Citrus Sinensis ID: 001991

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-----
Protein Sequence
MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEESQRQGFTSVSGNGEESPNGSDSSGSSKGSD
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccEEEEEcccccccccccEEEccccHHHHHHHccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEcccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEcccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccHHHHHHHHccccccEEEEEccccHHHHHHHHHHHHHcccccccEEEEccccccccccEEEEEEEcccccHHHHHHHHccccccccccccEEEEEEHHHHcHHHHHHHHccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHccccccccccccHHcccccccccccEccccccccccccccccccccccccccHccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccHHHHHHHHHccccccHHHHHccccccccccccccccHHHHHHHHHcccccEEEccccHHHHHHcccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHccccEEEEEccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEcccccccEEEEEEccHHHHHHHHHHHccccEcccEEEEEEccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHccccccEEEEEEcccccHcHHHHHHHHHHHccccEEEEEEEEcccccccEEEEEEEcccHHHHHHHHHHHccccccEccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mpfeimdhrsgsapthfseeirfpaerqigfwkpntmsdqqdgtvpmlggkfvasspmenfspvgipsvdwLELQQSTLARDKMKRLGivgeegaanlsenswnsvnhhpkswsnlavqpginslsgnrsgingiqsesslfsssLSDIFTRKMklsgneilsrqplnavashhqpeepfesLKEIEAQTIgnllpdeddlfsgvtddmghnfqantvddledfdlfssgggmelegddrlfavqknsdfvggvsnqgvsagsvvgehpygehpsrtLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALqnkplrrrkldihysipkdnpsekdanqgtLVVFNldssvsteELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLnrsdvagkqikleasrpggarrFMVQSEqeqddlnlcqipfddlssgqmvsSGVITstcmdngsiqvlhsatrspaialteshqtssvpnglpslarvgsigkqfghyepnlsldemkfgnqhpsfhphslpeyhdslanglpynspstiADIASSVgtkikdgldsrhirgvssnghlmeptggvfgsprngsyslhgnpyvwnnsnshqqhpsspmvwpnspsflnglhanrvahmpgfprvpplmlnatspahhhigsapavnpslwdrqhayagespetsnfhlgslgsggflgrspshhvdiasqnilshvggncmdmtknvgmrspqqichlfpgrnpmmsmqtsfdssnerMRNLsyrrnesnsnhadkkqyELDIDrilrgddsrttLMIKNIPNKYTSKMLLAAIDEHcrgtydfiylpidfknkcnvgyafinmidprqiipfhqafngkkwekfNSEKVASLAYARIQGKAALIAHFQnsslmnedkrcrpilfhtdgpnagdpepfpmgtnirsrlgkpringneesqrqgftsvsgngeespngsdssgsskgsd
Flexible Loop (DISEMBL)
mpfeimdhrsgsapthfseeIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKalqnkplrrrkLDIHysipkdnpsekdanqgTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTlnrsdvagkqikleasrpggaRRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTeshqtssvpngLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRgvssnghlmeptggVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSyrrnesnsnhadkkqyeldidrilrgddsrttlmiknipnkytSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHtdgpnagdpepFPMGTNIRSRLGKPRINGNEESQRQGFtsvsgngeespngsdssgsskgsd
Low Complexity Region (SEG)
MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQsesslfssslsDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWnnsnshqqhpsspMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHlgslgsggflgrsPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEESQRQGFTsvsgngeespngsdssgsskgsd
Disordered region (IsUnstruct)
***************************QIGFW****************************FSPVGIPSVDWLELQQSTLA*****RLGIV*******************************************************************************************************LL****DLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSN*GV**GSVVG***Y****SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL**********DIH****************TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN*********************************NLCQIPFDDLS**QMVSSGVITSTCMDNGSIQVL************************************************************************************************************************************PYVW*********************FLNGLHANRVAHMPGF******************************************************F*******HVDIASQNILSHVGGNCMDMTKNVG*****QICHLF*****************************************LDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILF***************************************************************
Disordered Region (DISOPRED)
****************FSEEIRFPAERQIGFWK************************************************************************************************************************************************************TIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRL**********************************RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI******************LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE**********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************DRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPN*********************************************************
Disordered Region (DISEMBL)
***************HFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIAL*********PNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNS***********VWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGN********************************
Disordered Region (DISPRO)
********************IRFPAERQIGFWKPN**************************SPV******WLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSV********************************************TRKMK**G*EILS*QPLN*********EPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFV*********************HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD**S***ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP************************DDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSM***************************KKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTD********P***************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEESQRQGFTSVSGNGEESPNGSDSSGSSKGSD
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	985	2.2.26 [Sep-21-2011]
Q64M78	1001	Protein MEI2-like 4 OS=Or	yes	no	0.963	0.948	0.524	0.0
Q8W4I9	915	Protein MEI2-like 1 OS=Ar	yes	no	0.917	0.987	0.520	0.0
Q9LYN7	907	Protein MEI2-like 4 OS=Ar	no	no	0.912	0.991	0.520	0.0
Q6ZI17	848	Protein MEI2-like 2 OS=Or	yes	no	0.690	0.801	0.484	1e-176
Q75M35	955	Protein MEI2-like 3 OS=Or	no	no	0.863	0.891	0.421	1e-175
Q6EQX3	811	Protein MEI2-like 5 OS=Or	no	no	0.724	0.880	0.439	1e-155
Q8VWF5	800	Protein MEI2-like 5 OS=Ar	no	no	0.315	0.388	0.581	1e-100
Q9SVV9	759	Protein MEI2-like 3 OS=Ar	no	no	0.292	0.379	0.574	3e-94
Q9SJG8	843	Protein MEI2-like 2 OS=Ar	no	no	0.144	0.168	0.615	1e-45
P08965	750	Meiosis protein mei2 OS=S	yes	no	0.157	0.206	0.525	3e-40

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

 Score =  895 bits (2313), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 542/1033 (52%), Positives = 676/1033 (65%), Gaps = 84/1033 (8%)

Query: 1    MPFEIMDHR----SGSAPT----HFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKF 52
            MP ++MD R      S PT     FSEE+R P ERQ+GFWK  ++          +G K 
Sbjct: 1    MPSQVMDQRHHMSQYSHPTLAASSFSEELRLPTERQVGFWKQESLPHH-------MGSKS 53

Query: 53   VASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGI----VGEEGAANLSENSWNSVNH 108
            VASSP+E   P+G      LEL Q    RD+     +     G+E  ANL  + W     
Sbjct: 54   VASSPIEKPQPIGTRMAGRLELLQPYKLRDQGAAFSLEHKLFGQERHANLPPSPW----- 108

Query: 109  HPKSWSNLAVQPGINS---LSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQ 165
             P   +       + S    S  R   NG  +E+ LFSSS+SDIF +K++L+    L  Q
Sbjct: 109  RPDQETGRQTDSSLKSAALFSDGRINPNGAYNENGLFSSSVSDIFDKKLRLTSKNGLVGQ 168

Query: 166  PLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD 225
             +  V  +H  +EPFE  +EIEAQ IGNLLPD+DDL SGV D++G+        D  D D
Sbjct: 169  SIEKVDLNHVDDEPFELTEEIEAQIIGNLLPDDDDLLSGVVDEVGYP-TNANNRDDADDD 227

Query: 226  LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQ-GVSAGSVVGEHPYGEHPSRTLFVRNIN 284
            +F +GGGMELE D+     +K  +F G  ++  G+  G + GEH Y E PSRTLFVRNIN
Sbjct: 228  IFYTGGGMELETDEN----KKLQEFNGSANDGIGLLNGVLNGEHLYREQPSRTLFVRNIN 283

Query: 285  SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI 344
            SNVEDSELK LFE FGDIR +YTACKHRGFVMISYYDIR+A NA   LQNK LRRRKLDI
Sbjct: 284  SNVEDSELKLLFEHFGDIRALYTACKHRGFVMISYYDIRSALNAKMELQNKALRRRKLDI 343

Query: 345  HYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEF 404
            HYSIPKDNPSEKD NQGT+V+FN+D S++ ++LH+IFG YGEI+EIRDT  K +HK IEF
Sbjct: 344  HYSIPKDNPSEKDINQGTIVLFNVDLSLTNDDLHKIFGDYGEIKEIRDTPQKGHHKIIEF 403

Query: 405  YDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFM--VQSEQEQDDLNLCQIPFDDLS 462
            YD+RAAE ALR LNR+D+AGK+IKLE SR G ARR    + SE  Q++  +C++     S
Sbjct: 404  YDVRAAEAALRALNRNDIAGKKIKLETSRLGAARRLSQHMSSELCQEEFGVCKLGSPSTS 463

Query: 463  SGQMVSSG-----VITSTCMDNGSIQVLHSATRSPAIALTESH---------QTSSVPNG 508
            S  + S G      ITST  +NGSIQ +HS  ++      E+          Q+ S P G
Sbjct: 464  SPPIASFGSTNLATITSTGHENGSIQGMHSGLQTSISQFRETSFPGLSSTIPQSLSTPIG 523

Query: 509  LPS------LARVG----SIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANG 558
            + S       A +G    S+G+  GH   N S   M       + HPHSLPE H+ + NG
Sbjct: 524  ISSGATHSNQAALGEISQSLGRMNGHM--NYSFQGMS------ALHPHSLPEVHNGVNNG 575

Query: 559  LPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSS---NGHLMEPTGGVFGSPRNGSYSLH 615
            +PYN  +++A + +   ++  + +D+RH+  V S   NGH  +   G  G  R+GS S+ 
Sbjct: 576  VPYNL-NSMAQVVNGTNSRTAEAVDNRHLHKVGSGNLNGHSFDRAEGALGFSRSGSSSVR 634

Query: 616  GNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPL-MLNATSPAHH 674
            G+  +WNNS++   HP+SP++WP+  SF+N + +   A M G PR P   M++   P HH
Sbjct: 635  GHQLMWNNSSNFHHHPNSPVLWPSPGSFVNNVPSRSPAQMHGVPRAPSSHMIDNVLPMHH 694

Query: 675  -HIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHV 733
             H+GSAPA+NPSLWDR+H YAGE  E  NFH GS+GS GF G    H +++   NI    
Sbjct: 695  LHVGSAPAINPSLWDRRHGYAGELTEAPNFHPGSVGSMGFPGSPQLHSMEL--NNIYPQT 752

Query: 734  GGNCMDMT---KNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNH 790
            GGNCMD T     +G  SPQQ   +F GRNPM+ +  SFDS  ERMR+   RRN+SN N 
Sbjct: 753  GGNCMDPTVSPAQIGGPSPQQRGSMFHGRNPMVPL-PSFDSPGERMRS---RRNDSNGNQ 808

Query: 791  AD-KKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFK 849
            +D KKQYELD+DRI+RGDDSRTTLMIKNIPNKYTSKMLLAAIDE+ +GTYDFIYLPIDFK
Sbjct: 809  SDNKKQYELDVDRIVRGDDSRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFIYLPIDFK 868

Query: 850  NKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSS 909
            NKCNVGYAFINM +P+ IIPF+Q FNGKKWEKFNSEKVASLAYARIQGK+ALIAHFQNSS
Sbjct: 869  NKCNVGYAFINMTNPQHIIPFYQTFNGKKWEKFNSEKVASLAYARIQGKSALIAHFQNSS 928

Query: 910  LMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEESQRQGFTSVSGNGE 969
            LMNEDKRCRPILFH+DGPNAGD EPFPMGTNIR+R G+ R +  EES  Q  +  S N +
Sbjct: 929  LMNEDKRCRPILFHSDGPNAGDQEPFPMGTNIRARSGRSRASSGEESH-QDISITSVNCD 987

Query: 970  ESPNGSDSSGSSK 982
             S NG D++G +K
Sbjct: 988  TSTNGVDTTGPAK 1000

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

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

 Score =  857 bits (2214), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 511/981 (52%), Positives = 655/981 (66%), Gaps = 77/981 (7%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMEN 60
           MP +IM+ R  S P+HF E+I   +ERQ GF K + M + Q G                 
Sbjct: 1   MPSDIMEQRGVSTPSHFHEDIHITSERQFGFMKTDMMPENQGG----------------- 43

Query: 61  FSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQP 120
                               RD++           +++ ++SW S ++  K  S+ +   
Sbjct: 44  --------------------RDRL-----------SSMPKSSWTSESYQLKPQSSFSGSH 72

Query: 121 GINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPF 180
              S +  R+  NG Q ESSLFSSS+SD+F+RK++L G+++LS    N V +H + EEP 
Sbjct: 73  PSGSPNA-RNTTNGSQWESSLFSSSMSDLFSRKLRLQGSDMLSTMSANTVVTH-REEEPS 130

Query: 181 ESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDR 240
           ESL+EIEAQTIGNLLPDEDDLF+ VT ++G   +ANT D+L++FDLFSS GGMEL+GD  
Sbjct: 131 ESLEEIEAQTIGNLLPDEDDLFAEVTGEVGRKSRANTGDELDEFDLFSSVGGMELDGDIF 190

Query: 241 LFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG 300
                +N +  G  S         VGE   GE PSRTL V NI+SNVED ELK LFEQFG
Sbjct: 191 SSVSHRNGERGGNNS---------VGELNRGEIPSRTLLVGNISSNVEDYELKVLFEQFG 241

Query: 301 DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
           DI+ ++TACK+RGF+M+SY DIRAA+NA +ALQNK LR  KLDI YSI K+NPS+KD ++
Sbjct: 242 DIQALHTACKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRYSISKENPSQKDTSK 301

Query: 361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 420
           G L+V NLDSS+S +EL+++   YGE++EIR T H ++  +IEF+D+RAA  AL  LN  
Sbjct: 302 GALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFDVRAAAAALGGLNGL 361

Query: 421 DVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVS--SGVITSTCMD 478
           +VAGK+++L  + P G R +  Q      +  L +  + + SSG +     G+I+ST  D
Sbjct: 362 EVAGKKLQLVPTYPEGTR-YTSQCAANDTEGCLPKTSYSNTSSGHIGRHFPGMISSTSSD 420

Query: 479 NGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGN 538
            GS++V+H++  SP  +  E H++ S+P G P  A   S  K  G  E     D    G 
Sbjct: 421 GGSMRVIHNSIGSPVNSFIERHRSLSIPIGFPPSANGISASKPVGLQEHGHHFDNSNMGI 480

Query: 539 QH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLM 597
           Q  P+ HPHS  EY D+ ANG PY S S  +++ S  G+K  +G    ++RGV       
Sbjct: 481 QSMPNLHPHSFSEYVDNFANGSPYTS-SAFSEMVSD-GSKANEGFMIHNVRGVEGF---- 534

Query: 598 EPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPG 657
             +GG  GSP + S     N  +W+NSN+ QQ+PSS M+WPNSPS +N +   R   +  
Sbjct: 535 --SGGGIGSPMHQSSRRPIN--LWSNSNTQQQNPSSGMMWPNSPSHINSIPTQRPP-VTV 589

Query: 658 FPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGR 716
           F R PP+M+N A+SP HHHIGSAP +N   WDR+ AY  ES E+S FH+GS GS G  G 
Sbjct: 590 FSRAPPIMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAESLESSGFHIGSHGSMGIPGS 649

Query: 717 SPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNER 775
           SPSH +DI S    S VGGN MD+ ++N  +RSPQQ+ HLFPGR+PM SM  SFDS NER
Sbjct: 650 SPSHPMDIGSHKTFS-VGGNRMDVNSQNAVLRSPQQLSHLFPGRSPMGSMPGSFDSPNER 708

Query: 776 MRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHC 835
            RNLS+RR+ES+S++ADKK YELD+DRILRG+D RTTLMIKNIPNKYTSKMLL+AIDEHC
Sbjct: 709 YRNLSHRRSESSSSNADKKLYELDVDRILRGEDRRTTLMIKNIPNKYTSKMLLSAIDEHC 768

Query: 836 RGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARI 895
           +GTYDF+YLPIDFKNKCNVGYAFIN+I+P +I+PF +AFNGKKWEKFNSEKVA+L YARI
Sbjct: 769 KGTYDFLYLPIDFKNKCNVGYAFINLIEPEKIVPFFKAFNGKKWEKFNSEKVATLTYARI 828

Query: 896 QGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEE 955
           QGK ALIAHFQNSSLMNEDKRCRPILFHTDGPNAGD EPFPMG+NIRSR GKPR +  + 
Sbjct: 829 QGKTALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQEPFPMGSNIRSRPGKPRSSSIDN 888

Query: 956 SQRQGFTSVSGNGEESPNGSD 976
                 +SVS N EE+PNG+D
Sbjct: 889 YNSFSISSVSENREETPNGTD 909

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  846 bits (2186), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 512/984 (52%), Positives = 650/984 (66%), Gaps = 85/984 (8%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMEN 60
           MP +I++ R    P+HF E+IR   E+Q GF K N M                       
Sbjct: 1   MPSDILEPRGVPTPSHFHEDIRITPEKQFGFMKNNPM----------------------- 37

Query: 61  FSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLA-VQ 119
             P G                         G + ++NL  +SW S ++     S+L+   
Sbjct: 38  --PEG-------------------------GVDRSSNLPTSSWTSDSYQLSQQSSLSGAL 70

Query: 120 PGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEP 179
           P    +   R+  N    ESSLFSSSLSD+F+RK++L  ++ L      A  S ++ EEP
Sbjct: 71  PSF--IPNGRTTTNDTHWESSLFSSSLSDLFSRKLRLPRSDKL------AFMSANREEEP 122

Query: 180 FESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDD 239
            ESL+E+EAQTIGNLLPDEDDLF+ V  +  H  +AN  DDL+D DLFSS GGMEL+GD 
Sbjct: 123 SESLEEMEAQTIGNLLPDEDDLFAEVVGEGVHKSRANGGDDLDDCDLFSSVGGMELDGD- 181

Query: 240 RLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQF 299
            +F+     D   G      S  S V EHP GE  SR LFVRN++S++ED EL  LF+QF
Sbjct: 182 -VFSSVSQRDGKRG------SNVSTVAEHPQGEILSRILFVRNVDSSIEDCELGVLFKQF 234

Query: 300 GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
           GD+R ++TA K+RGF+M+SYYDIRAA+ A +AL  + LR RKLDI YSIPK+NP E +++
Sbjct: 235 GDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYSIPKENPKE-NSS 293

Query: 360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           +G L V NLDSS+S EELH IF  YGEIRE+R T H+++  +IEF+D+R A+ AL+ LN 
Sbjct: 294 EGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGLNG 353

Query: 420 SDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVS--SGVITSTCM 477
            +VAG+Q+KL  + P G   F  Q   +  +  L ++ F++LSS  M     G++ ST +
Sbjct: 354 LEVAGRQLKLAPTCPEGTS-FWPQFASDDGEGGLPKMAFNNLSSAHMGRHFPGILASTSI 412

Query: 478 DNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFG 537
           D GSI+ +H++  SP  +  E HQ+  VP GLP  ARV S  K  G  E     D  K G
Sbjct: 413 DGGSIRGMHNSVGSPMNSFIERHQSLDVPIGLPPSARVISASKPVGLQEFGNPFDNSKTG 472

Query: 538 NQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHL 596
            Q  P+ HPH  P+Y D+ A+G PY S +T +++ S  G K  +G    ++RGV  +G  
Sbjct: 473 IQSMPNLHPH-FPDYLDNFASGSPYKSSTTFSEMVSD-GQKANEGFMMSNVRGVGVDGF- 529

Query: 597 MEPTGGVFGSPRN-GSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHM 655
               GGV GSP N GS+   GN  +W+NSNS Q + SS M+WPNSPS +NG+ + R+  +
Sbjct: 530 ---NGGVIGSPINQGSH--RGNLNLWSNSNSQQHNQSSGMMWPNSPSRVNGVPSQRIPPV 584

Query: 656 PGFPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFL 714
             F R  PLM+N A+SP HHHIGSAP +N   WDR+ AY  ESPE+S FHLGS GS GF 
Sbjct: 585 TAFSRASPLMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAESPESSGFHLGSPGSMGFP 644

Query: 715 GRSPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSN 773
           G SPSH +D  S  + SHVGGN M+  +KN  +RS +Q+ HLF GR+PM+S+  SFD  N
Sbjct: 645 GSSPSHPMDFGSHKVFSHVGGNRMEANSKNAVLRSSRQMPHLFTGRSPMLSVSGSFDLPN 704

Query: 774 ERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDE 833
           ER RNLS+RR+ESNS++A+KK YELD+DRILRG+DSRTTLMIKNIPNKYTSKMLLAAIDE
Sbjct: 705 ERYRNLSHRRSESNSSNAEKKLYELDVDRILRGEDSRTTLMIKNIPNKYTSKMLLAAIDE 764

Query: 834 HCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYA 893
           +C+GTYDF+YLPIDFKNKCNVGYAFIN+I+P  I+PF++AFNGKKWEKFNSEKVASLAY 
Sbjct: 765 YCKGTYDFLYLPIDFKNKCNVGYAFINLIEPENIVPFYKAFNGKKWEKFNSEKVASLAYG 824

Query: 894 RIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGN 953
           RIQGK+ALIAHFQNSSLMNEDKRCRPILFHT GPNAGD EPFPMG+NIRSR GK R N  
Sbjct: 825 RIQGKSALIAHFQNSSLMNEDKRCRPILFHTAGPNAGDQEPFPMGSNIRSRPGKHRTNSI 884

Query: 954 EESQRQGFTSVSGNGEESPNGSDS 977
           E      F+S S N +E  NG+DS
Sbjct: 885 E--NYTNFSSSSDNRDEPANGNDS 906

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  618 bits (1594), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 382/788 (48%), Positives = 496/788 (62%), Gaps = 108/788 (13%)

Query: 185 EIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD--DRLF 242
           + + + I +LLP+EDDLF+G+T+++    Q N++++LE+FD+F SGGGMEL+ D  + + 
Sbjct: 97  DFDLRQIDDLLPNEDDLFAGITNEIEPAGQTNSMEELEEFDVFGSGGGMELDTDPVESIT 156

Query: 243 AVQKNSDFVGGVSNQGV-------SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKAL 295
           A   N+    G+   GV       SA +V GEHPYGEHPSRTLFVRNINSNV+D+EL++L
Sbjct: 157 AGLGNTSIADGLRGNGVNHFGPSNSASTVAGEHPYGEHPSRTLFVRNINSNVDDTELRSL 216

Query: 296 FEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE 355
           FEQ+GDIRT+YTA KHRGFVMISY+DIRAAR AM+ LQNKPLRRRKLDIH+SIPK+NPS+
Sbjct: 217 FEQYGDIRTLYTATKHRGFVMISYFDIRAARGAMRGLQNKPLRRRKLDIHFSIPKENPSD 276

Query: 356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR 415
           KD NQGTLV+FNLD SVS EE+ QIFG YGE++EIR+T +K +HKFIEFYD+RAAE ALR
Sbjct: 277 KDLNQGTLVIFNLDPSVSNEEVRQIFGTYGEVKEIRETPNKKHHKFIEFYDVRAAEAALR 336

Query: 416 TLNRSDVAGKQIKLEASRPGGARRFMVQS---EQEQDDLNLCQIPFDDLSSGQMVSSG-- 470
           +LN+S++AGK+IKLE SRPGG RR ++Q    + +QD+    +IP      G  ++S   
Sbjct: 337 SLNKSEIAGKRIKLEPSRPGGTRRNLMQQLGHDIDQDEPRSYRIP----HVGSPIASSPP 392

Query: 471 ---VITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLP-----SLARVGSIGKQF 522
                 S+  DN  +Q  +++     ++          P G+P     +  ++  IGK  
Sbjct: 393 GAWAQYSSPTDNNLLQAFNASPTGNGMS----------PIGMPPSLISNAVKIAPIGK-- 440

Query: 523 GHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGL 582
              + N S  +  F N +    PH           G  +    +  D             
Sbjct: 441 ---DSNWSKYDKVFSNNN---QPH-----------GAAFQHSHSYQD------------H 471

Query: 583 DSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPS 642
            S H+   SS G L  P   ++GSP+   YS H    +W         PS      N+ S
Sbjct: 472 KSEHMS--SSPGTLTGPE-FLWGSPK--PYSEHAQSPIWRPPAIGHAIPS------NTRS 520

Query: 643 FLNG-LHANRVAHMPGFPRVPPLMLNATSPAHH-HIGSAPAVNPSLWDRQHAYAGESPET 700
              G L+  R A + G          +    HH H+GSAP+  P  ++    +  ESPET
Sbjct: 521 QGQGLLYGGRQASLFG----------SQDQLHHHHVGSAPSGAP--FESHFGFLPESPET 568

Query: 701 SNF------HLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNV--GMRSPQQI 752
           S        ++G++GSG        +    AS N +S + GN  D   +    + SP ++
Sbjct: 569 SYMNQVRFGNIGNIGSGRNGTGLMLNMAARASVNPVSALSGNMSDNNSSSFRPILSP-RL 627

Query: 753 CHLFPGRNPMMSMQTSF--DSSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDDS 809
              F G NP      SF  D+S ER RN   RR +S+   AD KKQY+LD+++I +GDD+
Sbjct: 628 GQSFYG-NPTYQGPGSFGLDNSIERGRN---RRVDSSVFQADSKKQYQLDLEKIRKGDDT 683

Query: 810 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIP 869
           RTTLMIKNIPNKYTSKMLLAAIDE  +GTYDF YLPIDFKNKCNVGYAFINMI P  I+ 
Sbjct: 684 RTTLMIKNIPNKYTSKMLLAAIDEFHKGTYDFFYLPIDFKNKCNVGYAFINMISPVHIVS 743

Query: 870 FHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNA 929
           F+QAFNGKKWEKFNSEKVASLAYARIQG+ ALI+HFQNSSLMNEDKRCRPILFH++GP+A
Sbjct: 744 FYQAFNGKKWEKFNSEKVASLAYARIQGRTALISHFQNSSLMNEDKRCRPILFHSNGPDA 803

Query: 930 GDPEPFPM 937
           G+ EPFP+
Sbjct: 804 GNQEPFPI 811

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  615 bits (1585), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 405/960 (42%), Positives = 545/960 (56%), Gaps = 109/960 (11%)

Query: 24  PAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQ--QSTLAR 81
           P ERQ+GFW   +M D +       G K V +SP+E   P G       E    Q+    
Sbjct: 34  PTERQVGFWNSESMVDHK-------GSKSVFASPLEKIQPNGANHAGDPETPGGQAFKGL 86

Query: 82  DKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLA------VQPGI--NSLSGNRSGIN 133
           D +    ++ +E A+     SW  +  +P S   L+      V+P      + G   G++
Sbjct: 87  DILSLSNLMRQENASGSPSLSWGEILTNPISRLGLSTRETAFVEPTTADQHVPGYGKGLS 146

Query: 134 GIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASH---HQPEEPFESLKEIEAQT 190
                    SSSLS++F+ K +    EI+S     +  +H   +  +EP ES++ IEAQT
Sbjct: 147 ---------SSSLSEVFSGKSR----EIVSGVLCQSTGTHTSIYDSDEPLESMEAIEAQT 193

Query: 191 IG-NLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSD 249
           IG  L  D+DDL SG+ D       +   DD  D D+F +GGGMELE +D +    K   
Sbjct: 194 IGDLLPDDDDDLISGIADGFEFTGMSTNQDD-ADEDIFCTGGGMELENNDSV----KGDK 248

Query: 250 FVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC 309
              G     +S+G     H   + PSRTL VRNI +N+EDS+L  LF+Q+GDIR +YT+ 
Sbjct: 249 VQDGSFKSQISSG-----HSINKQPSRTLVVRNITANIEDSDLTVLFQQYGDIRMLYTSF 303

Query: 310 KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLD 369
           KH GFV +SYYDIRAA+NAM+AL +KPL   KLD+ +S PK+N   KD ++G LVV N+D
Sbjct: 304 KHHGFVTVSYYDIRAAQNAMRALHSKPLGLMKLDVQFSFPKENVPGKDIDKGMLVVSNID 363

Query: 370 SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 429
           SS+S ++L Q+  +YG+++EI  +      KF+EFYD+RAAE AL  LN+  ++G + K+
Sbjct: 364 SSISNDDLLQMLSVYGDVKEISSSPISCTKKFVEFYDVRAAEEALHDLNKGGISGPKFKV 423

Query: 430 EASRPGGARRFMVQS---EQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLH 486
           E S+ G A   + Q    E +QD L     P    +S    + G + + C DN ++  L 
Sbjct: 424 ELSQHGEAGSCLRQQHSREWKQDSL-----PHQPKNSSPG-TIGKLGTKCQDNSTVHNLF 477

Query: 487 SATRSPAIALTESHQTSSVPNGLPSLARVGSI---GKQFGHYEPNLSLDEMKFGNQHPSF 543
           S       + T+   T+  P  L S  R+ S      Q    + +  L +  FG    + 
Sbjct: 478 SPVNQQLESPTQCISTTG-PQILSSPIRIKSTLQHNNQASVGDLSGPLGQGNFGRGIQTL 536

Query: 544 HPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDS--RHIRGVSSNGHLMEPTG 601
           HP SLPE+H+ + N    NS S    ++    +  +DG+D   + +      GH  +   
Sbjct: 537 HPRSLPEHHNRICN----NSKSMT--VSGRNASSRQDGVDHNIQKVGPAGFCGHSFDQNN 590

Query: 602 GVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRV 661
             FG    GS  LHG  Y WN++N   Q PS+P++W N              H+  +P V
Sbjct: 591 EAFGFTEIGSCPLHGYHYTWNHTNVFPQSPSAPILWSN---------LQHPMHVHSYPGV 641

Query: 662 PPLMLNATSPA--HHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRS-- 717
           PP MLN  S     HH+GSAP              G      +FH GSLGS G  G    
Sbjct: 642 PPHMLNTGSYPMDQHHLGSAP-----------DNGGSFGNVHSFHPGSLGSIGLHGSPQL 690

Query: 718 -PSHHVDIAS------QNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFD 770
            PS     AS      + + S VGG         G +S QQ+C+   GRNPM+ + TS+D
Sbjct: 691 YPSELSAFASSRGNFREALFSPVGG---------GFQSLQQMCNAINGRNPMIHVSTSYD 741

Query: 771 SSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLA 829
           ++N+RMR+   RR++ N   ++ K+Q+ELDIDRI +G+DSRTTLMIKNIPNKY  K+LLA
Sbjct: 742 ATNDRMRS---RRHDGNPAQSENKRQFELDIDRIAKGEDSRTTLMIKNIPNKYNCKLLLA 798

Query: 830 AIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVAS 889
            IDE+ RGTYDFIYLPIDFKNKCNVGYAFINM DP+ IIPF++ FNGKKWEKFNSEKVAS
Sbjct: 799 VIDENHRGTYDFIYLPIDFKNKCNVGYAFINMTDPQHIIPFYKTFNGKKWEKFNSEKVAS 858

Query: 890 LAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPR 949
           LAYARIQG++ALIAHFQNSSLMNEDK CRP+LFH DGPNAGD EPFP+G N+RSR G+ R
Sbjct: 859 LAYARIQGRSALIAHFQNSSLMNEDKWCRPMLFHKDGPNAGDQEPFPVGNNVRSRAGRNR 918

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  551 bits (1420), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 362/824 (43%), Positives = 477/824 (57%), Gaps = 110/824 (13%)

Query: 132 INGIQSESSLFSSSLSDIFTRKMKLSGNEI-LSRQPLNAV-ASHHQP---EEPFESLKEI 186
           +NG  S++ LFSSSL  +  +  KL G E   + QP + +     QP       + + ++
Sbjct: 38  VNG-SSDAVLFSSSLPSVL-QFGKLPGKEREYNAQPKDDMFPMMKQPGTNARVADPMDDV 95

Query: 187 EAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD---DRLFA 243
               IGNLLPD+++L +GV +D  H      V++ E++D+F + GGMEL+ D      F 
Sbjct: 96  AQHLIGNLLPDDEELLAGVIEDFDHVKLRTQVEESEEYDVFRNSGGMELDIDPLESITFG 155

Query: 244 VQKNS--DFVGGVSNQGV---SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQ 298
             K S  +  G  +NQ      AG+V GEHPYGEHPSRTLFVRNINSNVEDSEL++LFE 
Sbjct: 156 TAKASLVNGTGSSTNQYSIQNGAGTVTGEHPYGEHPSRTLFVRNINSNVEDSELRSLFEP 215

Query: 299 FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDA 358
           FGDIR++YTA KHRGFVMISYYDIR ARNA  ALQ+KPLRRRKLDIHYSIPK+NPS+KD 
Sbjct: 216 FGDIRSMYTATKHRGFVMISYYDIRHARNAKTALQSKPLRRRKLDIHYSIPKENPSDKDM 275

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           NQGTLV+FNL+ +VS EEL QIFG +GE+REIR+T HK +H+FIEFYD+RAAE+ALR+LN
Sbjct: 276 NQGTLVIFNLEPAVSNEELLQIFGAFGEVREIRETPHKRHHRFIEFYDVRAAESALRSLN 335

Query: 419 RSDVAGKQIKLEASRPGGARRFMVQS-----EQEQDDLNLCQIPFDDLSSGQMVSSGVIT 473
           +SD+AGK++KLE SRPGGARR  +Q      EQ++   N  QI     +S   + S + +
Sbjct: 336 KSDIAGKRVKLEPSRPGGARRSFIQHFNHEFEQDETKHNSFQIGSPSANSPPSLWSQLGS 395

Query: 474 STCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDE 533
            T  D   +  L+    +  ++   S+  S   +G P +     +GK    Y  N + D 
Sbjct: 396 PT--DENKLNALNETAFNGGMSPLGSNHLSGFSSGYPPMK--SPVGKS--SYWNNRA-DN 448

Query: 534 MKFGNQHPSFH-PHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSS 592
           +  G+  P+ H  HS PE+H  + +  P  S +  +   +S                   
Sbjct: 449 IFHGS--PTLHNSHSFPEHHGGIISASPLVSSAASSASTAS------------------- 487

Query: 593 NGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQH--PSSPMVWPNSPSFLNGLHAN 650
                            G  +L G  ++W N+N+ + H  PSS      S S        
Sbjct: 488 -----------------GFTALTGTSFLWGNNNNLRDHGQPSSIQSQALSNSLFPNNQPQ 530

Query: 651 RVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGS 710
           R +++  +  +      +   +  ++GSAP+V P  ++    Y  +SP+TS    G  G 
Sbjct: 531 RQSNL--YQNLRGSFGASEHFSQFNVGSAPSVFP--FESNFGYFSDSPDTSYMRQGKFGG 586

Query: 711 GGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQ---T 767
            G                  + V G+ M    N G          +P  N + SMQ    
Sbjct: 587 TG-----------------PTRVSGSLM---TNFGA---------YPRIN-VASMQNGSV 616

Query: 768 SFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKML 827
            F+   +R RN +     S      + QY+LD+++I+ G D+RTTLMIKNIPNKYTS ML
Sbjct: 617 GFEGLLDRGRNQTV--GNSGCQEDSRVQYQLDLEKIIAGKDTRTTLMIKNIPNKYTSNML 674

Query: 828 LAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKV 887
           L  IDE   GTYDF YLPIDFKNKCNVGYAFINM  P  I+ F +AF G+KWEKFNSEKV
Sbjct: 675 LEVIDETHEGTYDFFYLPIDFKNKCNVGYAFINMASPGYIVSFFKAFAGRKWEKFNSEKV 734

Query: 888 ASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILF---HTDGPN 928
            SLAYARIQGKAAL+ HFQNSSLMNEDKRCRP+LF   HT+  N
Sbjct: 735 VSLAYARIQGKAALVNHFQNSSLMNEDKRCRPMLFDPKHTENNN 778

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 =  366 bits (940), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 196/337 (58%), Positives = 248/337 (73%), Gaps = 26/337 (7%)

Query: 137 SESSLFSSSLSDIFTR-KMKLSGN-EILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNL 194
           S+++LFSSSL  +F R K++LS N +  S     AV+  ++  E   S  + E+ +IGNL
Sbjct: 26  SDATLFSSSLP-VFPRGKLQLSDNRDGFSLIDDTAVSRTNKFNE---SADDFESHSIGNL 81

Query: 195 LPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDR------------LF 242
           LPDE+DL +G+ DD+        + D +D+DLF SGGGMEL+ D R            L 
Sbjct: 82  LPDEEDLLTGMMDDL----DLGELPDADDYDLFGSGGGMELDADFRDNLSMSGPPRLSLS 137

Query: 243 AVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI 302
           ++  N+     + N    AG+V GEHPYGEHPSRTLFVRNINSNVEDSEL ALFEQ+GDI
Sbjct: 138 SLGGNAIPQFNIPN---GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELTALFEQYGDI 194

Query: 303 RTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT 362
           RT+YT CKHRGFVMISYYDIR+AR AM++LQNKPLRRRKLDIH+SIPKDNPSEKD NQGT
Sbjct: 195 RTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKDNPSEKDMNQGT 254

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 422
           LVVFNLD S+S ++LH IFG +GEI+EIR+T HK +HKF+EFYD+R AE AL+ LNR ++
Sbjct: 255 LVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAEAALKALNRCEI 314

Query: 423 AGKQIKLEASRPGGARR-FMVQSEQEQDDLNLCQIPF 458
           AGK+IK+E SRPGGARR  M+Q  Q+ ++ +L  +P 
Sbjct: 315 AGKRIKVEPSRPGGARRSLMLQLNQDLENDDLHYLPM 351

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 =  347 bits (889), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 182/317 (57%), Positives = 228/317 (71%), Gaps = 29/317 (9%)

Query: 161 ILSRQPLNAVASHHQPEEPFES------------LKEIEAQTIGNLLPD-EDDLFSGVTD 207
           ++  Q +N   S+HQ  +   S            L + ++  IGN+LPD E++LFSG+ D
Sbjct: 29  LIQHQNINPRDSYHQSVDEMASGLDHFSGGIGNMLDDGDSHPIGNMLPDDEEELFSGLMD 88

Query: 208 DMGHNFQANTVDDLEDFDLFSSGGGMELEGD---------DRLFAVQKNSDFV--GGVSN 256
           D+  +    T+DDLED+DLF SGGG+ELE D          R+     N D V    +  
Sbjct: 89  DLNLSSLPATLDDLEDYDLFGSGGGLELETDPYDSLNKGFSRMGFADSNVDNVMPQNIFQ 148

Query: 257 QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVM 316
            GV  GS+ GEHPYGEHPSRTLFVRNINSNVEDSEL+ALFEQ+G IRT+YTACK RGFVM
Sbjct: 149 NGV--GSIAGEHPYGEHPSRTLFVRNINSNVEDSELQALFEQYGHIRTLYTACKQRGFVM 206

Query: 317 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEE 376
           +SY DIRA+R AM+ALQ K L++RKLDIH+SIPKDNPSEKD NQGTLVVFNL  SVS  +
Sbjct: 207 VSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPSVSNRD 266

Query: 377 LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG 436
           L  IFG+YGEI+EIR+T +K +HKF+EF+D+R+A+ AL+ LNR+++AGK+IKLE SRPGG
Sbjct: 267 LENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADAALKALNRTEIAGKRIKLEHSRPGG 326

Query: 437 ARRFM---VQSEQEQDD 450
           ARR M   +  E EQDD
Sbjct: 327 ARRNMMLQMNPELEQDD 343

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  186 bits (471), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 88/143 (61%), Positives = 107/143 (74%), Gaps = 1/143 (0%)

Query: 792 DKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNK 851
           D  +Y +D+DRI  GD+ RTTL+IKNIPNKYT KML+A IDE  +G YDF+ LP DFKNK
Sbjct: 661 DGGRYHIDLDRIASGDEIRTTLIIKNIPNKYTYKMLVAEIDEKHKGDYDFLCLPTDFKNK 720

Query: 852 CNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLM 911
           CN+G+AFINM+ P  I+PF Q FNGK WEKFNS KVASLAYA IQGK+AL ++ Q  S M
Sbjct: 721 CNMGHAFINMVSPLHIVPFQQTFNGKIWEKFNSGKVASLAYAEIQGKSALASYMQTPSSM 780

Query: 912 NEDKRCRP-ILFHTDGPNAGDPE 933
            E K+  P + +H DG +A D E
Sbjct: 781 KEQKQLFPEVSYHDDGQDANDHE 803

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  168 bits (425), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 82/156 (52%), Positives = 106/156 (67%), Gaps = 1/156 (0%)

Query: 790 HADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFK 849
           HA  +   +D  +I  G D+RTT+MIKNIPNK+T +ML   ID   +GTYDF+YL IDF 
Sbjct: 577 HASDRN-SVDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKGTYDFLYLRIDFV 635

Query: 850 NKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSS 909
           NKCNVGYAFIN I+P+ II F +A  G +W  F+SEK+  ++YA IQGK  LI  F+NS 
Sbjct: 636 NKCNVGYAFINFIEPQSIITFGKARVGTQWNVFHSEKICDISYANIQGKDRLIEKFRNSC 695

Query: 910 LMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRL 945
           +M+E+   RP +F + GPN G  EPFP   N R +L
Sbjct: 696 VMDENPAYRPKIFVSHGPNRGMEEPFPAPNNARRKL 731

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	985
255540053	972	RNA-binding protein, putative [Ricinus c	0.978	0.991	0.721	0.0
297734509	998	unnamed protein product [Vitis vinifera]	0.998	0.985	0.690	0.0
359491581	991	PREDICTED: protein MEI2-like 4-like [Vit	0.993	0.987	0.691	0.0
224134156	919	predicted protein [Populus trichocarpa]	0.916	0.982	0.655	0.0
296085525	986	unnamed protein product [Vitis vinifera]	0.970	0.969	0.592	0.0
359473863	965	PREDICTED: protein MEI2-like 4-like [Vit	0.949	0.968	0.586	0.0
224075455	976	predicted protein [Populus trichocarpa]	0.968	0.977	0.574	0.0
356507390	976	PREDICTED: protein MEI2-like 4-like [Gly	0.966	0.975	0.566	0.0
356527581	955	PREDICTED: protein MEI2-like 1-like [Gly	0.957	0.987	0.556	0.0
242061760	997	hypothetical protein SORBIDRAFT_04g02113	0.967	0.955	0.524	0.0

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

 Score = 1420 bits (3676), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 709/982 (72%), Positives = 823/982 (83%), Gaps = 18/982 (1%)

Query: 6   MDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGT---VPMLGGKFVASSPMENFS 62
           MD R G+A +H+ E++  PAERQIGFWKP++M D Q GT   VP    K VA SP+E FS
Sbjct: 1   MDQRGGTASSHYFEDMLLPAERQIGFWKPHSMPDHQIGTGGMVPFPSSKLVAPSPLEKFS 60

Query: 63  PVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGI 122
           P G  SVD+++L  S LA D+ ++L I   EG+ N+ +NSWNSV+ + KSWS+L++QP  
Sbjct: 61  PGGALSVDYMQLPDSVLAMDQKEKLSI--GEGSTNMLKNSWNSVDQNAKSWSSLSMQPTS 118

Query: 123 NSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFES 182
            SL GNR+GI   Q ESSLFSSSLS++F  K++L  N+I SRQP   +A  ++ +EPFES
Sbjct: 119 YSLGGNRAGIGATQWESSLFSSSLSEVFNGKLRLLENDIQSRQPAKPIALPNEEDEPFES 178

Query: 183 LKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLF 242
           L+E+EAQTIGNLLP EDDLFSGVTD++GHN   N  DDLEDFDLF +GGGMELEGDDRL 
Sbjct: 179 LEELEAQTIGNLLPAEDDLFSGVTDELGHNAHTNGGDDLEDFDLFITGGGMELEGDDRLC 238

Query: 243 AVQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD 301
             Q+NSDFVG +SN QG S GSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQ+GD
Sbjct: 239 VGQRNSDFVGALSNLQGGSNGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQYGD 298

Query: 302 IRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
           IRT+YTACKHRGFVMISYYDIRAARNAM++LQNKPLRRRKLDIHYSIPKDNPSEKD NQG
Sbjct: 299 IRTLYTACKHRGFVMISYYDIRAARNAMRSLQNKPLRRRKLDIHYSIPKDNPSEKDINQG 358

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           TLV+FNLDSSVSTEELH+IFG+YGEI+EIR+T HK +HKFIE+YDIR+AE AL  LNRSD
Sbjct: 359 TLVIFNLDSSVSTEELHKIFGVYGEIKEIRETPHKRHHKFIEYYDIRSAEAALSALNRSD 418

Query: 422 VAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMV--SSGVITSTCMDN 479
           +AGKQIKLE SRPGG RR M + EQEQD+  LCQ PF+DLSSG++   S GVI S+CM+N
Sbjct: 419 IAGKQIKLEPSRPGGTRRLMTKPEQEQDESGLCQSPFEDLSSGRLATFSPGVIASSCMEN 478

Query: 480 GSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQ 539
           GS QV+HSA +SP  +  ESH++SSVPN LPS   V SI KQFG +EPN S+DEM FGNQ
Sbjct: 479 GSTQVIHSAIQSPVGSFIESHRSSSVPNNLPSPVSVTSISKQFGLHEPNRSMDEMMFGNQ 538

Query: 540 H-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLME 598
             PSFHPHSLPEY D LANG+P+NS S+I  +A SVG+K+ +G+ SRHI+ VSSNGHLME
Sbjct: 539 RIPSFHPHSLPEYPDGLANGVPFNSSSSIGGMAHSVGSKVTEGISSRHIQAVSSNGHLME 598

Query: 599 PTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGF 658
             GGVFGS  NGS  L G+ Y+WNNSN++QQH SS M+WPNS SF NG+HA+ + HMPGF
Sbjct: 599 LNGGVFGSSGNGS--LPGHHYMWNNSNTNQQHHSSRMIWPNSSSFTNGVHAHHLPHMPGF 656

Query: 659 PRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSP 718
           PR PP+MLN T PAHHH+GSAP+VNPS+W+R+HAYAGESPE S+FHLGSLGS G    SP
Sbjct: 657 PRAPPVMLN-TVPAHHHVGSAPSVNPSVWERRHAYAGESPEASSFHLGSLGSVG----SP 711

Query: 719 SHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRN 778
            H ++IAS NI SHVGGNCMDMTKN G+R+ Q +CH+FPGRNPM+SM  SFDS NER+RN
Sbjct: 712 -HPMEIASHNIFSHVGGNCMDMTKNAGLRTAQPMCHIFPGRNPMISMPASFDSPNERVRN 770

Query: 779 LSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGT 838
           LS+RR +SN NH+DKKQYELD+DRI+RG+DSRTTLMIKNIPNKYTSKMLLAAIDE+CRGT
Sbjct: 771 LSHRRIDSNPNHSDKKQYELDLDRIMRGEDSRTTLMIKNIPNKYTSKMLLAAIDEYCRGT 830

Query: 839 YDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGK 898
           YDFIYLPIDFKNKCNVGYAFINMIDP+QIIPFH+AFNGKKWEKFNSEKVASLAYARIQGK
Sbjct: 831 YDFIYLPIDFKNKCNVGYAFINMIDPQQIIPFHKAFNGKKWEKFNSEKVASLAYARIQGK 890

Query: 899 AALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEESQR 958
           +ALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTN+RSRLGK R +G+EE+  
Sbjct: 891 SALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNVRSRLGKLRTSGSEENH- 949

Query: 959 QGFTSVSGNGEESPNGSDSSGS 980
            G  S S NGE+S  G+DSSGS
Sbjct: 950 HGNPSTSANGEDSSVGTDSSGS 971

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 1320 bits (3417), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 690/999 (69%), Positives = 796/999 (79%), Gaps = 15/999 (1%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQ---DGTVPMLGGKFVASSP 57
           MPFE+MD R  SA +   ++I FPAERQ+GFWKP  MSD     DG   + G K V SSP
Sbjct: 1   MPFEVMDPRGVSASSPLFDDICFPAERQVGFWKPKIMSDHHAEGDGVARIPGSKSVTSSP 60

Query: 58  MENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLA 117
           +E   PVG  SVD+ E  +S LARD+ ++L +  EEG ANLS   W +V+H+ K+WSNL 
Sbjct: 61  LEKLLPVGSKSVDYSEGPESYLARDQKEKLQVNREEGTANLSRTPWRTVDHNSKTWSNLY 120

Query: 118 VQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPE 177
           VQP  + +   ++ ING   ESSLFSSSLS+IF RK+++S +++LS Q    VA H + E
Sbjct: 121 VQPASSYVEVKKTSINGALYESSLFSSSLSEIFNRKLRVSTSDVLSHQSAGTVAPHSEEE 180

Query: 178 EPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEG 237
           + F+SL+EIE QT+GNLLPDED+LFSGV DDMG+N  AN  DD EDFDLFSSGGGMELEG
Sbjct: 181 KLFKSLEEIEVQTLGNLLPDEDELFSGVVDDMGYNAHANNGDDFEDFDLFSSGGGMELEG 240

Query: 238 DDRLFAVQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALF 296
           DD L   Q++SDF GG+ N QG S GS+  EHPYGEHPSRTLFVRNINSNVEDSEL+ LF
Sbjct: 241 DDHLCISQRHSDFNGGIPNSQGGSNGSLASEHPYGEHPSRTLFVRNINSNVEDSELRDLF 300

Query: 297 EQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 356
           EQ+GDIRT+YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDNPSEK
Sbjct: 301 EQYGDIRTLYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPSEK 360

Query: 357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT 416
           D NQGTLVVFNLDSSVS ++L QIFGIYGEI+EIR+T HK +HKFIEF+D+RAAE ALR 
Sbjct: 361 DINQGTLVVFNLDSSVSNDDLRQIFGIYGEIKEIRETPHKRHHKFIEFFDVRAAEAALRA 420

Query: 417 LNRSDVAGKQIKLEASRPGGARRFMVQ---SEQEQDDLNLCQIPFDDLSSGQM-VSSGVI 472
           LNRSD+AGK+IKLE SRPGG+RR ++Q   SE EQD+  LCQ P D+LSSG M VS G+ 
Sbjct: 421 LNRSDIAGKRIKLEPSRPGGSRRCLMQLCSSELEQDESILCQSPDDNLSSGCMAVSPGIK 480

Query: 473 TSTCMDNGSIQVLHSATRSPAIALTE---SHQTSSVPNGLPSLARVGSIGKQFGHYEPNL 529
           TS+CMDN SIQ LHSA R P  +  E   SH +SSVPN LPS  RV SI  +FG  E + 
Sbjct: 481 TSSCMDNVSIQDLHSAVRMPIGSFVENATSHGSSSVPNTLPSPMRVVSIINEFGLGETSN 540

Query: 530 SLDEMKFGNQ-HPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIR 588
           +LD+MKFGNQ  P++HPHSLPEYHD+LAN + YNS STI D+   VG +I +G+D+RHI 
Sbjct: 541 TLDQMKFGNQSFPNYHPHSLPEYHDNLANAIRYNSSSTIGDMTGHVGPRITEGIDNRHIH 600

Query: 589 GVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLH 648
            V SNGH +E  GG FGS  NGS  +HG    W NS+S+Q H SSPM+WPNSPSF NG+H
Sbjct: 601 RVGSNGHPIELNGGAFGSSGNGSCPVHGLHRAWGNSSSYQHHSSSPMIWPNSPSFSNGVH 660

Query: 649 ANRVAHMPGFPRVPPLMLNATSPAHHH-IGSAPAVNPSLWDRQHAYAGESPETSNFHLGS 707
           A R   +PGFPR PP MLN  SP HHH +GSAPAVNPSLWDR+HAY+GESPETS FHLGS
Sbjct: 661 AQRPTQVPGFPRPPPHMLNIVSPVHHHHVGSAPAVNPSLWDRRHAYSGESPETSGFHLGS 720

Query: 708 LGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQT 767
           LGS GF G SP H +++AS  I  HVGGNCMD++ NVG+RSPQQICH+FPGRN M+S+ +
Sbjct: 721 LGSVGFPGSSPLHPLEMASH-IFPHVGGNCMDISANVGLRSPQQICHVFPGRNSMLSIPS 779

Query: 768 SFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKML 827
           SFD   ER+RNLS+RR E+NSNH DKKQYELDIDRILRG+D RTTLMIKNIPNKYTSKML
Sbjct: 780 SFDLPMERVRNLSHRRTEANSNHTDKKQYELDIDRILRGEDCRTTLMIKNIPNKYTSKML 839

Query: 828 LAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKV 887
           LAAIDEH RGTYDFIYLPIDFKNKCNVGYAF+NMIDP  I+PFHQAFNGKKWEKFNSEKV
Sbjct: 840 LAAIDEHHRGTYDFIYLPIDFKNKCNVGYAFVNMIDPLHIVPFHQAFNGKKWEKFNSEKV 899

Query: 888 ASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGK 947
           ASLAYARIQGK ALIAHFQNSSLMNEDKRCRPILFHTDGPNAGD EPFPMG+NIRSR GK
Sbjct: 900 ASLAYARIQGKTALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQEPFPMGSNIRSRPGK 959

Query: 948 PRINGNEESQRQGFTSVSGNGEESPNGSDS-SGSSKGSD 985
            R +G EESQ QG  + S NGEES NG+ +  GS+K SD
Sbjct: 960 ARTSGGEESQHQGSPTTSANGEESSNGAVTLLGSAKDSD 998

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359491581|ref|XP_002280892.2| PREDICTED: protein MEI2-like 4-like [Vitis vinifera]

 Score = 1308 bits (3386), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 686/992 (69%), Positives = 789/992 (79%), Gaps = 13/992 (1%)

Query: 6   MDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQ--DGTVPMLGGKFVASSPMENFSP 63
           MD R  SA +   ++I FPAERQ+GFWKP  MSD    DG   + G K V SSP+E   P
Sbjct: 1   MDPRGVSASSPLFDDICFPAERQVGFWKPKIMSDHHEGDGVARIPGSKSVTSSPLEKLLP 60

Query: 64  VGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGIN 123
           VG  SVD+ E  +S LARD+ ++L +  EEG ANLS   W +V+H+ K+WSNL VQP  +
Sbjct: 61  VGSKSVDYSEGPESYLARDQKEKLQVNREEGTANLSRTPWRTVDHNSKTWSNLYVQPASS 120

Query: 124 SLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESL 183
            +   ++ ING   ESSLFSSSLS+IF RK+++S +++LS Q    VA H + E+ F+SL
Sbjct: 121 YVEVKKTSINGALYESSLFSSSLSEIFNRKLRVSTSDVLSHQSAGTVAPHSEEEKLFKSL 180

Query: 184 KEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFA 243
           +EIE QT+GNLLPDED+LFSGV DDMG+N  AN  DD EDFDLFSSGGGMELEGDD L  
Sbjct: 181 EEIEVQTLGNLLPDEDELFSGVVDDMGYNAHANNGDDFEDFDLFSSGGGMELEGDDHLCI 240

Query: 244 VQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI 302
            Q++SDF GG+ N QG S GS+  EHPYGEHPSRTLFVRNINSNVEDSEL+ LFEQ+GDI
Sbjct: 241 SQRHSDFNGGIPNSQGGSNGSLASEHPYGEHPSRTLFVRNINSNVEDSELRDLFEQYGDI 300

Query: 303 RTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT 362
           RT+YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDNPSEKD NQGT
Sbjct: 301 RTLYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPSEKDINQGT 360

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 422
           LVVFNLDSSVS ++L QIFGIYGEI+EIR+T HK +HKFIEF+D+RAAE ALR LNRSD+
Sbjct: 361 LVVFNLDSSVSNDDLRQIFGIYGEIKEIRETPHKRHHKFIEFFDVRAAEAALRALNRSDI 420

Query: 423 AGKQIKLEASRPGGARRFM--VQSEQEQDDLNLCQIPFDDLSSGQM-VSSGVITSTCMDN 479
           AGK+IKLE SRPGG+RR M    SE EQD+  LCQ P D+LSSG M VS G+ TS+CMDN
Sbjct: 421 AGKRIKLEPSRPGGSRRLMQLCSSELEQDESILCQSPDDNLSSGCMAVSPGIKTSSCMDN 480

Query: 480 GSIQVLHSATRSPAIALTE---SHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKF 536
            SIQ LHSA R P  +  E   SH +SSVPN LPS  RV SI  +FG  E + +LD+MKF
Sbjct: 481 VSIQDLHSAVRMPIGSFVENATSHGSSSVPNTLPSPMRVVSIINEFGLGETSNTLDQMKF 540

Query: 537 GNQ-HPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGH 595
           GNQ  P++HPHSLPEYHD+LAN + YNS STI D+   VG +I +G+D+RHI  V SNGH
Sbjct: 541 GNQSFPNYHPHSLPEYHDNLANAIRYNSSSTIGDMTGHVGPRITEGIDNRHIHRVGSNGH 600

Query: 596 LMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHM 655
            +E  GG FGS  NGS  +HG    W NS+S+Q H SSPM+WPNSPSF NG+HA R   +
Sbjct: 601 PIELNGGAFGSSGNGSCPVHGLHRAWGNSSSYQHHSSSPMIWPNSPSFSNGVHAQRPTQV 660

Query: 656 PGFPRVPPLMLNATSPAHHH-IGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFL 714
           PGFPR PP MLN  SP HHH +GSAPAVNPSLWDR+HAY+GESPETS FHLGSLGS GF 
Sbjct: 661 PGFPRPPPHMLNIVSPVHHHHVGSAPAVNPSLWDRRHAYSGESPETSGFHLGSLGSVGFP 720

Query: 715 GRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNE 774
           G SP H +++AS  I  HVGGNCMD++ NVG+RSPQQICH+FPGRN M+S+ +SFD   E
Sbjct: 721 GSSPLHPLEMASH-IFPHVGGNCMDISANVGLRSPQQICHVFPGRNSMLSIPSSFDLPME 779

Query: 775 RMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEH 834
           R+RNLS+RR E+NSNH DKKQYELDIDRILRG+D RTTLMIKNIPNKYTSKMLLAAIDEH
Sbjct: 780 RVRNLSHRRTEANSNHTDKKQYELDIDRILRGEDCRTTLMIKNIPNKYTSKMLLAAIDEH 839

Query: 835 CRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYAR 894
            RGTYDFIYLPIDFKNKCNVGYAF+NMIDP  I+PFHQAFNGKKWEKFNSEKVASLAYAR
Sbjct: 840 HRGTYDFIYLPIDFKNKCNVGYAFVNMIDPLHIVPFHQAFNGKKWEKFNSEKVASLAYAR 899

Query: 895 IQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNE 954
           IQGK ALIAHFQNSSLMNEDKRCRPILFHTDGPNAGD EPFPMG+NIRSR GK R +G E
Sbjct: 900 IQGKTALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQEPFPMGSNIRSRPGKARTSGGE 959

Query: 955 ESQRQGFTSVSGNGEESPNGSDS-SGSSKGSD 985
           ESQ QG  + S NGEES NG+ +  GS+K SD
Sbjct: 960 ESQHQGSPTTSANGEESSNGAVTLLGSAKDSD 991

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134156|ref|XP_002321750.1| predicted protein [Populus trichocarpa] gi|222868746|gb|EEF05877.1| predicted protein [Populus trichocarpa]

 Score = 1204 bits (3116), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 647/987 (65%), Positives = 745/987 (75%), Gaps = 84/987 (8%)

Query: 1   MPFEIMDHR-SGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPME 59
           MPFE+MDHR S +A +H+ ++I FPAERQIGFWKPN M D Q                  
Sbjct: 1   MPFEVMDHRGSTAASSHYFDDIHFPAERQIGFWKPNVMPDHQ------------------ 42

Query: 60  NFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQ 119
                                          G EG+AN S+++W+S++HHPKSWS+L++Q
Sbjct: 43  -------------------------------GCEGSANTSKHAWSSMDHHPKSWSSLSMQ 71

Query: 120 PGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEP 179
           P   S   +R  I+G Q ESSLFSSS S+IF+RK++ S N+I S QP   + S H+ EEP
Sbjct: 72  PASYSTGRSRVDISGTQWESSLFSSSFSEIFSRKLRSSRNDIQSHQPAKTITSSHEEEEP 131

Query: 180 FESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDD 239
           FESL+E+EA+TIGNLLP ED+LFSGVT + G + Q N +DDLEDFDLF SGGGMELEGD 
Sbjct: 132 FESLEELEAKTIGNLLPTEDNLFSGVTTEFGRDAQINNLDDLEDFDLFGSGGGMELEGD- 190

Query: 240 RLFAVQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQ 298
                + NS  + GVSN QG S GS+V  HP     SRTLFVRNINSNVE SELKALFEQ
Sbjct: 191 ---VARGNSGLLRGVSNGQGDSNGSIVVGHP-----SRTLFVRNINSNVEVSELKALFEQ 242

Query: 299 FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDA 358
           +GDIRT+YTACKHRGFVMISYYDIRAARNAM ALQNKPL+ R LDIHYSIPKDNPSEKD 
Sbjct: 243 YGDIRTLYTACKHRGFVMISYYDIRAARNAMSALQNKPLKHRNLDIHYSIPKDNPSEKDM 302

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRDTQHKHNHKFIEFYDIRAAETALRTL 417
           NQGTLVVFNLDSSV+ +EL QIFG+YGEI+E IR++ HKH+HKF+E+YDIRAAE AL  L
Sbjct: 303 NQGTLVVFNLDSSVTIDELRQIFGVYGEIKEVIRESPHKHHHKFVEYYDIRAAEAALSAL 362

Query: 418 NRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMV--SSGVITST 475
           NRSDVAGKQIK+E+S PGG R  M Q E EQ + NL Q PF+DLSSG +   S GV  S+
Sbjct: 363 NRSDVAGKQIKIESSHPGGTRSLMQQPEHEQAERNLLQSPFNDLSSGPLATFSPGVSASS 422

Query: 476 CMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMK 535
            M NGS QVLHSA  S   A  E H++SSV N LPS     S  KQF       S+DEMK
Sbjct: 423 YMANGSSQVLHSAIPSQLGAFAELHRSSSVSNNLPSPV-TASAAKQF-------SIDEMK 474

Query: 536 FGNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNG 594
           FGN+  PS HPHSLPEYHDS AN +PYNSPSTI D+ SS  +K+ +G++S HIRGV SNG
Sbjct: 475 FGNKCIPSIHPHSLPEYHDSFANTIPYNSPSTIRDMPSSFTSKVTEGINSLHIRGVGSNG 534

Query: 595 HLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAH 654
           H+ME  GGVFGSP  GS +L G+ YVW NS S QQHPS+ M+W NSPSF NG+HA+ V H
Sbjct: 535 HMMELNGGVFGSPGTGSCTLPGHHYVWKNSKSGQQHPSNAMIWSNSPSFANGVHAHHVPH 594

Query: 655 MPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFL 714
           MPGFPR   +MLN ++PA HHIGSAPAVNPSLWDR+  ++GESPE S+FHLG+LGS GF 
Sbjct: 595 MPGFPRGHTVMLN-SAPAPHHIGSAPAVNPSLWDRRQTFSGESPEASSFHLGALGSVGFP 653

Query: 715 GRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNE 774
           G SP H ++IAS NI SH GG+CMDMTK  G+ +  Q+C +FPGRNPM+SM  SF S NE
Sbjct: 654 GSSPPHPMEIASHNIFSH-GGSCMDMTKGTGLPASPQMCQMFPGRNPMISMPASFGSPNE 712

Query: 775 RMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEH 834
           R+RN S+RR ESNSNH+DKKQYELDID ILRGDD+RTTLMIKNIPNKYTSKMLLAAIDE 
Sbjct: 713 RVRNFSHRRIESNSNHSDKKQYELDIDCILRGDDNRTTLMIKNIPNKYTSKMLLAAIDEQ 772

Query: 835 CRGTYDFIYLPIDFK----------NKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNS 884
           CRGTYDFIYLPIDFK          NKCNVGYAFINMIDP+QIIPFH+AFNGKKWEKFNS
Sbjct: 773 CRGTYDFIYLPIDFKASEFSGGSTLNKCNVGYAFINMIDPQQIIPFHKAFNGKKWEKFNS 832

Query: 885 EKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSR 944
           EKVASLAYARIQGK ALIAHFQNSSLMNEDKRCRPILFH+DGPNAGDPEPFPMGT+IRSR
Sbjct: 833 EKVASLAYARIQGKTALIAHFQNSSLMNEDKRCRPILFHSDGPNAGDPEPFPMGTHIRSR 892

Query: 945 LGKPRINGNEESQRQGFTSVSGNGEES 971
           LGKPR +GNEE+   G  S   NGE+S
Sbjct: 893 LGKPRSSGNEENHHSGSPSTLANGEDS 919

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 1053 bits (2724), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 599/1011 (59%), Positives = 712/1011 (70%), Gaps = 55/1011 (5%)

Query: 5   IMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPV 64
           + D    S  ++FSEE   P+ERQ+GFWK  TM+D+        GGK +ASSPME   P 
Sbjct: 1   MTDLHGWSRSSYFSEEACLPSERQVGFWKAETMADRN------AGGKSIASSPMEKLIPT 54

Query: 65  GIPSVDWLELQQSTLARDKMKRLG----IVGEEGAANLSENSWNSVNHHPKSWSNLAVQP 120
              +V+  E  +  L RD+   L      VG E     S + W +V H   + SN  V  
Sbjct: 55  ESQTVNCWEQSEPYLIRDQKVNLSSERHAVGAERVVRNSLDMWRTVEHDLGTRSNANVHS 114

Query: 121 GINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPF 180
               + G++  + G Q E+ LFSSSLS++F RK++LS N  L    ++ VA HH+ E+ F
Sbjct: 115 ASYFMEGDKINMTGSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPHHEEEDLF 174

Query: 181 ESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDR 240
           ESL+EIEAQTIGNLLP+EDDL SGV D + +  Q +  DDLED DLFSS GGM+L GDD 
Sbjct: 175 ESLEEIEAQTIGNLLPNEDDLLSGVADVLDYVVQPSNGDDLEDIDLFSSVGGMDL-GDDG 233

Query: 241 LFAVQKNSDFVGGVSN--QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQ 298
             A Q+NS++ GG+SN   G S GS VGEHPYGEHPSRTLFVRNINSNVEDSEL+ LFEQ
Sbjct: 234 SSAGQRNSEYPGGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSELRILFEQ 293

Query: 299 FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDA 358
           +GDIR +YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDNP EKD 
Sbjct: 294 YGDIRALYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPPEKDV 353

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           NQGTLVVFNLD SV+ +EL QIFG+YGEI+EIR+T H+ +HKF+EFYDIRAAE ALR LN
Sbjct: 354 NQGTLVVFNLDPSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAEAALRALN 413

Query: 419 RSDVAGKQIKLEASRPGGARRFMVQ--SEQEQDD--LNLCQIPFDDLSSGQM---VSSGV 471
           RSD+AGK+IKLE SRPGGARR M Q  SE E+D+  L L Q    + S+       S G 
Sbjct: 414 RSDIAGKRIKLEPSRPGGARRLMQQFPSELEEDESGLYLQQNNTPNNSTTGFPGPASLGA 473

Query: 472 ITSTCMDNGSIQVLHSATRSPAIALTE--SHQ--TSSVPNGLPSLARVGSIGKQFGHYEP 527
           ITS+ M+NG+I  +HS    P     E  SH   +SSVPN LPSL  V S+G Q G  E 
Sbjct: 474 ITSSSMENGTIMGVHSGIPFPIRPFLENVSHHGISSSVPNTLPSLLSVESVGSQSGLAES 533

Query: 528 NLSLDEMKF---GNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDS 584
           + S  ++KF   G Q  S HPHSLPEY+D LANG P N    +  +A+++  +  + +++
Sbjct: 534 SRSQGQLKFDFRGTQ--SLHPHSLPEYNDGLANGAPCN---PVGTMAANINPR-PERIEN 587

Query: 585 RHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSP-MVWPNSPSF 643
           R + G +SNG  +E   GVFGS  NGS  L G+ Y+W+NS     HP SP M+WPNSPSF
Sbjct: 588 RQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNS----HHPQSPGMMWPNSPSF 643

Query: 644 LNGLHANRVAHMP----GFPRVPPLMLNAT-SPAHHHIGSAPAVNPSLWDRQHAYAGESP 698
           +NG+     AH P    G PR P  MLN   S  +HH+GSAP VNPS+WDR+H YAGES 
Sbjct: 644 MNGIG---TAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSIWDRRHTYAGESS 700

Query: 699 ETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMT---KNVGMRSPQQICHL 755
           E S FH GSLGS      S  H ++ A  NI   VGGNC+D++   KNVG+ S  Q C +
Sbjct: 701 EASGFHPGSLGSMRISNNS-LHPLEFAPHNIFPSVGGNCIDLSIPPKNVGLHSHHQRCLM 759

Query: 756 FPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDDSRTTLM 814
           FPGR+ ++ M +SFD  NER R+   RRN+++SN  D KKQYELDIDRILRG+D+RTTLM
Sbjct: 760 FPGRSQLIPMMSSFDPPNERSRS---RRNDNSSNQVDNKKQYELDIDRILRGEDTRTTLM 816

Query: 815 IKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAF 874
           IKNIPNKYTSKMLLAAIDE  RGTYDFIYLPIDFKNKCNVGYAFINM DP QIIPF+QAF
Sbjct: 817 IKNIPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAFINMTDPCQIIPFYQAF 876

Query: 875 NGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEP 934
           NGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGD  P
Sbjct: 877 NGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQVP 936

Query: 935 FPMGTNIRSRLGKPRINGNEESQRQGFTSVSGNGEESPNGSDSSGSSKGSD 985
           FPMG N+RSR GK R + NE++  QG       GE+  NG  SSGS+K SD
Sbjct: 937 FPMGVNVRSRPGKTRTSSNEDNH-QGSPPNLTTGEDYSNGDSSSGSTKDSD 986

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 1040 bits (2688), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 595/1015 (58%), Positives = 708/1015 (69%), Gaps = 80/1015 (7%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMEN 60
           MP ++ D    S  ++FSEE   P+ERQ+GFWK  TM+D+        GGK +ASSPME 
Sbjct: 1   MPSKMTDLHGWSRSSYFSEEACLPSERQVGFWKAETMADRN------AGGKSIASSPMEK 54

Query: 61  FSPVGIPSVDWLELQQSTLARDKMKRLG----IVGEEGAANLSENSWNSVNHHPKSWSNL 116
             P    +V+  E  +  L RD+   L      VG E +A+                   
Sbjct: 55  LIPTESQTVNCWEQSEPYLIRDQKVNLSSERHAVGAERSASYF----------------- 97

Query: 117 AVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQP 176
                   + G++  + G Q E+ LFSSSLS++F RK++LS N  L    ++ VA HH+ 
Sbjct: 98  --------MEGDKINMTGSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPHHEE 149

Query: 177 EEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELE 236
           E+ FESL+EIEAQTIGNLLP+EDDL SGV D + +  Q +  DDLED DLFSS GGM+L 
Sbjct: 150 EDLFESLEEIEAQTIGNLLPNEDDLLSGVADVLDYVVQPSNGDDLEDIDLFSSVGGMDL- 208

Query: 237 GDDRLFAVQKNSDFVGGVSN--QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKA 294
           GDD   A Q+NS++ GG+SN   G S GS VGEHPYGEHPSRTLFVRNINSNVEDSEL+ 
Sbjct: 209 GDDGSSAGQRNSEYPGGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSELRI 268

Query: 295 LFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
           LFEQ+GDIR +YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDNP 
Sbjct: 269 LFEQYGDIRALYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPP 328

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL 414
           EKD NQGTLVVFNLD SV+ +EL QIFG+YGEI+EIR+T H+ +HKF+EFYDIRAAE AL
Sbjct: 329 EKDVNQGTLVVFNLDPSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAEAAL 388

Query: 415 RTLNRSDVAGKQIKLEASRPGGARRFMVQ--SEQEQDD--LNLCQIPFDDLSSGQM---V 467
           R LNRSD+AGK+IKLE SRPGGARR M Q  SE E+D+  L L Q    + S+       
Sbjct: 389 RALNRSDIAGKRIKLEPSRPGGARRLMQQFPSELEEDESGLYLQQNNTPNNSTTGFPGPA 448

Query: 468 SSGVITSTCMDNGSIQVLHSATRSPAIALTE--SHQ--TSSVPNGLPSLARVGSIGKQFG 523
           S G ITS+ M+NG+I  +HS    P     E  SH   +SSVPN LPSL  V S+G Q G
Sbjct: 449 SLGAITSSSMENGTIMGVHSGIPFPIRPFLENVSHHGISSSVPNTLPSLLSVESVGSQSG 508

Query: 524 HYEPNLSLDEMKF---GNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKD 580
             E + S  ++KF   G Q  S HPHSLPEY+D LANG P N    +  +A+++  +  +
Sbjct: 509 LAESSRSQGQLKFDFRGTQ--SLHPHSLPEYNDGLANGAPCN---PVGTMAANINPR-PE 562

Query: 581 GLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSP-MVWPN 639
            +++R + G +SNG  +E   GVFGS  NGS  L G+ Y+W+NS     HP SP M+WPN
Sbjct: 563 RIENRQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNS----HHPQSPGMMWPN 618

Query: 640 SPSFLNGLHANRVAHMP----GFPRVPPLMLNAT-SPAHHHIGSAPAVNPSLWDRQHAYA 694
           SPSF+NG+     AH P    G PR P  MLN   S  +HH+GSAP VNPS+WDR+H YA
Sbjct: 619 SPSFMNGIG---TAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSIWDRRHTYA 675

Query: 695 GESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMT---KNVGMRSPQQ 751
           GES E S FH GSLGS      S  H ++ A  NI   VGGNC+D++   KNVG+ S  Q
Sbjct: 676 GESSEASGFHPGSLGSMRISNNS-LHPLEFAPHNIFPSVGGNCIDLSIPPKNVGLHSHHQ 734

Query: 752 ICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDDSR 810
            C +FPGR+ ++ M +SFD  NER R+   RRN+++SN  D KKQYELDIDRILRG+D+R
Sbjct: 735 RCLMFPGRSQLIPMMSSFDPPNERSRS---RRNDNSSNQVDNKKQYELDIDRILRGEDTR 791

Query: 811 TTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPF 870
           TTLMIKNIPNKYTSKMLLAAIDE  RGTYDFIYLPIDFKNKCNVGYAFINM DP QIIPF
Sbjct: 792 TTLMIKNIPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAFINMTDPCQIIPF 851

Query: 871 HQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAG 930
           +QAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAG
Sbjct: 852 YQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAG 911

Query: 931 DPEPFPMGTNIRSRLGKPRINGNEESQRQGFTSVSGNGEESPNGSDSSGSSKGSD 985
           D  PFPMG N+RSR GK R + NE++  QG       GE+  NG  SSGS+K SD
Sbjct: 912 DQVPFPMGVNVRSRPGKTRTSSNEDNH-QGSPPNLTTGEDYSNGDSSSGSTKDSD 965

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  986 bits (2550), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 579/1007 (57%), Positives = 703/1007 (69%), Gaps = 53/1007 (5%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQDGTVPMLGGKFVASSPMEN 60
           MP EIMD +  S+ + FSE+  FP+ERQ+GFWK +TM DQ+   +    GK    SP E 
Sbjct: 1   MPSEIMDLQGLSSSSFFSEDASFPSERQVGFWKSDTMPDQRGQYIRDTLGKSYVLSPSEK 60

Query: 61  FSPVGIPSVDWLELQQSTLARDKMKRLGI----VGEEGAANLSENSWNSVNHHPKSWSNL 116
              V + SV  LE  Q +L  D+     +    VG E A N S      V++   + ++L
Sbjct: 61  L--VAVESVQSLEHPQPSLMHDQKMNHSLDKHAVGAERALNRSFTLLRPVDNDTGTGTSL 118

Query: 117 AVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQP 176
            VQP        +      Q E+SLFSSSLS++F+RK++LS    L    ++ +ASH + 
Sbjct: 119 NVQPTSYFAEVGKVNAMATQHENSLFSSSLSELFSRKLRLSSTNSLYGHSVDTIASHFEE 178

Query: 177 EEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELE 236
           EEPF+SL+EIEAQTIGNLLP++DDLFSGVTD + +    +  DD+ED D FSS GGM+L 
Sbjct: 179 EEPFQSLEEIEAQTIGNLLPNDDDLFSGVTDRVENINHPSGGDDMEDLDFFSSVGGMDL- 237

Query: 237 GDDRLFAVQKNSDFVGGVSNQGVSAG--SVVGEHPYGEHPSRTLFVRNINSNVEDSELKA 294
           GDD   A Q +S+F GG SN  + A   SV GEHPYGEHPSRTLFVRNINSNVE+SEL+A
Sbjct: 238 GDDGSVA-QIDSEFHGGASNGQLGACNLSVAGEHPYGEHPSRTLFVRNINSNVEESELRA 296

Query: 295 LFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
           +FEQ+GDIRT+YTACKHRGFVMISYYDIRAA+NAMKALQN+PLR RKLDIHYSIPKDNPS
Sbjct: 297 IFEQYGDIRTLYTACKHRGFVMISYYDIRAAKNAMKALQNRPLRCRKLDIHYSIPKDNPS 356

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL 414
           EKD NQGTL VFNLDSSVS ++L +IFG+YGEI+EIR+T H+++HKF+EFYD+RAAE AL
Sbjct: 357 EKDFNQGTLAVFNLDSSVSNDDLRRIFGVYGEIKEIRETPHRNHHKFVEFYDVRAAEAAL 416

Query: 415 RTLNRSDVAGKQIKLEASRPGGARRFMVQ--SEQEQDDLNLCQIPFDDLSSGQMVS---- 468
             LN+SD+AGK+IKLEAS PGG RR + Q   E EQD+      PF   SS    S    
Sbjct: 417 HALNKSDIAGKRIKLEASCPGGLRRLLHQIPPELEQDEFG----PFVQQSSPPNNSTTEF 472

Query: 469 SGVITSTCMDNGSIQVLHSATRSPAIALTESHQT-SSVPNGLPSLARVGSIGKQFGHYEP 527
           SG + ST MDNG I   HSAT++P       H   SSVPN + SL+RV S G Q G  E 
Sbjct: 473 SGTVISTGMDNGPILGAHSATQAPFFESALHHGISSSVPNSMSSLSRVESAGNQTGFAEL 532

Query: 528 NLSLDEMKFGNQHP-SFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRH 586
           + S   +KF  Q   +FHPHSLPEY D L +G+  NSP     +A+++  ++ + +D+RH
Sbjct: 533 SHSPGHLKFDIQSTLNFHPHSLPEY-DGLNSGVHCNSPGA---MAANINPRLLERIDTRH 588

Query: 587 IRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNG 646
           +  +S NG+ +E + GVFGS RNGS S  G+ Y W NS  HQ      M+WPNSPSF+NG
Sbjct: 589 LARISPNGNPIEFSEGVFGSARNGSCSRPGHHYTWGNSYHHQ---PPGMIWPNSPSFVNG 645

Query: 647 LHANRVAH----MPGFPRVPPLMLNATSPA-HHHIGSAPAVNPSLWDRQHAYAGESPETS 701
           +    VAH    + G PR PP MLN   P  + H+GS PAVNPSLWDRQHAYAGESP+ S
Sbjct: 646 I---SVAHPGPRLHGPPRAPPPMLNPVLPINNQHVGSVPAVNPSLWDRQHAYAGESPDAS 702

Query: 702 NFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDM---TKNVGMRSPQQICHLFPG 758
            FH  SLGS      S  H ++  S  +  HVGGNC+++    +NVG +S QQ   +FPG
Sbjct: 703 GFHPCSLGSMRISNNS-LHSMEFLSPKMFPHVGGNCLELPMPPQNVGFQSQQQRSMVFPG 761

Query: 759 RNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNI 818
           R  M+ M  +FD+  ER R+   RRNE +++ ADKKQYELDIDRIL+G+D+RTTLMIKNI
Sbjct: 762 RGQMIPMINTFDAPGERARS---RRNEGSTSQADKKQYELDIDRILQGEDNRTTLMIKNI 818

Query: 819 PNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKK 878
           PNKYTSKMLLAAIDE  +GTY+F        NKCNVGYAFINMIDPRQIIPF+QAFNGKK
Sbjct: 819 PNKYTSKMLLAAIDERHKGTYNF--------NKCNVGYAFINMIDPRQIIPFYQAFNGKK 870

Query: 879 WEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMG 938
           WEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILF+TDGPNAGD  PFPMG
Sbjct: 871 WEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFNTDGPNAGDQVPFPMG 930

Query: 939 TNIRSRLGKPRINGNEESQRQGFTSVSGNGEESPNGSDSSGSSKGSD 985
            N+R+R GKPR   +EE+Q QG  S    GE+S NG  SSGS K SD
Sbjct: 931 VNVRTRPGKPRTITHEENQ-QGSPSNLAGGEDSSNGDASSGSGKESD 976

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507390|ref|XP_003522450.1| PREDICTED: protein MEI2-like 4-like [Glycine max]

 Score =  983 bits (2540), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 559/986 (56%), Positives = 687/986 (69%), Gaps = 34/986 (3%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQ-QDGTVPML---GGKFVASS 56
           MP EIM+ R  SA + F ++I + +E+  G  KP  + D    G   M    G  F  SS
Sbjct: 1   MPSEIMEKRGVSASSRFLDDISYVSEKNTGLRKPKFIHDHFLQGKSEMAASPGIIFNTSS 60

Query: 57  PMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAAN-LSENSWNSVNHHPKSWSN 115
           P E  +  G      L + Q+TL+R+  + L    E G    L +++  S+N+H +SWSN
Sbjct: 61  PHETNAKTG------LLMSQTTLSREITEDLHFGREAGNIEMLKDSTTESLNYHKRSWSN 114

Query: 116 LAVQPGINS--LSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASH 173
           +  QP  +S  L G++   N    ESSLFSSSLSD+F++K++L GN +LS QP+  V S 
Sbjct: 115 VHRQPASSSYGLVGSKIVTNAASRESSLFSSSLSDMFSQKLRLLGNGVLSGQPI-TVGSL 173

Query: 174 HQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM 233
            + EEP++SL+EIEA+TIGNLLPDEDDLFSGV D++G + +    DD EDFDLFSS GGM
Sbjct: 174 PE-EEPYKSLEEIEAETIGNLLPDEDDLFSGVNDELGCSTRTRMNDDFEDFDLFSSSGGM 232

Query: 234 ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELK 293
           ELEGD+ L + ++ S         GVS G +    P+GE  SRTLFVRNINSNVEDSELK
Sbjct: 233 ELEGDEHLISGKRTSCGDEDPDYFGVSKGKI----PFGEQSSRTLFVRNINSNVEDSELK 288

Query: 294 ALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP 353
           ALFEQ+G+IRTIYTACK+RGFVMISYYD+RAA+NAMKALQN+ LR RKLDIHYSIPK N 
Sbjct: 289 ALFEQYGNIRTIYTACKYRGFVMISYYDLRAAQNAMKALQNRSLRSRKLDIHYSIPKGNS 348

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 413
            EKD   GTL++ NLDSSV  +EL QIFG YGEIREI +    ++ KFIEFYD+RAAE +
Sbjct: 349 PEKDIGHGTLMISNLDSSVLDDELKQIFGFYGEIREIYEYPQLNHVKFIEFYDVRAAEAS 408

Query: 414 LRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQM--VSSGV 471
           LR LN    AGK IKLE   P  A   M QS + +D+ ++     D++S      VSSG 
Sbjct: 409 LRALNGICFAGKHIKLEPGLPKIATCMMHQSHKGKDEPDVGHSLSDNISLRHKAGVSSGF 468

Query: 472 ITS-TCMDNGSIQVLHSATRSPA-IALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNL 529
           I S + ++NG  Q  HSAT+ PA I  +  H  SS+      + R  S GK  G +E + 
Sbjct: 469 IASGSSLENGYNQGFHSATQLPAFIDNSPFHVNSSIHK----ITRGASAGKVSGVFEASN 524

Query: 530 SLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRG 589
           + D MKF +    FHPHSLPEY +SLA G PYN  STI + AS++GT   +  +SRHI+G
Sbjct: 525 AFDAMKFASI-SRFHPHSLPEYRESLATGSPYNFSSTI-NTASNIGTGSTESSESRHIQG 582

Query: 590 VSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHA 649
           +SS G+L E   G FG   NG++  HG  ++WN SN HQQ  S+ M+W  +PSF+NG  +
Sbjct: 583 MSSTGNLAEFNAGDFGPSGNGNHPHHGLYHMWNGSNLHQQPSSNAMLWQKTPSFVNGACS 642

Query: 650 NRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLG 709
             +  +P FPR PP +L A S   H +GSAP V  S WDRQH++ GESP+ S F LGS+G
Sbjct: 643 PGLPQIPSFPRTPPHVLRA-SHIDHQVGSAPVVTASPWDRQHSFLGESPDASGFRLGSVG 701

Query: 710 SGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSF 769
           S GF G    H    AS NI SHVGGN  ++T N G  SP+Q+ H+FPG+ PM ++ + F
Sbjct: 702 SPGFHGSWQLH--PPASHNIFSHVGGNGTELTSNAGQGSPKQLSHVFPGKLPM-TLVSKF 758

Query: 770 DSSNERMRNLSYRRNESNSNH-ADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLL 828
           D++NERMRNL  RR+E N+N+ ADKKQYELD+ RILRGDD+RTTLMIKNIPNKYTSKMLL
Sbjct: 759 DTTNERMRNLYSRRSEPNTNNNADKKQYELDLGRILRGDDNRTTLMIKNIPNKYTSKMLL 818

Query: 829 AAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVA 888
            AIDE CRGTYDF+YLPIDFKNKCNVGYAFINMIDP QIIPFH+AF+GKKWEKFNSEKVA
Sbjct: 819 VAIDEQCRGTYDFLYLPIDFKNKCNVGYAFINMIDPGQIIPFHKAFHGKKWEKFNSEKVA 878

Query: 889 SLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKP 948
            LAYARIQGK+ALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFP+G NIR R GK 
Sbjct: 879 VLAYARIQGKSALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPLGNNIRVRPGKI 938

Query: 949 RINGNEESQRQGFTSVSGNGEESPNG 974
           RINGNEE++ QG  S   +GEES N 
Sbjct: 939 RINGNEENRSQGNPSSLASGEESGNA 964

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356527581|ref|XP_003532387.1| PREDICTED: protein MEI2-like 1-like [Glycine max]

 Score =  974 bits (2517), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 549/986 (55%), Positives = 672/986 (68%), Gaps = 43/986 (4%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQ----QDGTVPMLGGKFVASS 56
           MPF+IMD R  SA +H+ ++I F +ER +G  KP +++D      +G V   G    A+ 
Sbjct: 1   MPFQIMDQRGVSASSHYFDDISFRSERNVGLRKPKSINDHYPQGNNGMVASPGNILNATP 60

Query: 57  PMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNL 116
           P++  +  G      L L Q++L  D +                +S  S N+  KS SN 
Sbjct: 61  PLDVNAKAG------LLLPQASLPGDNI----------------HSTESSNYRTKSLSNA 98

Query: 117 AVQ--PGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHH 174
            +Q  P    L GN+   N    ESSLFSSS+S+IF++K++  GN++ S  P+ A +   
Sbjct: 99  CLQSAPTSYGLIGNKIVTNAAPFESSLFSSSMSEIFSQKLRFFGNDVRSDHPITAGSP-- 156

Query: 175 QPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGME 234
             EEP++SL+E+EA TIGNLLPDEDDLFSGV D++G +  A T DD EDFDLFSSGGGME
Sbjct: 157 PKEEPYKSLEEMEADTIGNLLPDEDDLFSGVVDELGCSSHARTNDDFEDFDLFSSGGGME 216

Query: 235 LEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKA 294
           +EGD+ L + ++ S   G     G S G +    P  E PSRTLFVRNINSNVEDSELKA
Sbjct: 217 MEGDEHLSSGKRMSALDGDFGFFGSSKGKL----PLVEQPSRTLFVRNINSNVEDSELKA 272

Query: 295 LFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
           LFEQ+GDIRTIYTA KHRGFVMISY D+RAA+NAM+ALQN+PL  RKLDIHYSIPK N  
Sbjct: 273 LFEQYGDIRTIYTASKHRGFVMISYQDLRAAQNAMQALQNRPLGSRKLDIHYSIPKVNAP 332

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL 414
           EKD   GTL++  LDS V  +EL QIFG YGEI+EI +    +NHKFIEFYD+RAAE AL
Sbjct: 333 EKDIGHGTLMLSGLDSPVLNDELKQIFGFYGEIKEIYEYSEMNNHKFIEFYDVRAAEAAL 392

Query: 415 RTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVS--SGVI 472
           R LN+ D+AGKQIKLE   P      M QS++ Q++ +L Q   D+LS  Q  +  SGVI
Sbjct: 393 RALNKIDIAGKQIKLEPGHPS----LMHQSQKGQEERDLGQSIIDNLSLRQKATLPSGVI 448

Query: 473 TSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLD 532
            S C++NG  Q   S  R P  A  + +    V +G+ +  R    GK     E +  +D
Sbjct: 449 GSGCLENGYNQRFQSTVRQPLNAFMD-NAFIHVNSGIHNTVRGAPAGKVSSVCESSNFVD 507

Query: 533 EMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSS 592
            MKF +    FHPHSLPEY DSLANG PYN  S+I+++A+++G    +  D RHI+G+ S
Sbjct: 508 AMKFASGS-RFHPHSLPEYRDSLANGSPYNFSSSISNMANNIGAGATEASDGRHIQGMGS 566

Query: 593 NGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRV 652
            G+L E   G F S  NG     G  ++WN+SN  QQ  SS M+W  SPSF+N   +  +
Sbjct: 567 TGNLAEFNAGYFCSSGNGIRPHQGLYHMWNSSNLQQQPSSSTMLWQKSPSFVNDASSPGL 626

Query: 653 AHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGG 712
             M  F R PP ML       HH+GSAP V  S W+RQ++Y G SPE S F LGSLGSGG
Sbjct: 627 PQMSSFARTPPHMLRTPHMMDHHVGSAPVVTASPWERQNSYLGGSPEASGFRLGSLGSGG 686

Query: 713 FLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSS 772
           F G    H +D  S N+ SHVGGN  ++T N G  SP+Q+ H+FP R+PM SM + FD+S
Sbjct: 687 FHGSWQMHPLDFPSHNMFSHVGGNGTELTTNAGQNSPKQLSHVFPVRHPMSSM-SKFDAS 745

Query: 773 NERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAID 832
           NERMRNL +R+NE+++N+ DKK YELD+ RILRG+DSRTTLMIKNIPNKYTSKMLLAAID
Sbjct: 746 NERMRNLYHRKNEASTNNVDKKLYELDLGRILRGEDSRTTLMIKNIPNKYTSKMLLAAID 805

Query: 833 EHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAY 892
           E C+GTYDF+YLPIDFKNKCNVGYAFINMIDP QIIPFHQAF+GKKWEKFNSEKVASLAY
Sbjct: 806 EQCKGTYDFLYLPIDFKNKCNVGYAFINMIDPGQIIPFHQAFDGKKWEKFNSEKVASLAY 865

Query: 893 ARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRING 952
           ARIQGK +LIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMG NIR R GK R  G
Sbjct: 866 ARIQGKGSLIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGANIRLRPGKSRTAG 925

Query: 953 NEESQRQGFTSVSGNGEESPNGSDSS 978
           NEE++ QG  S   +GEES NG DSS
Sbjct: 926 NEENRSQGSPSTLSSGEESANGIDSS 951

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242061760|ref|XP_002452169.1| hypothetical protein SORBIDRAFT_04g021130 [Sorghum bicolor] gi|241932000|gb|EES05145.1| hypothetical protein SORBIDRAFT_04g021130 [Sorghum bicolor]

 Score =  952 bits (2462), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 540/1029 (52%), Positives = 686/1029 (66%), Gaps = 76/1029 (7%)

Query: 1   MPFEIMDHRS--------GSAPTHFSEE-IRFPAERQIGFWKPNTMSDQQDGTVPMLGGK 51
           MP ++MD R           A + FSEE +R P ERQ+GFWK  ++          +G K
Sbjct: 1   MPSQVMDPRRHLSQFSNPTLAASSFSEEQLRLPTERQVGFWKQESLHH--------IGSK 52

Query: 52  FVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGI----VGEEGAANLSENSWNSVN 107
            VASSP+E   P+G  +V  ++ Q   L RD+     +     G+E   NL  + W + +
Sbjct: 53  SVASSPIEKPQPIGTKTVARIDPQPYKL-RDQKTAFSLEHKTFGQERHVNLPPSLWRT-D 110

Query: 108 HHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPL 167
             P   S+ ++ P      G R+  N   +E+ LFSSSLS+IF RK+ L   ++L RQP+
Sbjct: 111 QDPNLQSDSSLFP-----DGRRTNPNEAYNENGLFSSSLSEIFDRKLGLRSKDVLLRQPV 165

Query: 168 NAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLF 227
             V   H  EEPFE  +EIEAQ IGN+LPD+DDL SGV D +G+   AN  DD++D D+F
Sbjct: 166 EKVDPTHVDEEPFELTEEIEAQIIGNILPDDDDLLSGVLD-VGYTAHANNGDDVDD-DIF 223

Query: 228 SSGGGMELEGDDRLFAVQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSN 286
            +GGGMELE D+     +KN++  GG ++  G+  G++ GEHPYGEHPSRTLFVRNINSN
Sbjct: 224 YTGGGMELETDEN----KKNTETNGGANDGLGLLNGTMNGEHPYGEHPSRTLFVRNINSN 279

Query: 287 VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY 346
           VEDSEL+ LFE +G+I  +YTACKHRGFVMISYYDIR+A NAM+ALQNKPLRRRKLDIHY
Sbjct: 280 VEDSELRLLFEHYGEISNLYTACKHRGFVMISYYDIRSAWNAMRALQNKPLRRRKLDIHY 339

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYD 406
           SIPKDNPSEKD NQG LVVFN+D SV+  ++HQIF  YGEI+EIRD   K +HK IEFYD
Sbjct: 340 SIPKDNPSEKDINQGMLVVFNVDPSVTNNDIHQIFSDYGEIKEIRDAPQKGHHKIIEFYD 399

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQE--QDDLNLCQI-------- 456
           +RAAE+A+R LNRSD+AGK+IKLE  R   ARR      +E  Q++  +C++        
Sbjct: 400 VRAAESAVRALNRSDLAGKKIKLETGRLSAARRLTQHMSKELGQEEFGVCKLGSPSTNSP 459

Query: 457 PFDDLSSGQMVSSGVITSTCMDNGSIQVLHSA---TRSPAIALTESHQTSSVPNGLPS-- 511
           P   L S  M +   +TS+  +NGSI  LHS    + SP    +    +S++P  L S  
Sbjct: 460 PLASLGSSNMAA---MTSSGRENGSIHGLHSGLLTSMSPFREASFPGLSSTIPQSLSSPI 516

Query: 512 -LARVGSIGKQFGHYEPNLSLDEMK----FGNQ-HPSFHPHSLPEYHDSLANGLPYNSPS 565
            +A   +   Q    E + SL  M     +G Q   + HPHSLPE H+   NG PYN  +
Sbjct: 517 GIASAATHSSQASLGELSHSLSRMNGHMNYGFQGMGALHPHSLPEVHNGANNGTPYNL-N 575

Query: 566 TIADIASSVGTKIKDGLDSRHIRGVSS---NGHLMEPTG-GVFGSPRNGSYSLHGNPYVW 621
           T+A I  +  ++  + +DSRH+  V S   +GH  +  G G  G  R+GS  + G+  +W
Sbjct: 576 TMAPIGVNSNSRTAEAVDSRHLHKVGSGNLSGHSFDRVGEGAMGFSRSGSGPVRGHQLMW 635

Query: 622 NNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHH-IGSAP 680
           NNSN+  +HP+SP++W N  SF+N + +   A M G PR P  M+    P HHH +GSAP
Sbjct: 636 NNSNNFHRHPNSPVLWQNPGSFVNNVPSRPPAQMHGVPRAPSHMIENVLPMHHHHVGSAP 695

Query: 681 AVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDM 740
           A+NPSLWDR+H YAGE  E S+FH GS+GS GF G    H +++ S  I SH  GN MD 
Sbjct: 696 AINPSLWDRRHGYAGELTEASSFHPGSVGSMGFPGSPQLHGLELNS--IFSHTSGNRMDP 753

Query: 741 T---KNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHAD-KKQY 796
           T     +   SPQQ   +F GRNPM+ +  SFDS  ERMR+   RRN+S +N +D K+QY
Sbjct: 754 TVSSAQISAPSPQQRGPMFHGRNPMVPL-PSFDSPGERMRS---RRNDSGANQSDNKRQY 809

Query: 797 ELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGY 856
           ELD+DRI+RG+DSRTTLMIKNIPNKYTSKMLLAAIDE  +GTYDFIYLPIDFKNKCNVGY
Sbjct: 810 ELDVDRIMRGEDSRTTLMIKNIPNKYTSKMLLAAIDESHKGTYDFIYLPIDFKNKCNVGY 869

Query: 857 AFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKR 916
           AFINM +P+ IIPF+Q FNGKKWEKFNSEKVASLAYARIQGK ALIAHFQNSSLMNEDKR
Sbjct: 870 AFINMTNPQHIIPFYQTFNGKKWEKFNSEKVASLAYARIQGKTALIAHFQNSSLMNEDKR 929

Query: 917 CRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEESQRQGFTSVSGNGEESPNGSD 976
           CRPILFH++GPNAGD EPFPMGTNIR+R G+ R +  EE+      +V  NG+ S NG+D
Sbjct: 930 CRPILFHSEGPNAGDQEPFPMGTNIRARSGRSRTSSGEENHHD-IQTVLTNGDTSSNGAD 988

Query: 977 SSGSSKGSD 985
           +SGS+K ++
Sbjct: 989 ASGSTKDTE 997

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	985
TAIR|locus:2182885	907	ML4 "MEI2-like 4" [Arabidopsis	0.786	0.854	0.555	4.2e-230
TAIR|locus:2156166	915	ML1 "MEI2-like protein 1" [Ara	0.715	0.770	0.543	2.3e-205
TAIR|locus:2013583	800	ML5 "MEI2-like protein 5" [Ara	0.361	0.445	0.530	1.2e-162
TAIR|locus:2117706	759	ML3 "MEI2-like 3" [Arabidopsis	0.384	0.499	0.493	6.2e-152
TAIR|locus:2045605	843	ML2 "MEI2-like 2" [Arabidopsis	0.425	0.497	0.456	1.3e-130
TAIR|locus:2090350	615	TEL1 "terminal EAR1-like 1" [A	0.121	0.195	0.422	3.6e-50
POMBASE|SPAC27D7.03c	750	mei2 "RNA-binding protein invo	0.168	0.221	0.505	7.1e-44
TAIR|locus:2008530	527	TEL2 "terminal EAR1-like 2" [A	0.128	0.240	0.416	7.7e-44
DICTYBASE|DDB_G0279255	1698	DDB_G0279255 [Dictyostelium di	0.175	0.101	0.313	3.7e-35
GENEDB_PFALCIPARUM|PFF1125c	427	PFF1125c "RNA-binding protein	0.134	0.309	0.478	7.4e-28

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

 Score = 2152 (762.6 bits), Expect = 4.2e-230, Sum P(2) = 4.2e-230
 Identities = 444/799 (55%), Positives = 555/799 (69%)

Query:   162 LSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDL 221
             L R    A  S ++ EEP ESL+E+EAQTIGNLLPDEDDLF+ V  +  H  +AN  DDL
Sbjct:   105 LPRSDKLAFMSANREEEPSESLEEMEAQTIGNLLPDEDDLFAEVVGEGVHKSRANGGDDL 164

Query:   222 EDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVR 281
             +D DLFSS GGMEL+GD  +F+     D   G SN      S V EHP GE  SR LFVR
Sbjct:   165 DDCDLFSSVGGMELDGD--VFSSVSQRDGKRG-SNV-----STVAEHPQGEILSRILFVR 216

Query:   282 NINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK 341
             N++S++ED EL  LF+QFGD+R ++TA K+RGF+M+SYYDIRAA+ A +AL  + LR RK
Sbjct:   217 NVDSSIEDCELGVLFKQFGDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRK 276

Query:   342 LDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKF 401
             LDI YSIPK+NP E ++++G L V NLDSS+S EELH IF  YGEIRE+R T H+++  +
Sbjct:   277 LDIRYSIPKENPKE-NSSEGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVY 335

Query:   402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDL 461
             IEF+D+R A+ AL+ LN  +VAG+Q+KL  + P G   F  Q   +  +  L ++ F++L
Sbjct:   336 IEFFDVRKAKVALQGLNGLEVAGRQLKLAPTCPEGTS-FWPQFASDDGEGGLPKMAFNNL 394

Query:   462 SSGQMVSS--GVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIG 519
             SS  M     G++ ST +D GSI+ +H++  SP  +  E HQ+  VP GLP  ARV S  
Sbjct:   395 SSAHMGRHFPGILASTSIDGGSIRGMHNSVGSPMNSFIERHQSLDVPIGLPPSARVISAS 454

Query:   520 KQFGHYEPNLSLDEMKFGNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKI 578
             K  G  E     D  K G Q  P+ HPH  P+Y D+ A+G PY S +T +++ S  G K 
Sbjct:   455 KPVGLQEFGNPFDNSKTGIQSMPNLHPH-FPDYLDNFASGSPYKSSTTFSEMVSD-GQKA 512

Query:   579 KDGLDSRHIRGVSSNGHLMEPTGGVFGSPRN-GSYSLHGNPYVWXXXXXXXXXXXXXMVW 637
              +G    ++RGV  +G      GGV GSP N GS+   GN  +W             M+W
Sbjct:   513 NEGFMMSNVRGVGVDGF----NGGVIGSPINQGSH--RGNLNLWSNSNSQQHNQSSGMMW 566

Query:   638 PNSPSFLNGLHANRVAHMPGFPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGE 696
             PNSPS +NG+ + R+  +  F R  PLM+N A+SP HHHIGSAP +N   WDR+ AY  E
Sbjct:   567 PNSPSRVNGVPSQRIPPVTAFSRASPLMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAE 626

Query:   697 SPETSNFHXXXXXXXXXXXXXPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHL 755
             SPE+S FH             PSH +D  S  + SHVGGN M+  +KN  +RS +Q+ HL
Sbjct:   627 SPESSGFHLGSPGSMGFPGSSPSHPMDFGSHKVFSHVGGNRMEANSKNAVLRSSRQMPHL 686

Query:   756 FPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMI 815
             F GR+PM+S+  SFD  NER RNLS+RR+ESNS++A+KK YELD+DRILRG+DSRTTLMI
Sbjct:   687 FTGRSPMLSVSGSFDLPNERYRNLSHRRSESNSSNAEKKLYELDVDRILRGEDSRTTLMI 746

Query:   816 KNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFN 875
             KNIPNKYTSKMLLAAIDE+C+GTYDF+YLPIDFKNKCNVGYAFIN+I+P  I+PF++AFN
Sbjct:   747 KNIPNKYTSKMLLAAIDEYCKGTYDFLYLPIDFKNKCNVGYAFINLIEPENIVPFYKAFN 806

Query:   876 GKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPF 935
             GKKWEKFNSEKVASLAY RIQGK+ALIAHFQNSSLMNEDKRCRPILFHT GPNAGD EPF
Sbjct:   807 GKKWEKFNSEKVASLAYGRIQGKSALIAHFQNSSLMNEDKRCRPILFHTAGPNAGDQEPF 866

Query:   936 PMGTNIRSRLGKPRINGNE 954
             PMG+NIRSR GK R N  E
Sbjct:   867 PMGSNIRSRPGKHRTNSIE 885

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

 Score = 1902 (674.6 bits), Expect = 2.3e-205, Sum P(2) = 2.3e-205
 Identities = 396/728 (54%), Positives = 497/728 (68%)

Query:   232 GMELEGDDRLFAV---QKNSDFVGGVSNQGVSAG--SVVGEHPYGEHPSRTLFVRNINSN 286
             G EL+  D   +V   + + D    VS++    G  + VGE   GE PSRTL V NI+SN
Sbjct:   168 GDELDEFDLFSSVGGMELDGDIFSSVSHRNGERGGNNSVGELNRGEIPSRTLLVGNISSN 227

Query:   287 VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY 346
             VED ELK LFEQFGDI+ ++TACK+RGF+M+SY DIRAA+NA +ALQNK LR  KLDI Y
Sbjct:   228 VEDYELKVLFEQFGDIQALHTACKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRY 287

Query:   347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYD 406
             SI K+NPS+KD ++G L+V NLDSS+S +EL+++   YGE++EIR T H ++  +IEF+D
Sbjct:   288 SISKENPSQKDTSKGALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFD 347

Query:   407 IRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQM 466
             +RAA  AL  LN  +VAGK+++L  + P G R +  Q      +  L +  + + SSG +
Sbjct:   348 VRAAAAALGGLNGLEVAGKKLQLVPTYPEGTR-YTSQCAANDTEGCLPKTSYSNTSSGHI 406

Query:   467 VSS--GVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGH 524
                  G+I+ST  D GS++V+H++  SP  +  E H++ S+P G P  A   S  K  G 
Sbjct:   407 GRHFPGMISSTSSDGGSMRVIHNSIGSPVNSFIERHRSLSIPIGFPPSANGISASKPVGL 466

Query:   525 YEPNLSLDEMKFGNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLD 583
              E     D    G Q  P+ HPHS  EY D+ ANG PY S S  +++ S  G+K  +G  
Sbjct:   467 QEHGHHFDNSNMGIQSMPNLHPHSFSEYVDNFANGSPYTS-SAFSEMVSD-GSKANEGFM 524

Query:   584 SRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWXXXXXXXXXXXXXMVWPNSPSF 643
               ++RGV   G     +GG  GSP + S     N  +W             M+WPNSPS 
Sbjct:   525 IHNVRGVE--GF----SGGGIGSPMHQSSRRPIN--LWSNSNTQQQNPSSGMMWPNSPSH 576

Query:   644 LNGLHANRVAHMPGFPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSN 702
             +N +   R   +  F R PP+M+N A+SP HHHIGSAP +N   WDR+ AY  ES E+S 
Sbjct:   577 INSIPTQRPP-VTVFSRAPPIMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAESLESSG 635

Query:   703 FHXXXXXXXXXXXXXPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHLFPGRNP 761
             FH             PSH +DI S    S VGGN MD+ ++N  +RSPQQ+ HLFPGR+P
Sbjct:   636 FHIGSHGSMGIPGSSPSHPMDIGSHKTFS-VGGNRMDVNSQNAVLRSPQQLSHLFPGRSP 694

Query:   762 MMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNK 821
             M SM  SFDS NER RNLS+RR+ES+S++ADKK YELD+DRILRG+D RTTLMIKNIPNK
Sbjct:   695 MGSMPGSFDSPNERYRNLSHRRSESSSSNADKKLYELDVDRILRGEDRRTTLMIKNIPNK 754

Query:   822 YTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEK 881
             YTSKMLL+AIDEHC+GTYDF+YLPIDFKNKCNVGYAFIN+I+P +I+PF +AFNGKKWEK
Sbjct:   755 YTSKMLLSAIDEHCKGTYDFLYLPIDFKNKCNVGYAFINLIEPEKIVPFFKAFNGKKWEK 814

Query:   882 FNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNI 941
             FNSEKVA+L YARIQGK ALIAHFQNSSLMNEDKRCRPILFHTDGPNAGD EPFPMG+NI
Sbjct:   815 FNSEKVATLTYARIQGKTALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDQEPFPMGSNI 874

Query:   942 RSRLGKPR 949
             RSR GKPR
Sbjct:   875 RSRPGKPR 882

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

 Score = 930 (332.4 bits), Expect = 1.2e-162, Sum P(2) = 1.2e-162
 Identities = 206/388 (53%), Positives = 261/388 (67%)

Query:   181 ESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD-- 238
             ES  + E+ +IGNLLPDE+DL +G+ DD+        + D +D+DLF SGGGMEL+ D  
Sbjct:    68 ESADDFESHSIGNLLPDEEDLLTGMMDDL----DLGELPDADDYDLFGSGGGMELDADFR 123

Query:   239 DRLFAV---QKNSDFVGGVS----NQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSE 291
             D L      + +   +GG +    N    AG+V GEHPYGEHPSRTLFVRNINSNVEDSE
Sbjct:   124 DNLSMSGPPRLSLSSLGGNAIPQFNIPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSE 183

Query:   292 LKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD 351
             L ALFEQ+GDIRT+YT CKHRGFVMISYYDIR+AR AM++LQNKPLRRRKLDIH+SIPKD
Sbjct:   184 LTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKD 243

Query:   352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 411
             NPSEKD NQGTLVVFNLD S+S ++LH IFG +GEI+EIR+T HK +HKF+EFYD+R AE
Sbjct:   244 NPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAE 303

Query:   412 TALRTLNRSDVAGKQIKLEASRPGGARR-FMVQSEQ--EQDDLNLCQIPFDDLSSGQMVS 468
              AL+ LNR ++AGK+IK+E SRPGGARR  M+Q  Q  E DDL+   +    +++   + 
Sbjct:   304 AALKALNRCEIAGKRIKVEPSRPGGARRSLMLQLNQDLENDDLHYLPMIGSPMANSPPMQ 363

Query:   469 SGVITSTCMDNGSIQVLHSATRSPAIAL--TESHQTSSVPNGL----PS--LARVG--SI 518
                  ++ ++   +Q + S  RSP   L  T +   S + + L    PS  LA +G   I
Sbjct:   364 GNWPLNSPVEGSPLQSVLS--RSPVFGLSPTRNGHLSGLASALNSQGPSSKLAPIGRGQI 421

Query:   519 G----KQFGHYEPNLSLDEMKFGNQHPS 542
             G    +Q  H      +D    GN  PS
Sbjct:   422 GSNGFQQSSHLFQEPKMDNKYTGNLSPS 449

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

 Score = 877 (313.8 bits), Expect = 6.2e-152, Sum P(3) = 6.2e-152
 Identities = 203/411 (49%), Positives = 264/411 (64%)

Query:   183 LKEIEAQTIGNLLPD-EDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD--D 239
             L + ++  IGN+LPD E++LFSG+ DD+  +    T+DDLED+DLF SGGG+ELE D  D
Sbjct:    63 LDDGDSHPIGNMLPDDEEELFSGLMDDLNLSSLPATLDDLEDYDLFGSGGGLELETDPYD 122

Query:   240 RL---FAVQKNSDF-VGGVSNQGV---SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSEL 292
              L   F+    +D  V  V  Q +     GS+ GEHPYGEHPSRTLFVRNINSNVEDSEL
Sbjct:   123 SLNKGFSRMGFADSNVDNVMPQNIFQNGVGSIAGEHPYGEHPSRTLFVRNINSNVEDSEL 182

Query:   293 KALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
             +ALFEQ+G IRT+YTACK RGFVM+SY DIRA+R AM+ALQ K L++RKLDIH+SIPKDN
Sbjct:   183 QALFEQYGHIRTLYTACKQRGFVMVSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDN 242

Query:   353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 412
             PSEKD NQGTLVVFNL  SVS  +L  IFG+YGEI+EIR+T +K +HKF+EF+D+R+A+ 
Sbjct:   243 PSEKDVNQGTLVVFNLAPSVSNRDLENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADA 302

Query:   413 ALRTLNRSDVAGKQIKLEASRPGGARR-FMVQS--EQEQDD----LNLCQIPFDDLSSGQ 465
             AL+ LNR+++AGK+IKLE SRPGGARR  M+Q   E EQDD    LN  + P      G 
Sbjct:   303 ALKALNRTEIAGKRIKLEHSRPGGARRNMMLQMNPELEQDDSYSYLNHVESPLASSPIGN 362

Query:   466 MVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSI--GKQFG 523
               +S +      D+     L S ++SP        +    P      A V +   G++F 
Sbjct:   363 WRNSPI------DHP----LQSFSKSPIFGNLSPTKNIRYPEFSMKTASVNNDQEGRRFS 412

Query:   524 HYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNS-PSTIADIASS 573
             H +   S     + N          P+   S+++    NS PS +  ++ S
Sbjct:   413 HLDHLFS--SSSYNNASHKASTFQQPQSFGSVSSFGSLNSHPSHVETLSGS 461

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 = 823 (294.8 bits), Expect = 1.3e-130, Sum P(2) = 1.3e-130
 Identities = 215/471 (45%), Positives = 284/471 (60%)

Query:   181 ESLKEIEAQTIGNLLP-DEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMEL--EG 237
             +SL+++E   +  LLP DE++L  G+ D++      + +DDLE+ D+F +GGGMEL  E 
Sbjct:    93 DSLEDVEPDALEILLPEDENELLPGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVES 152

Query:   238 DDRLFAVQKNSDFVG--GVSNQGV------SAGSVVGEHPYGEHPSRTLFVRNINSNVED 289
              D   AV  +   +   G +N  V      +AG V  EHP GEHPSRTLFVRNINS+VED
Sbjct:   153 QDN-HAVDASGMQISDRGAANAFVPRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVED 211

Query:   290 SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP 349
             SEL ALFE FG+IR++YTACK RGFVMISYYDIRAA  AM+ALQN  LR+R LDIH+SIP
Sbjct:   212 SELSALFEPFGEIRSLYTACKSRGFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIP 271

Query:   350 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRA 409
             K+NPSEKD NQGTLV+FN+D++VS +EL Q+FG YGEIREIR+T ++  H+FIE+YD+R 
Sbjct:   272 KENPSEKDMNQGTLVIFNVDTTVSNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRD 331

Query:   410 AETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSS 469
             AETAL+ LNRS++ GK IKLE SRPGGARR  V S+ +  DL   ++     +    V S
Sbjct:   332 AETALKALNRSEIGGKCIKLELSRPGGARRLSVPSQSQ--DLERTEVT----NFYNQVGS 385

Query:   470 GVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSV-P---NGLPSLARV-GSIGKQFGH 524
              V  S     G+  +      SP+ A T  H    V P   + +P LA +  +    F  
Sbjct:   386 HVANSP---PGNWPIGSPVKGSPSHAFTRPHGLGMVRPVNSDNMPGLASILPAHPSSFHG 442

Query:   525 YEPNLSLDE--MKFGNQ--------HP-SF-HPHSLPEYHDSLANGLPYNSPSTIADIAS 572
             + P +S D+  +   NQ        H  S+  PHSLPE+   +  G+  NS   IA  +S
Sbjct:   443 FSP-VSNDQGLLNHSNQTILNKGLMHNISYGQPHSLPEH---ITGGIS-NSMRFIAPHSS 497

Query:   573 SVGTKIKDGLDSRHIRGVSSNGHLMEP--TG-GVFGSPRNGSYSL-HGNPY 619
               GT      D R+  G S   H+  P  TG     S     +++ HG P+
Sbjct:   498 GFGTSS----DHRYRWG-SPPQHMNYPGYTGVSSSSSSTERPFTVRHGFPF 543

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 = 258 (95.9 bits), Expect = 3.6e-50, Sum P(4) = 3.6e-50
 Identities = 52/123 (42%), Positives = 71/123 (57%)

Query:   838 TYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQG 897
             +YDF+YLP+DF NKCNVGY F+NM  P     F++AF+G++WE FNS K+  + YAR+QG
Sbjct:   455 SYDFVYLPMDFNNKCNVGYGFVNMTSPEAAWRFYKAFHGQRWEVFNSHKICQITYARVQG 514

Query:   898 KAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRLGKPRINGNEESQ 957
                L  HF++S    E +   P++F    P  G     P+  NI    G  R+N N   Q
Sbjct:   515 LEDLKEHFKSSKFPCEAELYLPVVFSP--PRDGKQLTEPVSINITIN-GCTRLNHNHFEQ 571

Query:   958 RQG 960
               G
Sbjct:   572 TVG 574

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

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

 Score = 411 (149.7 bits), Expect = 7.1e-44, Sum P(2) = 7.1e-44
 Identities = 85/168 (50%), Positives = 110/168 (65%)

Query:   778 NLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRG 837
             NL  R   +   HA  +   +D  +I  G D+RTT+MIKNIPNK+T +ML   ID   +G
Sbjct:   566 NLQ-RYTPTVEKHASDRN-SVDYAQIASGIDTRTTVMIKNIPNKFTQQMLRDYIDVTNKG 623

Query:   838 TYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQG 897
             TYDF+YL IDF NKCNVGYAFIN I+P+ II F +A  G +W  F+SEK+  ++YA IQG
Sbjct:   624 TYDFLYLRIDFVNKCNVGYAFINFIEPQSIITFGKARVGTQWNVFHSEKICDISYANIQG 683

Query:   898 KAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDPEPFPMGTNIRSRL 945
             K  LI  F+NS +M+E+   RP +F + GPN G  EPFP   N R +L
Sbjct:   684 KDRLIEKFRNSCVMDENPAYRPKIFVSHGPNRGMEEPFPAPNNARRKL 731

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

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

 Score = 283 (104.7 bits), Expect = 7.7e-44, Sum P(3) = 7.7e-44
 Identities = 60/144 (41%), Positives = 80/144 (55%)

Query:   808 DSRTTLMIKNIPNKYTSKMLLAAIDEHCR---------------GTYDFIYLPIDFKNKC 852
             D RTT+MIKNIPNKYT K+LL  +D HC+                +YDF+YLPIDF NK 
Sbjct:   334 DGRTTVMIKNIPNKYTQKLLLKMLDTHCKDCNQSVIKEGNKTPMSSYDFVYLPIDFSNKS 393

Query:   853 NVGYAFINMIDPRQIIPFHQAFNGKKWEKFNS-EKVASLAYARIQGKAALIAHFQNSSLM 911
             NVGY F+NM  P  +   +++F+ + W  F +  K+  + YARIQG  +L  HF+N  L 
Sbjct:   394 NVGYGFVNMTSPEAVWRLYKSFHNQHWRDFTTTRKICEVTYARIQGLESLREHFKNVRLA 453

Query:   912 N-EDKRCRPILFHTDGPNAGDPEP 934
               E     P++F         PEP
Sbjct:   454 GVEIDEYMPVVFSPPRDGRLSPEP 477

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

 Score = 254 (94.5 bits), Expect = 3.7e-35, Sum P(3) = 3.7e-35
 Identities = 57/182 (31%), Positives = 96/182 (52%)

Query:   759 RNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDI------DRILRGDDSRTT 812
             +N +   Q   + +N  +RN +  + +       + +  +D       + I+ G D+RT+
Sbjct:  1516 KNQLQQQQPKKNQNNGTLRNSTNSKGKKELKEPKEPKEPVDPTCILIPENIISGVDTRTS 1575

Query:   813 LMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQ 872
             LMI+NIPN+ T + L A IDE  + TYDF+ +P+D   K + GYAFIN  D   +  FHQ
Sbjct:  1576 LMIRNIPNRLTQQTLTALIDEEFKDTYDFLNMPLDPHTKVSRGYAFINFKDHMNVYRFHQ 1635

Query:   873 AFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDP 932
              F   +W+ +N +K+  + YA IQG+ AL+   Q+     E  + +  +   D  +A + 
Sbjct:  1636 KFFHTRWKNYNHDKICEINYAIIQGEEALL---QSIKKKQEKLQLKKGITSNDENSASEE 1692

Query:   933 EP 934
             +P
Sbjct:  1693 KP 1694

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 = 311 (114.5 bits), Expect = 7.4e-28, Sum P(2) = 7.4e-28
 Identities = 66/138 (47%), Positives = 87/138 (63%)

Query:   811 TTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPF 870
             TT+M++NIPNKYT  ML+  ++EH +G YDF YLPIDF+NKCNVGYAFIN I P     F
Sbjct:   290 TTVMLRNIPNKYTQNMLMDVMNEHFKGLYDFFYLPIDFRNKCNVGYAFINFIHPYYAELF 349

Query:   871 HQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNED-KRCRPILFHTDGPNA 929
              + FN  K   F S KV S+ + R+QG  A I H++NS++M     + +PILF  +G   
Sbjct:   350 IKFFNNYKLNAFKSNKVCSVTWGRVQGLKANIEHYRNSAIMTIPIPQYKPILFQ-NGITV 408

Query:   930 GDPE---PFPMGTNIRSR 944
               PE   P P    +RS+
Sbjct:   409 SWPESDGPLP-SIKLRSQ 425

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)
Q64M78	OML4_ORYSJ	No assigned EC number	0.5246	0.9634	0.9480	yes	no
Q8W4I9	AML1_ARATH	No assigned EC number	0.5208	0.9177	0.9879	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	985
pfam04059	97	pfam04059, RRM_2, RNA recognition motif 2	3e-63
cd12531	86	cd12531, RRM3_MEI2_like, RNA recognition motif 3 i	5e-61
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	4e-49
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	5e-44
cd12530	101	cd12530, RRM3_EAR1_like, RNA recognition motif 3 i	4e-38
cd12532	90	cd12532, RRM3_MEI2_fungi, RNA recognition motif 3	2e-37
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-35
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	3e-28
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	1e-27
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-24
smart00360	73	smart00360, RRM, RNA recognition motif	4e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-13
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	1e-12
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-12
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	3e-12
smart00360	73	smart00360, RRM, RNA recognition motif	7e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-10
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-09
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	2e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-08
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	3e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-08
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	4e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	6e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-08
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	7e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-08
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	8e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	2e-07
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	2e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-07
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	4e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-07
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	5e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-07
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	6e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	7e-07
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	9e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-06
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	2e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-06
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	4e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	6e-06
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	6e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	7e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	8e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	9e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	2e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	4e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-05
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	5e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	7e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	7e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	9e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	1e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	2e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	2e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	3e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	4e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	4e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	4e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	4e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	4e-04
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	4e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	5e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	5e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	5e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-04
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	6e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	6e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	7e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	7e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	8e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	8e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	9e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	9e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	0.001
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.001
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	0.001
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.001
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.001
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.002
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.002
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.002
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.002
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.002
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.002
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.002
smart00360	73	smart00360, RRM, RNA recognition motif	0.003
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.003
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.003
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.003
cd12752	87	cd12752, RRM1_RBM5, RNA recognition motif 1 in ver	0.003
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.003
cd12455	88	cd12455, RRM_like_Smg4_UPF3, RNA recognition motif	0.003
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.004
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.004
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.004
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.004
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.004
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.004
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.004
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.004
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.004

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

 Score =  208 bits (530), Expect = 3e-63
 Identities = 86/97 (88%), Positives = 91/97 (93%)

Query: 810 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIP 869
           RTTLMIKNIPNKYT KMLLAAIDE  +GTYDF+YLPIDFKNKCNVGYAFINMI+P+ IIP
Sbjct: 1   RTTLMIKNIPNKYTQKMLLAAIDEKNKGTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIP 60

Query: 870 FHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQ 906
           F +AFNGKKWEKFNSEKVASLAYARIQGK ALIAHFQ
Sbjct: 61  FGKAFNGKKWEKFNSEKVASLAYARIQGKDALIAHFQ 97

Length = 97

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

 Score =  201 bits (513), Expect = 5e-61
 Identities = 75/86 (87%), Positives = 78/86 (90%)

Query: 813 LMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQ 872
           LMIKNIPNKYT KMLLAAIDE  RGTYDF YLPIDFKNKCNVGYAFINMI P  I+PF++
Sbjct: 1   LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYK 60

Query: 873 AFNGKKWEKFNSEKVASLAYARIQGK 898
           AFNGKKWEKFNSEKV SLAYARIQGK
Sbjct: 61  AFNGKKWEKFNSEKVCSLAYARIQGK 86

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

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

 Score =  167 bits (425), Expect = 4e-49
 Identities = 63/77 (81%), Positives = 69/77 (89%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           SRTLFVRNINSNVED EL+ALFEQFGDIRT+YTACKHRGF+M+SYYDIRAAR A +ALQ 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 335 KPLRRRKLDIHYSIPKD 351
             L  RKLDIH+SIPKD
Sbjct: 61  TELGGRKLDIHFSIPKD 77

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

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

 Score =  153 bits (389), Expect = 5e-44
 Identities = 56/86 (65%), Positives = 69/86 (80%), Gaps = 1/86 (1%)

Query: 813 LMIKNIPNKYTSKMLLAAIDEHCRG-TYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFH 871
           +MI+NIPNKYT +MLL  +DEH +G  YDF+YLPIDFKNKCNVGYAFIN ++P     F+
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFY 60

Query: 872 QAFNGKKWEKFNSEKVASLAYARIQG 897
           +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 = 4e-38
 Identities = 53/101 (52%), Positives = 69/101 (68%), Gaps = 13/101 (12%)

Query: 810 RTTLMIKNIPNKYTSKMLLAAIDEHC-------------RGTYDFIYLPIDFKNKCNVGY 856
           RTTLMIKNIPNKY+ K+LL  +D HC               +YDF+YLPIDFKNKCN+GY
Sbjct: 1   RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHIEDSSQPVSSYDFVYLPIDFKNKCNLGY 60

Query: 857 AFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQG 897
           AF+N   P     F++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 =  134 bits (340), Expect = 2e-37
 Identities = 55/89 (61%), Positives = 66/89 (74%)

Query: 810 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIP 869
           RTT+M+KNIPNK+T +ML   IDE   GTYDF+YL IDF N CNVGYAF+N I+P  II 
Sbjct: 1   RTTVMLKNIPNKFTQQMLRKYIDETNPGTYDFMYLRIDFNNSCNVGYAFVNFIEPISIIT 60

Query: 870 FHQAFNGKKWEKFNSEKVASLAYARIQGK 898
           F +A  G KW  F+SEKV  ++YA IQGK
Sbjct: 61  FGKARVGTKWNMFHSEKVCDISYANIQGK 89

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

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

 Score =  127 bits (321), Expect = 3e-35
 Identities = 52/71 (73%), Positives = 64/71 (90%)

Query: 360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           QGTLVVFNLD SVS ++LHQIFG YGEI+EIR+T +K +HKFIEFYD+R+AE AL+ LNR
Sbjct: 1   QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 420 SDVAGKQIKLE 430
           S++AGK+IKLE
Sbjct: 61  SEIAGKRIKLE 71

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

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

 Score =  108 bits (271), Expect = 3e-28
 Identities = 36/71 (50%), Positives = 52/71 (73%)

Query: 360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           QGTL+VFNLDS +S +EL  +F  +GE+++IR+T  + + KF+EFYDIRAAE AL  LN 
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 420 SDVAGKQIKLE 430
               G ++K++
Sbjct: 61  RPFLGGRLKVK 71

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

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

 Score =  106 bits (266), Expect = 1e-27
 Identities = 26/71 (36%), Positives = 44/71 (61%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           SR+LFV N+  +V +S L+ LFE +GD+R + T     G V + +YDIR A+ A++ L  
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60

Query: 335 KPLRRRKLDIH 345
           + ++++ 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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 97.2 bits (242), Expect = 2e-24
 Identities = 34/71 (47%), Positives = 53/71 (74%)

Query: 360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           QGTLV+FNLD +VS+E L  IF +YG+++E+R+T  K   +F+EF+D+R A  ALR +N 
Sbjct: 1   QGTLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 420 SDVAGKQIKLE 430
            +++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|214636 smart00360, RRM, RNA recognition motif

 Score = 64.9 bits (159), Expect = 4e-13
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKA 331
           TLFV N+  +  + EL+ LF +FG + ++         K +GF  + +     A  A++A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 332 LQNKPLRRRKLDI 344
           L  K L  R L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 63.9 bits (156), Expect = 9e-13
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARNAMKALQ 333
           LFV N+  +  + +L+ LF +FG+I ++        K +GF  + +     A  A++AL 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 334 NKPLRRRKLDIH 345
            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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 63.7 bits (156), Expect = 1e-12
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 277 TLFVRNINSNVEDSELK----ALFEQFGDIRTIYTACK---HRGFVMISYYDIRAARNAM 329
           TL++ N+N  ++  ELK    ALF QFG +  I  A K    RG   + + D+ +A NA+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIV-ASKTLKMRGQAFVVFKDVESATNAL 59

Query: 330 KALQNKPLRRRKLDIHYS 347
           +ALQ  P   + + I Y+
Sbjct: 60  RALQGFPFYDKPMRIQYA 77

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

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

 Score = 63.1 bits (154), Expect = 2e-12
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           TL V N++S+V  EEL  +F  +G+IR +           + +YDIRAA  A R L  ++
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 422 VAGKQIKLEASRP 434
           + 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 = 62.2 bits (152), Expect = 3e-12
 Identities = 25/68 (36%), Positives = 39/68 (57%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 336
           TL V N++S + D EL++LF QFG+++ I           + +YDIRAA  A+ AL  +P
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRP 62

Query: 337 LRRRKLDI 344
               +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 = 7e-12
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHK--FIEFYDIRAAETALRT 416
           TL V NL    + EEL ++F  +G++  +R   D +   +    F+EF     AE AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 417 LNRSDVAGKQIKL 429
           LN  ++ G+ +K+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 60.8 bits (148), Expect = 1e-11
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLN 418
           L V NL    + E+L ++F  +GEI  +R             F+EF     AE AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 419 RSDVAGKQIKLE 430
             ++ 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 = 57.2 bits (139), Expect = 2e-10
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAMKALQ 333
           LFV N+  +  + +LK LF +FG I +I        + +GF  + + D   A  A++AL 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 334 NKPLRRRKL 342
            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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLN 418
           L V NL    + E+L  +F  +G I  IR    +T       F+EF D   AE AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 419 RSDVAGKQIK 428
             ++ 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 56.4 bits (137), Expect = 3e-10
 Identities = 17/56 (30%), Positives = 24/56 (42%)

Query: 292 LKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS 347
           L  LF  FG++  I    K  GF  + +    AA  A++ L       R L + YS
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 55.1 bits (133), Expect = 1e-09
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVMISYYDIRAARNAMKA 331
           +L+VRN+       +L+ LF ++G I  +Y          RGF  + + D+R A +A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 332 LQNKPLRRRKLDIHYS 347
           L       R+++I ++
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|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 = 54.9 bits (133), Expect = 2e-09
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALR 415
             L V  L +  + +EL  +F  +G + E+   +     +     F+ F  +  A+ A+R
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 416 TLNRSDVAGKQIKLEASR 433
            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|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal Mei2-like proteins

 Score = 54.3 bits (131), Expect = 2e-09
 Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-RGFVMISYYDIRAARNAMKALQ 333
           +R L V  +  +V  S LK +FE+ GD++ I+      +G V++S++D+R A  A K LQ
Sbjct: 1   TRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFHDLRQAIKAYKDLQ 60

Query: 334 NKPL 337
           +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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 53.8 bits (130), Expect = 4e-09
 Identities = 20/77 (25%), Positives = 43/77 (55%), Gaps = 9/77 (11%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDIRAARN 327
           R ++VRN++  +++ +L+ +F +FG++ +I    K        + GF  +++ D  +A N
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 328 AMKALQNKPLRRRKLDI 344
           A++ L    L  RK+ +
Sbjct: 61  ALQ-LNGTELGGRKISV 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 = 52.2 bits (126), Expect = 1e-08
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 331
           TLFVRN+  +  D +L+  F + G I+  +        K RGF  +++     A+ A++ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 332 LQNKPLRRRKLDIHYSIPK 350
            +      RK+ + ++  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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 10/82 (12%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTI----------YTACKHRGFVMISYYDIRAA 325
            TLFV+N+N    +  LK  FE+ G +R++                 G+  + +    AA
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 326 RNAMKALQNKPLRRRKLDIHYS 347
           + A+K 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 56.8 bits (137), Expect = 3e-08
 Identities = 52/205 (25%), Positives = 93/205 (45%), Gaps = 24/205 (11%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAAR 326
           E   RT+FV  +     + +L   F + G +R +       + + +G   + +YD+ +  
Sbjct: 86  ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVI 145

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN--QGT------LVVFNLDSSVSTEELH 378
            A+ AL  + L  R + +  S  + N + K A    G       L V NL  +++ +EL 
Sbjct: 146 KAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELR 204

Query: 379 QIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS- 432
           QIF  +G+I +++     +T       FI+F+D   A+ AL  +N  ++AG+ IK+  + 
Sbjct: 205 QIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ 264

Query: 433 ----RPGGARRFMVQSEQEQDDLNL 453
                   A  F    +Q+Q   NL
Sbjct: 265 DSTYLLDAANTFEDIDKQQQMGKNL 289

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 = 50.8 bits (122), Expect = 3e-08
 Identities = 15/59 (25%), Positives = 34/59 (57%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           SR L +  +  ++ +++L+   EQ+G +R +       G V + +YD+R A +A++ ++
Sbjct: 1   SRALLLSGVPPHIPETQLRRDLEQWGAVRAVQMDAMAEGIVTVHFYDLRHAEDALRDIR 59

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

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

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 2/65 (3%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRS 420
           L V NL   +S+EEL+ +FG YG IR+IR  +T+      F+ + DI  A+ A   L+  
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64

Query: 421 DVAGK 425
           +VA +
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|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 51.1 bits (122), Expect = 4e-08
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 277 TLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMK 330
           T+++ N+N  V+  ELK    A+F QFG I  I      K RG   + + DI +A NA++
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60

Query: 331 ALQNKPLRRRKLDIHYS 347
           ++Q  P   + + I YS
Sbjct: 61  SMQGFPFYDKPMRIAYS 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|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 = 50.7 bits (122), Expect = 5e-08
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           T+ V NL   ++ EEL + F  +G I E+R       + F+ F    AA TA+  +N + 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVR-VFKDKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 422 VAGKQIK 428
           + 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 50.3 bits (121), Expect = 6e-08
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH--RGFVMISYYDIRAARNAMKAL 332
           +R L+VRN+   +   EL  LF ++G IR I        RG   + Y DI  A+NA   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 333 QNKPLRRRKLDIHY 346
               +  R L + Y
Sbjct: 62  SGFNVANRYLVVLY 75

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

 Score = 50.3 bits (121), Expect = 6e-08
 Identities = 23/70 (32%), Positives = 36/70 (51%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 424
           V NL    +  EL   F  YG +R +   ++     F+EF D R AE A+R L+   + G
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRICG 63

Query: 425 KQIKLEASRP 434
            ++++E SR 
Sbjct: 64  NRVRVELSRG 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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 50.0 bits (120), Expect = 7e-08
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL-RTLNRS 420
           TL V  L   V+ ++L   F  +GEIR I     +    F+ F    AAE A  R  N+ 
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVV-PRQQCAFVTFTTREAAEKAAERLFNKL 61

Query: 421 DVAGKQIKL 429
            + G+++KL
Sbjct: 62  IINGRRLKL 70

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

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

 Score = 56.0 bits (135), Expect = 7e-08
 Identities = 62/325 (19%), Positives = 116/325 (35%), Gaps = 36/325 (11%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVMISYYDIRAARNAMKAL 332
           L+V+N++ +V + +L+ LF +FG+I T     K      RGF  +++     A  A++ +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEI-TSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 333 QNKPLRRRKL-DIHYSIPKDNPSEKDA----------------NQGT-LVVFNLDSSVST 374
             K +   K     Y       +E++A                 QG  L V NLD +V+ 
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299

Query: 375 EELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
           E+L ++F   GEI   +    +        F+ F +   A  A+  ++   + GK + + 
Sbjct: 300 EKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVA 359

Query: 431 ASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATR 490
            ++    RR  +Q +  Q    + Q+P      G M                Q       
Sbjct: 360 LAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQ----GPQQQFNGQPLG 415

Query: 491 SPAIAL---TESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHS 547
            P +++            PNGL  +  V +  +   +      +  + +   + S  P S
Sbjct: 416 WPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYPPNYQS-LPLS 474

Query: 548 LPEYHDSLANGLPYNSPSTIADIAS 572
                          +      +AS
Sbjct: 475 QDLPQPQSTASQGGQNKKLAQVLAS 499

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|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 = 50.0 bits (120), Expect = 8e-08
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           S TL++ +++  V + +LK LFE++G+I++I      RG   +     + A  A++ L+N
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI-DMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 335 KPLRRRKLDIHYSIPK 350
             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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 49.1 bits (117), Expect = 2e-07
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLN 418
           L V NLD  V+ + L QIF + G ++ ++          N+ F+E++    AE AL+TLN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 419 RSDVAGKQIKL 429
              +   +I++
Sbjct: 61  GRQIENNEIRV 71

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

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

 Score = 54.4 bits (131), Expect = 2e-07
 Identities = 42/175 (24%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           PS  + VRN+  +V +++L      FG + +       +   ++ + D  +A+  +    
Sbjct: 1   PSPVVHVRNLPQDVVEADLVEALIPFGPV-SYVMMLPGKRQALVEFEDEESAKACVNFAT 59

Query: 334 NKP--LRRRKLDIHYS----IPKDNPSEKDANQGTLV----VFNLDSSVSTEELHQIFGI 383
           + P  +R +    +YS    I +D  S+ D+     V    V N    ++ + L+QIF  
Sbjct: 60  SVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNP 119

Query: 384 YGEIREIRDTQHKHN--HKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEASRP 434
           YG++  I  T  K+N     +EF  + +A+ A   LN +D+      +K+E ++P
Sbjct: 120 YGKVLRIV-TFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKP 173

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 48.7 bits (117), Expect = 2e-07
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           L+VRN+  +V + +L+  F  +G +   R +    + RGF  + +     A  A+K L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 335 KPLRRRKL 342
             L  R L
Sbjct: 61  LVLDGRTL 68

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

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

 Score = 47.9 bits (114), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 38/68 (55%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 336
           TL V N++ +V + +L  +F  +G+I+ I      R    I +YD+R+A  A+KAL    
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 337 LRRRKLDI 344
           +  +++ +
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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 48.4 bits (116), Expect = 4e-07
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 14/84 (16%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIR----TIYTACKH---RGFVMISYYDIRAARNA 328
           RT+F+RN+  +  + ELK LF QFG+++           H     FV   +    +A+  
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFV--KFKTKESAQKC 58

Query: 329 MKALQNKP-----LRRRKLDIHYS 347
           ++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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 48.5 bits (115), Expect = 5e-07
 Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 6/80 (7%)

Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A N
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A++++Q  P   + + I Y+
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|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 = 48.0 bits (115), Expect = 5e-07
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACK----HRGFVMISYYDIRAARNAMKAL 332
            L VRN+       EL+ LF  FG ++++    K    HRGF  + +   + A+NAM+AL
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 333 QNKPLRRRKLDIHYS 347
           ++  L  R L + Y+
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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L V NL  +V+ E+L  +FG +GE+        R+T       F+E      A  A+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 417 LNRSDVAGKQIKLEASRP 434
           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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 47.6 bits (114), Expect = 6e-07
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQF-G--DIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           P++ LF++N+        L+ LF QF G  ++R +      RG   + +     A  A++
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV----PRRGIAFVEFETEEQATVALQ 56

Query: 331 ALQN 334
           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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 46.7 bits (112), Expect = 7e-07
 Identities = 15/54 (27%), Positives = 31/54 (57%)

Query: 377 LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
           L+++F  +G + +I+  + K    F+EF    AAE A++ LN     G+ ++++
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54

(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|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 = 47.0 bits (112), Expect = 9e-07
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHKFIEFYDIRAAETALRTLN 418
           T+ V  +D S+S ++L + F   GE+  +R   D QH     F+EF D  +A +AL  L+
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALN-LS 60

Query: 419 RSDVAGKQIKLEASR 433
            + + G  +++  S+
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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 52.1 bits (125), Expect = 1e-06
 Identities = 33/150 (22%), Positives = 68/150 (45%), Gaps = 9/150 (6%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAMKALQ 333
           +FV+N++ +V++  L   F +FG+I +   A     K RG+  + +    +A+ A++ + 
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 334 NKPLRRRKLDI-HYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD 392
              L  +++ +  +    +  +        L V NLD SV+ ++L ++F  +GEI     
Sbjct: 151 GMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV 210

Query: 393 TQHKHNHK----FIEFYDIRAAETALRTLN 418
            +          F+ F     A  A+  +N
Sbjct: 211 MKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

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

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

 Score = 51.5 bits (122), Expect = 1e-06
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 5/90 (5%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAAR 326
           +  + TLFV N+  +V + +L+ LF++FG ++ +         K RGF  + +    +A 
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDNPSEK 356
            A++ L  K L  R L +  + P   P  +
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSE 201

Length = 306

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

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKAL 332
           LFVRN+  + ++ +L+ LF +FG++  ++ A      K +GF  + + D   A  A K L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 333 QNKPLRRRKLDI 344
             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|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 = 46.4 bits (111), Expect = 2e-06
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKA 331
            LFV  +++   + EL+ALF +FG +  +         + RGF  +++  +  A  A++ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 332 LQNKPLRRRKLDI 344
           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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 46.1 bits (110), Expect = 2e-06
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 9/74 (12%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREIR------DTQHKHNH--KFIEFYDIRAAETALRT 416
           V NLD  +  ++L  IF  +GE+  IR      + Q + N+   F+ F D  +AE AL+ 
Sbjct: 5   VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ- 63

Query: 417 LNRSDVAGKQIKLE 430
           LN +++ G++I + 
Sbjct: 64  LNGTELGGRKISVS 77

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

 Score = 51.7 bits (124), Expect = 2e-06
 Identities = 39/181 (21%), Positives = 87/181 (48%), Gaps = 21/181 (11%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC------KHRGFVMISYYDIRAARNAMK 330
           +L+V +++ +V +++L  LF+ FG + ++   C      +  G+  +++ +   A  A++
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSV-RVCRDSVTRRSLGYGYVNFQNPADAERALE 60

Query: 331 ALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI 390
            +  K L  + + I +S  + +PS + +  G + V NLD SV  + L   F  +G I   
Sbjct: 61  TMNFKRLGGKPIRIMWS--QRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSC 118

Query: 391 R----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQ 446
           +    +      + F+ F    +A+ A++ +N   +  K++ +         RF+ + E+
Sbjct: 119 KVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVG--------RFIKKHER 170

Query: 447 E 447
           E
Sbjct: 171 E 171

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

 Score = 46.5 bits (111), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTL 417
           T+ V NLD + + ++L + F   GE++ +R    +TQ    + F+EF +  +   AL+ L
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPT-RYAFVEFAEQTSVINALK-L 63

Query: 418 NRSDVAGKQIKLEASR 433
           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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 45.8 bits (109), Expect = 2e-06
 Identities = 24/68 (35%), Positives = 43/68 (63%), Gaps = 2/68 (2%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHN-HKFIEFYDIRAAETALRTLNRS 420
           L V NLD +V+ + L ++F   G I+  +   +H ++ + F+E+YD R+A  AL+T+N  
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 421 DVAGKQIK 428
            + G++IK
Sbjct: 61  LILGQEIK 68

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

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAM 329
           L+V  +   V++  L A F  FGDI+ I     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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 45.4 bits (108), Expect = 4e-06
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           ++ V  L   V+ EEL++ F  +G+I E   I+   H +   FI+F   +AA  A+ + N
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 419 RSDVAGKQIKLE 430
            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|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 = 45.2 bits (108), Expect = 4e-06
 Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           + + NL   V+ + LHQ+F  YG + +I    ++      ++F  + +AE A + LN  +
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 422 VAGKQIKLE 430
           +      L+
Sbjct: 64  IYDGCCTLD 72

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

 Score = 45.3 bits (108), Expect = 5e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMK 330
           +TLFV  +N +  +S+L+  FE++G I+ I         K RG+  I +   R  + A K
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 331 ALQNKPL--RRRKLDI 344
               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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 44.7 bits (106), Expect = 6e-06
 Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHN---HKFIEFYDIRAAETALRTLN 418
           TL + NL+ + +  +L + F  +GEI +I D + +     + FI++ DI +   A+R ++
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDI-DIKKQGGNPAYAFIQYADIASVVKAMRKMD 62

Query: 419 RSDVAGKQIKL 429
              +   ++KL
Sbjct: 63  GEYLGNNRVKL 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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 45.4 bits (107), Expect = 6e-06
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 6/79 (7%)

Query: 275 SRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNA 328
           + T+++ N+N  ++  ELK    ALF QFG +  I      K RG   + + ++ +A NA
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNA 60

Query: 329 MKALQNKPLRRRKLDIHYS 347
           ++ LQ  P   + + I Y+
Sbjct: 61  LRQLQGFPFYGKPMRIQYA 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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 44.5 bits (106), Expect = 7e-06
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           L+V  +      +EL+  F++FG IR I      R +  I Y  I AA+ A +AL+  PL
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI-DYDPGRNYAYIEYESIEAAQAAKEALRGFPL 59

Query: 338 RR--RKLDIHYS 347
               R+L + ++
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|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 = 44.2 bits (105), Expect = 8e-06
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKAL 332
           LFVRN+     + EL+ LFE FG+I  ++        + +GF  +S+     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 333 QNKPLRRRKLDI 344
                + 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 44.1 bits (105), Expect = 9e-06
 Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 12/73 (16%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC--------KHRGFVMISYYDIRAARNAM 329
           ++V+N+  +++D +LK LF ++G I    T+         K +GF  +++ +  AA+ A+
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKI----TSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59

Query: 330 KALQNKPLRRRKL 342
           + 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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 43.8 bits (104), Expect = 1e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
           T+ V NL  S++  +LH+IF  YG++ ++   + K   K     FI F D   A   ++ 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 417 LNRSDVAGKQIK 428
           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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 48.1 bits (114), Expect = 1e-05
 Identities = 46/175 (26%), Positives = 75/175 (42%), Gaps = 15/175 (8%)

Query: 255 SNQGVSAGSVVGEHPYGEHPSRT-LFVRNINSNVEDSELKALFEQFGDIRTI-----YTA 308
           S   +++    G      + S T L V  +  ++ D EL ALF   G I T      Y  
Sbjct: 86  STNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKT 145

Query: 309 CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNL 368
               G+  + +     ++ A+K L    +R ++L + Y+ P    S KD N   L V NL
Sbjct: 146 GYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP-GGESIKDTN---LYVTNL 201

Query: 369 DSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLN 418
             +++ ++L  IFG YG+I +    + K         F+ F     A+ A+  LN
Sbjct: 202 PRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 417
           L+V  L   ++ EEL  +F   G I   +  + +   +     F+++ D   A+ A+ TL
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 418 NRSDVAGKQIK 428
           N  ++  K++K
Sbjct: 63  NGFEIRNKRLK 73

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

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAMKA 331
           TLFVRN+  +V   +L   F     I+     T     + RG+  +++  +  A+ A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 332 LQNKPL--RRRKLDI 344
           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|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL 417
           +L V N+   V+   L ++F +YG++R ++  +       + FYDIR A+ A+R 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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---D--TQHKHNHKFIEFYDIRAAETALRT 416
           +L V N+  +   ++L ++FG YG I ++    D  T+      +++F D+R AE AL  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 417 LNRSDVAGKQIKLE 430
           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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMK 330
           +RTLF+ N+      S+L+  FE+FG+I  I    K +G    +  I Y DI +   AM+
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEIIDI--DIKKQGGNPAYAFIQYADIASVVKAMR 59

Query: 331 ALQNKPLRRRKL 342
            +  + 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 9/61 (14%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARNAMKALQN 334
           LFV N+       EL+ALFE++G +    T C   K+ GFV +   +   A +A+KAL  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV----TECDVVKNYGFVHME--EEEDAEDAIKALNG 55

Query: 335 K 335
            
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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 43.6 bits (102), Expect = 2e-05
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 5/81 (6%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 413
           ++  L+V  L  +++ EEL  +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 414 LRTLNRSDVAGKQIKLEASRP 434
           + TLN   +  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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 43.5 bits (102), Expect = 2e-05
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 416
           +L V N+  +   E+L + FG YG I ++       T+      +I+F D+R AE AL  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 417 LNRSDVAGKQIKLE 430
           LNR  V G+QI+++
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|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 43.4 bits (102), Expect = 2e-05
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 331
           +LFVRNI  +    +L+  F ++G I  +Y        + RGF  + + D+R A +A+  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 332 LQNKPLRRRKLDIHYS 347
           L  K +  R+++I ++
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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKAL 332
           L V N+       +L+ +FE++G++  +Y        + RGF  + +YD R A +AM A+
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 333 QNKPLRRRKL 342
             K L  R+L
Sbjct: 61  DGKELDGREL 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|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 = 21/71 (29%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRTLNR 419
           V N+    + E+L +IF   G +   R     DT     + F EF DI  A +A+R LN 
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 420 SDVAGKQIKLE 430
            +  G+ ++++
Sbjct: 63  YEFNGRALRVD 73

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

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 424
           V NL +     EL + F  YG +R +   ++     F+EF D R AE A+R L+   + G
Sbjct: 4   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 63

Query: 425 KQIKLEASRPGGARR 439
            ++++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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 17/65 (26%), Positives = 36/65 (55%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           ++V N+       EL+  FE++G +R+++ A    GF  + + D R A +A++AL  + +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 338 RRRKL 342
              ++
Sbjct: 62  CGNRV 66

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 = 42.5 bits (101), Expect = 3e-05
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETALRTLNR 419
           L V NL  SV+ E+L + F  YG++  +R  ++K   +   F+EF     AE AL+ LN 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 420 SDVAGKQIK 428
             + G+ ++
Sbjct: 61  LVLDGRTLR 69

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

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

 Score = 42.9 bits (102), Expect = 3e-05
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKAL 332
           LFV  +     + +++ALFE++G+I  +         + +G   + +     A+ A++AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 333 QNK 335
             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|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 43.1 bits (101), Expect = 3e-05
 Identities = 22/68 (32%), Positives = 38/68 (55%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 424
           V NL ++ +  EL + FG YG +R +   ++     F+EF D R A  A+R L+   + G
Sbjct: 9   VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 68

Query: 425 KQIKLEAS 432
            ++++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|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHNHKFIEFYDIRAAETALRTLNRS 420
           T+      +S    ++ ++F   G +R++   ++    H FI F ++ AA+ A+ TLN +
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 421 DVAGKQIKLE 430
            V 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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 43.4 bits (103), Expect = 3e-05
 Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 10/89 (11%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIRAAETALRT 416
           TL V  L    + E L ++F  YG+IR +R  +         + F+E+   R A  A R 
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 417 LNRSDVAGKQI--KLEASR--PGG-ARRF 440
            ++  + G +I    E  R  PG   RR 
Sbjct: 65  AHKLVIDGSEIFVDFERERTLPGWIPRRL 93

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

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 14/69 (20%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 335
           + L+VRN+  +  + +L+ LF ++G++  +    K + +  + + +   A  AM+ +  K
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK---KIKDYAFVHFEERDDAVKAMEEMNGK 58

Query: 336 PLRRRKLDI 344
            L    +++
Sbjct: 59  ELEGSPIEV 67

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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 10/83 (12%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFG---DIRTIYT---ACKHRGFVMISYYDIRAARN 327
           P+R +FV  I  +  + EL+  F +FG   D++ I       K  GFV  ++     A  
Sbjct: 2   PNR-IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFV--TFETQEDAEK 58

Query: 328 AMKALQNKPLRRRKLDIHYSIPK 350
              A+ N   R +KL+I  +I K
Sbjct: 59  I-LAMGNLNFRGKKLNIGPAIRK 80

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

 Score = 42.1 bits (100), Expect = 4e-05
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 362 TLVVFNLDSSVSTEE----LHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALR 415
           TL + NL+  +  +E    L+ +F  +G + +I    T       F+ F D+ +A  ALR
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 416 TLNRSDVAGKQIKLEASR 433
            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|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 42.6 bits (100), Expect = 4e-05
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
           +L V N+     +E+L + FG YG I ++      +  +     +++F D+R AE AL  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 417 LNRSDVAGKQIKLE 430
           L+R  + G+QI+++
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 = 42.2 bits (100), Expect = 4e-05
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 9/75 (12%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           L V NL  S + E+L ++F  YGE+   ++I+D      + F+ F +   A  A+  +N 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD------YAFVHFEERDDAVKAMEEMNG 57

Query: 420 SDVAGKQIKLEASRP 434
            ++ 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 = 42.2 bits (99), Expect = 4e-05
 Identities = 22/69 (31%), Positives = 36/69 (52%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            LVV NL  S S + L ++F     IR  ++      + F+EF     A+ AL + N ++
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 422 VAGKQIKLE 430
           + 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|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 = 42.2 bits (100), Expect = 5e-05
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 416
            L+V N+    + +EL ++F  +G+++ +R     D  H+    F+EF   + A+ A+  
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHR-GFAFVEFVTKQEAQNAMEA 60

Query: 417 LNRSDVAGKQIKLE 430
           L  + + G+ + LE
Sbjct: 61  LKSTHLYGRHLVLE 74

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

 Score = 42.4 bits (100), Expect = 5e-05
 Identities = 17/72 (23%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           SR +++ NI+ ++ + +L+  F Q+G+I ++    + +    +++ +I  A  A+  +++
Sbjct: 3   SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNY-LREKNCAFVNFTNISNAIKAIDGVKS 61

Query: 335 KPLRRRKLDIHY 346
            PL  +K  I Y
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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 42.4 bits (100), Expect = 5e-05
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIRAAETALRT 416
            L++  L  +++ EE   +F   G ++  +  + K     +   F+++     A+ A+RT
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 417 LNRSDVAGKQIKLEASRPGG 436
           LN   +  K+IK+  +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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 42.1 bits (100), Expect = 5e-05
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAARNAMKA 331
           T+ V N++ + ++ +L+ LF  FG I  +Y A      + RGF  ++++    A  A++ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 332 LQ 333
           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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 41.9 bits (99), Expect = 6e-05
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTI-YTACKHRGFVMISYYDIRAARNAMKALQN 334
            TL+V  +   V + +L+  F QFG+IR+I     +   FV  ++    AA  A + L N
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFV--TFTTREAAEKAAERLFN 59

Query: 335 K 335
           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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 42.0 bits (99), Expect = 6e-05
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKH----NHKFIEFYDIRAAETALRTL 417
            L V  L  SV+ EEL ++F  +G ++ +R   ++        ++E+ +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 418 NRSDVAGKQIKLEASRPG 435
           + +++  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|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 = 41.8 bits (99), Expect = 7e-05
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 279 FVRNINSNVEDSELKALFEQFGDI---RTIY--TACKHRGFVMISYYDIRAARNAMKALQ 333
           FV NI  +  + +L  +F + G +   R +      K +G+    + DI  A +A++ L 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 334 NKPLRRRKLDIHYS 347
                 R L + ++
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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 275 SRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           SR +FV N+N++ V   +L+ +F ++G I  I     H+G+  + + +   AR A+    
Sbjct: 1   SR-VFVGNLNTDKVSKEDLEEIFSKYGKILGISL---HKGYGFVQFDNEEDARAAVAGEN 56

Query: 334 NKPLRRRKLDI 344
            + +  +KLDI
Sbjct: 57  GREIAGQKLDI 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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 41.5 bits (98), Expect = 8e-05
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 12/71 (16%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA------ 331
           LFV N+ +++ + E K LF ++G++  ++   K +GF  I   D R   NA KA      
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRT--NAEKAKAELDG 59

Query: 332 --LQNKPLRRR 340
              + + LR R
Sbjct: 60  IMRKGRQLRVR 70

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 41.2 bits (97), Expect = 9e-05
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFG---DIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
           + L V NI     D +L+ +F QFG   D+  I+     +GF  +++ +   A  A + L
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 333 QNKPLRRRKLDIHYS 347
               +  RK++++ +
Sbjct: 61  HGTVVEGRKIEVNNA 75

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

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 331
           +LFVRN+       +L+  F ++G I  +Y        + RGF  I + D+R A +A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 332 LQNKPLRRRKLDIHYS 347
           L  K +  R+++I ++
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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)

Query: 368 LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI 427
           L   V  +++ + FG YG++ EI     K+ + F+EF D R A+ A+  LN  D+ G+++
Sbjct: 7   LSYHVREKDIQRFFGGYGKLLEI---DLKNGYGFVEFEDSRDADDAVYELNGKDLCGERV 63

Query: 428 KLEASR 433
            +E +R
Sbjct: 64  IVEHAR 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKAL 332
           LFV N++    + EL+A F + G IR +         K +GF  + + +I  A NA+K  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK-- 58

Query: 333 QNKPLRRRKLDIHY 346
             K L  R L + Y
Sbjct: 59  -GKHLNGRALRVEY 71

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 277 TLFVRNINSNVEDSELKALFEQFG---DIRTIY---TACKHRGFVMISYYDIRAARNAMK 330
            L+V N+  NV + +LK LF QFG     R I    T  + RGF  +       A  A++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETG-RSRGFGFVEMETAEEANAAIE 59

Query: 331 ALQNKPLRRRKL 342
            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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRGFVMISYYDIRAARNAMKA 331
           + VRNI       EL+ LF  FG+++T+    K      HRGF  + +   + A+ A KA
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 332 LQ 333
           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|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 = 40.8 bits (96), Expect = 2e-04
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRA 324
            +  +  LFV  I  N+E+ +L+ LFEQFG I      +  YT   H+G   ++Y    +
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTG-MHKGCAFLTYCARES 59

Query: 325 ARNAMKALQNK 335
           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|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 = 40.5 bits (95), Expect = 2e-04
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 362 TLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 420
           TL V   D  +   E++ ++F  +G +        +    F+EF D   A  AL  L+ S
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCD---IRKTFAFVEFEDSEDATKALEALHGS 57

Query: 421 DVAGKQIKLE 430
            + 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|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 = 40.4 bits (95), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQ 333
           T+FV  ++  V + EL++LF  FG+I  +Y      K  GFV   +    AA  A++ LQ
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEI--VYVKIPPGKGCGFV--QFVHRAAAEAAIQQLQ 58

Query: 334 NKPL 337
              +
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|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 363 LVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           L+V NL+   V+ + L  +FG+YG++  ++   +K +   I+  D + A+TAL  LN   
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61

Query: 422 VAGKQIKLEASR 433
           + 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEI--------REIRDTQHKHNHKFIEFYDIRAAETAL 414
           L V NL+  V+ E L Q FG +G +        R   + +   N  F+ F +   AE AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 415 RTLNRSDVAGKQIKL 429
             L+  DV 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 417
           L V  L  +V+ + L +IF  YG ++++     R+      + ++EF     AE A++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 418 NRSDVAGKQIKLE 430
           +   + 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|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 = 40.0 bits (94), Expect = 3e-04
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           T+ V  LD +V+ +EL  +FG +GEI  ++    K    F++F    AAE A++ L  + 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGC-GFVQFVHRAAAEAAIQQLQGTI 61

Query: 422 VAGKQIKL 429
           + G +I+L
Sbjct: 62  IGGSRIRL 69

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

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 40.5 bits (94), Expect = 3e-04
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 5/81 (6%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 413
           ++  L+V  L  +++ EE   +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 414 LRTLNRSDVAGKQIKLEASRP 434
           + TLN   +  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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 40.2 bits (94), Expect = 3e-04
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIR-TIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           +RTLFV+N+  N+   ELK +FE   DIR         +G   I+Y + +    A KAL+
Sbjct: 3   ARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKG---IAYIEFKTEAEAEKALE 59

Query: 334 NK 335
            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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 40.0 bits (94), Expect = 3e-04
 Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           V N+D   + EEL + F   G I  I     + T       +IEF D  + E AL  LN 
Sbjct: 4   VGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLNE 62

Query: 420 SDVAGKQIK 428
           S+  G+QIK
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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 367 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ 426
            L       ++ + F  YG IREI     K+   F+EF D R A+ A+  LN  ++ G++
Sbjct: 6   RLPYRARERDVERFFKGYGRIREI---NLKNGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 427 IKLEASRP 434
           + +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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREI---RD--TQHKHNHKFIEFYDIRAAETALRTL 417
           L V NL  +++ ++L  IF  +GEI  +   RD  T     + FI+F D   A+ AL  L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 418 NRSDVAGKQIKL 429
           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|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 361 GTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALR 415
           G L +  L    + + L Q+F  YG+I E+     R+TQ      F+ F +   A+ A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 416 TLNRSDVAGKQIKLE 430
            +N   V G+QI+++
Sbjct: 61  AMNGKSVDGRQIRVD 75

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 422
           V NL   +   ++  +F  YG I+ I  ++ +      F+EF D R AE A+R  +  D 
Sbjct: 4   VGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGYDF 63

Query: 423 AGKQIKLE 430
            G ++++E
Sbjct: 64  DGYRLRVE 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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 4/61 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIY-TACK-HRGFVMISYYDIRAARNAMKALQN 334
           TL + N++  V    L+++F+ +GD++ +  T CK  + FV   ++D+R A  A++A+  
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFV--EFFDVRDAAKALRAMNG 60

Query: 335 K 335
           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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 7/61 (11%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRAARNAMKA 331
           L+V N++ N+ + +L+ +FE FG+I      R   T  + +G+  I + D   A+ A++ 
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETG-RSKGYGFIQFADAEDAKKALEQ 59

Query: 332 L 332
           L
Sbjct: 60  L 60

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

 Score = 39.5 bits (92), Expect = 4e-04
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           LFV N+  ++ + E++ LFE++G    I+   K +GF  I       A  A   L N PL
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIH-KDKGFGFIRLETRTLAEIAKAELDNMPL 62

Query: 338 RRRKLDIHY 346
           R ++L + +
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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 39.7 bits (93), Expect = 4e-04
 Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 367 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN-RSDVAGK 425
           NL  S S EEL +    +G I +I+  + K N  F+ F  I  A   + TL    D A +
Sbjct: 10  NLPESYSEEELREDLEKFGPIDQIKIVKEK-NIAFVHFLSIANAIKVVTTLPCEPDYASR 68

Query: 426 QI 427
           +I
Sbjct: 69  RI 70

This subgroup corresponds to the RRM2 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 = 78

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

 Score = 39.6 bits (92), Expect = 4e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           TL V NL   V+   + Q+F   G  +    I DT     + F+EF++ R A  +L  +N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 419 RSDVAGKQIKL 429
              + 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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----RGFVMISYYDIRAARNAMKALQ 333
           + V+N+       +++ LF  +G ++++    K     RGF  + +   + A NAM AL+
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 334 NKPLRRRKLDIHYS 347
           +  L  R+L + Y+
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|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 2 (PTBP2)

 Score = 40.4 bits (94), Expect = 4e-04
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 353 PSEKDANQGTLVVFNL-DSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 411
           P         L+V NL +  V+ + L  +FG+YG+++ ++   +K +   I+  D   ++
Sbjct: 6   PGVSAGGNTVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQ 65

Query: 412 TALRTLNRSDVAGKQIKLEASR 433
            A+  LN   + GK I++  S+
Sbjct: 66  LAMSHLNGQKMYGKIIRVTLSK 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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 39.1 bits (92), Expect = 5e-04
 Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           L V  L    S  EL + F  +G IR I D     N+ +IE+  I AA+ A   L 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI-DYDPGRNYAYIEYESIEAAQAAKEALR 55

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

 Score = 39.6 bits (92), Expect = 5e-04
 Identities = 17/60 (28%), Positives = 34/60 (56%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           ++V N+ +N   +EL+  F  +G +R+++ A    GF  + + D R A +A++ 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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 39.2 bits (91), Expect = 5e-04
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 422
           L V NL ++V+ E L + FG +G++  ++  +   ++ FI F +   A  A+  +N  ++
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLK---DYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 423 AGKQIKLEASRP 434
            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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRAARNAMKA 331
           +FV +++  ++   L+A F  FG+I      + + T  K +G+  +S+     A NA+++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTG-KSKGYGFVSFVKKEDAENAIQS 60

Query: 332 LQNKPLRRRKL 342
           +  + 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 417
           L V NL    + ++L ++F  YGE+ ++     R T+      F+ FYD R AE A+  +
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 418 NRSDVAGKQIK 428
           +  ++ 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|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 = 6e-04
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 371 SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
            VS E+L +IF  YGE+ +I     K+ + F++F    +   A+       + G+++ LE
Sbjct: 11  RVSKEDLFRIFSTYGELAQI---VLKNAYGFVQFDSPESCANAINCEQGKMIRGRKLHLE 67

Query: 431 ASRP 434
            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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 39.3 bits (92), Expect = 6e-04
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMK 330
           +RTLFV N+   + + EL+  FE++G +  +      RG    +  + + ++  A  A  
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 331 ALQNKPLRRRKLDIHY 346
           A+  + + R ++ I Y
Sbjct: 62  AMSGQYIGRNQIKIGY 77

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

 Score = 39.5 bits (93), Expect = 7e-04
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 7/67 (10%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRAARN 327
           P  TLFV  ++    +  L+ +F ++GDI      R I T    +G+  + Y   R A  
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTG-FSKGYAFVEYEHERDALR 60

Query: 328 AMKALQN 334
           A +    
Sbjct: 61  AYRDAHK 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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 39.6 bits (93), Expect = 7e-04
 Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 275 SRTLFVRNINSNVED-SELKALFEQFGDIRTIYTACKH----RGFVMISYYDIRAARNAM 329
           SR LFV  +     D S L+ LF Q G       A       RGF  + Y     A  A 
Sbjct: 2   SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 330 KALQNKPLRRRKLDIHYSIP 349
           +AL    L+   + + +  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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMI-----SYYDIRAARNAMKAL 332
           LFV N+ +++ + + K LFE++G+   ++   + RGF  I     +  +I  A      L
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 62

Query: 333 QNKPLRRR 340
           +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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 38.7 bits (91), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREI---RDTQHKHNHK---FIEFYDIRAAETALRT 416
           L V  L   V  + LH  F  +G+I++I    D      H+   F+EF +   A  A+  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLD-YETQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 417 LNRSDVAGKQIK 428
           +N S++ G+ I+
Sbjct: 60  MNESELFGRTIR 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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 38.7 bits (91), Expect = 8e-04
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREI---RD--TQHKHNHKFIEFYDIRAAETALRTL 417
           L V +L   V+   L++IF   G +  I   RD  T+    + ++ F +   AE AL TL
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 418 NRSDVAGKQIKL 429
           N   + GK I++
Sbjct: 62  NFDVIKGKPIRI 73

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

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKF-----IEFYDIRAAETALRTL 417
           L V NL      + +++ FG YGEI  +R      + +      +EF    AA+ AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 418 NRSDVAGKQIKLE 430
             +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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 42.2 bits (99), Expect = 9e-04
 Identities = 47/192 (24%), Positives = 83/192 (43%), Gaps = 26/192 (13%)

Query: 275 SRT-LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRA 324
           S+T L V  +   +   E+++LF   G+I +    CK           G+  ++Y     
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIES----CKLVRDKVTGQSLGYGFVNYVRPED 57

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 384
           A  A+ +L    L+ + + + Y+ P  + S K AN   L V  L  +++  EL  IF  +
Sbjct: 58  AEKAVNSLNGLRLQNKTIKVSYARPS-SDSIKGAN---LYVSGLPKTMTQHELESIFSPF 113

Query: 385 GEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAG--KQIKLE-ASRPGG 436
           G+I   R              FI F     A+ A++TLN +  +G  + I ++ A+ P  
Sbjct: 114 GQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSS 173

Query: 437 ARRFMVQSEQEQ 448
           +    + S+ E 
Sbjct: 174 SNSKGLLSQLEA 185

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 38.5 bits (90), Expect = 9e-04
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFG---DIRTIYT--ACKHRGFVMISYYDIRAARNAMKA 331
           TLFV N++ +V+D  LKA FE+FG     R I      + RGF  + +     A+ A++A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 332 LQNKPLRRRKLDIHYS 347
           +  K L  R +++ +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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 38.8 bits (91), Expect = 9e-04
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 9/73 (12%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGD------IRTIYT-ACKHRGFVMISYYDIRAARNAM 329
            +FV N+  + ++S L  LF  FG       IR + T  CK  GFV ++ Y+   A +A+
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE--EAYSAI 60

Query: 330 KALQNKPLRRRKL 342
            +L    L  R L
Sbjct: 61  ASLNGYRLGGRVL 73

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 39.2 bits (92), Expect = 9e-04
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTI 305
           RT+FV N+    +  +LK LF+QFG I ++
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESV 30

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

 Score = 38.4 bits (90), Expect = 9e-04
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 5/68 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-HKHNHK---FIEFYDIRAAETALRTL 417
           T+ V NLD SV  +EL ++F   GEI ++R  + +K   K   ++EF +  + + AL  L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-KL 59

Query: 418 NRSDVAGK 425
           +R  + 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMK 330
             L V  +  ++   EL++LFE  G I +          +  G+  + Y D   A+ A+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 331 ALQNKPLRRRKLDIHY 346
            L    +R ++L + Y
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|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 18/68 (26%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 363 LVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           L+V+ LD   ++ ++L  +F +YG +  I+  + K     ++  D +AAE A+  LN   
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVV 61

Query: 422 VAGKQIKL 429
           + G+++++
Sbjct: 62  LFGQKLEV 69

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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----RGFVMISYYDIRAARNAMKAL 332
           TLFV N++ + E  +L+  F++ G++  +  A       +GF  + +     A+ A+   
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59

Query: 333 QNKPLRRRKL 342
             + L  R++
Sbjct: 60  SGEELLGREI 69

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|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRT-IYTACKHRGFVMISYYDIRAARNAMKALQ 333
           SRTLF   +  N+ + +L++ F +FG++++ I    K   FV +  Y+ R A NA +A++
Sbjct: 3   SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKM--YNRRDAENAREAME 60

Query: 334 NKP 336
              
Sbjct: 61  QYK 63

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

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

 Score = 38.2 bits (88), Expect = 0.001
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHN--HKFIEFYDIRAAETALRTLN 418
           TL V NL   V+   + Q+F   G  +  +  T+H  N  + F+EFY+ R A  AL  +N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 419 RSDVAGKQIKLE-ASRPGGAR 438
              + GK++K+  A+ P   +
Sbjct: 61  GRKILGKEVKVNWATTPSSQK 81

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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 16/84 (19%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
           TL + +L+  +    ++  F   GE+  ++  ++K   K     F+EF    AAE AL++
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 417 LNRSDVAGKQIKLEASRPGGARRF 440
           LN     GK I      P   +RF
Sbjct: 61  LN-----GKPI------PNTQQRF 73

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

>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 = 37.4 bits (87), Expect = 0.002
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARNAMKAL 332
            LFV  +  +V   EL+ LF++ G ++++      + K +G   + Y +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 333 QNKPLRRRKLDIHYSIP 349
               ++ + + +  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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 12/77 (15%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI--------RTIYTACKHR--GFVMISYYDIRAARN 327
           L+V N+N  V +  L   F +FG +        RT     ++R  GFV  ++ +   A  
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFV--AFMNRADAER 61

Query: 328 AMKALQNKPLRRRKLDI 344
           A+  L  K +   +L +
Sbjct: 62  ALDELDGKDVMGYELKL 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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK----FIEFYDIRAAETALRTLN 418
           L+V NL    +  +L ++F  +G + E+   +     K    F++F     AE A++ +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 419 RSDVAGKQI 427
              + G+ +
Sbjct: 62  GKKIKGRPV 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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 37.9 bits (89), Expect = 0.002
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 11/63 (17%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTI--------YTACKHRGFVMISYYDIRAARNAM 329
           L+V N++    + ++  LF + GDI+ I         T C   GF  + YY    A NA+
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPC---GFCFVEYYTREDAENAV 57

Query: 330 KAL 332
           K L
Sbjct: 58  KYL 60

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 37.5 bits (88), Expect = 0.002
 Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 417
           L V NL    + E+++++F   G+I+ I     +         F+E+Y    AE A++ L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 418 NRSDVAGKQIKLE 430
           N + +  + I+++
Sbjct: 61  NGTKLDDRIIRVD 73

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 37.6 bits (87), Expect = 0.002
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           LFV N+ +++ + E K LF ++G+   ++   K +GF  I       A  A   L + P+
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFIN-KGKGFGFIKLESRALAEIAKAELDDTPM 62

Query: 338 RRRKLDIHY 346
           R R+L + +
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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAM 329
            +++ ++     + ELK  F QFG ++ +  A        KH GF  I + +   A  A 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGF--IQFLNPEVAAIAA 58

Query: 330 KALQNKPLRRRKLDIHY 346
           K++ N  L  + L +H 
Sbjct: 59  KSMNNYLLMGKVLQVHV 75

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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           T+ V NL   +   E+  +F  YG I +I  +       + FIEF D R AE A+R  + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 420 SDVAGKQIKLE 430
            D  G+++++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|214636 smart00360, RRM, RNA recognition motif

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 812 TLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFH 871
           TL + N+P   T + L     +   G  + + L  D +   + G+AF+            
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKF--GKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58

Query: 872 QAFNGKKWE 880
           +A NGK+ +
Sbjct: 59  EALNGKELD 67

Length = 73

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

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
            L + NL    + E L  +F  +   +E+R    +    F+EF     A  AL+ L 
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQFPGFKEVR-LVPRRGIAFVEFETEEQATVALQALQ 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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARNAMKALQ 333
           L VRN+     +++LK LF  FG +  +        K +GF  + +     A  A+K + 
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 334 NKPLRRRKLDIHYSI 348
            K ++ R + + +++
Sbjct: 62  GKKIKGRPVAVDWAV 76

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

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK--------HNHKFIEFYDIRAAETA 413
            L + NLDS ++   L ++F  YG+I++     HK          + F+ F     AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 414 LRTLNRSDVAGKQI 427
           L++LN     GK++
Sbjct: 61  LKSLNGKTALGKKL 74

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

 Score = 37.7 bits (87), Expect = 0.003
 Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 7/86 (8%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQF-----GDIRTIYTACK-HRGFVMISYYDIRAA 325
           E  S+T+ +R +  N+ +++++ L E F      D+R +       RGF  + +Y ++ A
Sbjct: 2   EKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDA 61

Query: 326 RNAMKALQNK-PLRRRKLDIHYSIPK 350
            + M+A Q K  ++ + + +HYS P+
Sbjct: 62  TSWMEANQKKLVIQGKTIAMHYSNPR 87

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 4/69 (5%)

Query: 278 LFVRNINSNVEDSELKALFEQFG---DIR-TIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           +FV  I  ++ + EL  LFE+ G   ++R  +  +  +RG+  ++Y +  AA+ A+K L 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 334 NKPLRRRKL 342
           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|240901 cd12455, RRM_like_Smg4_UPF3, RNA recognition motif-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 7/87 (8%)

Query: 813 LMIKNIPNKYTSKMLLAAIDEHCRGTYDFIY-----LPIDFKNKCNVGYAFINMIDPRQI 867
           ++I+ +P   T +  L  +    + T D+ Y        DFK       A+IN  +P  +
Sbjct: 2   VVIRRLPPSLTEEEFLEQVSPLIKPTVDWYYFVGGKSSKDFKPPIY-SRAYINFKNPEDL 60

Query: 868 IPFHQAFNGKKWE-KFNSEKVASLAYA 893
           + F + F+G  +     +E  A + YA
Sbjct: 61  LEFARRFDGHVFVDSKGNEYKAIVEYA 87

This subfamily corresponds to the RRM-like Smg4_UPF3 domain found in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. Upf3p, also termed nonsense-mediated mRNA decay protein 3, or Sua6p, a surveillance factor encoded by UPF3 gene from Saccharomyces cerevisiae. It is required for nonsense-mediated mRNA decay (NMD) in yeast. Upf3p is primarily cytoplasmic but accumulates inside the nucleus. Its nuclear import is mediated by the Srp1p (importin-alpha)/beta heterodimer while its nuclear export is mediated by a leucine-rich nuclear export sequence (NES-A), but not the Crm1p exportin. C. elegans SMG-4 is a nuclear shuttling protein that shuttles between the cytoplasm and nucleus through nuclear import and export signals similar to that of the yeast Upf3p. It is regulated by phosphorylation. Human orthologs of yeast Upf3p and C. elegans SMG-4 include Upf3A and Upf3B, which derive from two genes, UPF3A and X-linked UPF3B, respectively. Both, Upf3A (Up-frameshift suppressor 3 homolog A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A) and Upf3B (Up-frameshift suppressor 3 homolog B on chromosome X, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B), are nucleocytoplasmic shuttling proteins. They associate selectively with spliced beta-globin mRNA in vivo, and tethering of any human Upf protein to the 3'UTR of beta-globin mRNA prevents NMD. The function of the Upf proteins in identifying and targeting nonsense mRNAs for rapid decay is conserved among eukaryotes. Besides, all Upf proteins in this family contain a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that they may be RNA binding proteins. . Length = 88

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

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           TL + +L   V+ E+L  +F  YGEI+ I D        ++     + A  AL+ L    
Sbjct: 4   TLWIGHLSKKVTEEDLKNLFEEYGEIQSI-DMIPPRGCAYVCMETRQDAHRALQKLRNVK 62

Query: 422 VAGKQIKL 429
           +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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG---FVMISYYDIRAARNAMKAL 332
           RT++V N++      +L   F Q G+++ +  A        +  + + +  +  NA+K L
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALK-L 63

Query: 333 QNKPLRRRKLDIHYSI 348
                  R L +++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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 37.2 bits (87), Expect = 0.004
 Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 18/89 (20%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
           TL V  L+   +  +L + F  YG I+ IR  + K   K     FIEF   R  + A + 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK- 61

Query: 417 LNRSDVAGKQIKLEASRPGGARRFMVQSE 445
                  GK+I          RR +V  E
Sbjct: 62  ----YADGKKID--------GRRVLVDVE 78

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

 Score = 36.9 bits (85), Expect = 0.004
 Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           ++V N+ +     EL+  F  +G +RT++ A    GF  + + D R A +A++ L  K +
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 338 --RRRKLDIHYSIPK 350
              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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 335
           + LFVRN+ + V +  L+  F QFG +  +    K + +  I + +   A  AM+ +  K
Sbjct: 2   KVLFVRNLANTVTEEILEKAFGQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGK 58

Query: 336 PLRRRKLDIHYSIP 349
            L    ++I ++ P
Sbjct: 59  ELEGENIEIVFAKP 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIR--TIYT--ACKHRGFVMISYYDIRAARNAMKA 331
           RTLFV N+++ V +  L  LF Q G +    I      K + F  +++    +   A++ 
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 332 LQNKPLRRRKLDI 344
           L    L  R+L I
Sbjct: 62  LNGIRLFGRELRI 74

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>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 = 36.8 bits (86), Expect = 0.004
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI-RTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 336
           L +RN+  +V +S+L AL   FG +   +    K++  V      + +A++ +      P
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALV--EMDSVESAKSMVDYYLTVP 59

Query: 337 LRRRKLDIH--YS 347
              R   ++  YS
Sbjct: 60  ALIRGRRVYIQYS 72

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|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 = 40/77 (51%), Gaps = 5/77 (6%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETALRTL 417
           L+V  L  +++ +EL  +F   GE+     IRD    H   + F+ + + + AE A+ TL
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 418 NRSDVAGKQIKLEASRP 434
           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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMK 330
           +RTLF+ N++  V +++L+  F++FG I  +      RG    +  + + ++  A  A  
Sbjct: 7   NRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKL 66

Query: 331 ALQNKPLRRRKLDIHY 346
           A+  K LRR  + I Y
Sbjct: 67  AMSGKVLRRNPIKIGY 82

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, 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 possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain 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. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	985
KOG4660	549	consensus Protein Mei2, essential for commitment t	100.0
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.97
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.94
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.92
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.91
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.91
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.89
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.88
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.88
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.87
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.86
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.86
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.85
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.83
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.82
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.77
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.75
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.71
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.71
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.71
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.7
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.66
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.61
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.59
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.59
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.59
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.56
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.55
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.43
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.41
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.41
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.39
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.38
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.36
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.3
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.3
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.29
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.28
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.28
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.25
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.23
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.23
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.22
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.2
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.12
PLN03120	260	nucleic acid binding protein; Provisional	99.1
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.1
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.09
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.08
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.08
smart00362	72	RRM_2 RNA recognition motif.	99.08
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.06
PLN03120	260	nucleic acid binding protein; Provisional	99.05
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.05
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.04
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.03
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.03
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.02
KOG0122	270	consensus Translation initiation factor 3, subunit	99.01
PLN03213	759	repressor of silencing 3; Provisional	99.0
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.98
KOG0122	270	consensus Translation initiation factor 3, subunit	98.97
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.95
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.94
smart00362	72	RRM_2 RNA recognition motif.	98.93
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.92
smart00360	71	RRM RNA recognition motif.	98.92
PLN03121	243	nucleic acid binding protein; Provisional	98.91
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.91
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.91
PLN03213	759	repressor of silencing 3; Provisional	98.91
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.89
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.86
PLN03121	243	nucleic acid binding protein; Provisional	98.86
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.85
smart00360	71	RRM RNA recognition motif.	98.83
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.82
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.82
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.8
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.75
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.75
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.74
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.73
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.7
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.67
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.66
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.65
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.63
smart00361	70	RRM_1 RNA recognition motif.	98.61
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.6
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.6
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.57
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.54
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.52
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.49
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.46
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.44
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.44
smart00361	70	RRM_1 RNA recognition motif.	98.43
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.41
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.41
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.32
KOG4210	285	consensus Nuclear localization sequence binding pr	98.31
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.28
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.25
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.22
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.21
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.15
KOG0226	290	consensus RNA-binding proteins [General function p	98.13
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.04
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	98.01
KOG0151	877	consensus Predicted splicing regulator, contains R	97.98
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.97
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.9
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.9
KOG0151	877	consensus Predicted splicing regulator, contains R	97.86
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.77
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.72
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.68
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.66
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.63
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.62
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.61
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.59
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.48
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.44
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.43
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.35
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.35
KOG4210	285	consensus Nuclear localization sequence binding pr	97.3
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.26
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.18
KOG0226	290	consensus RNA-binding proteins [General function p	97.17
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.16
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.09
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.93
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.9
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.78
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.54
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.43
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.4
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.18
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.14
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.11
KOG3152	278	consensus TBP-binding protein, activator of basal	96.03
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.84
KOG1995	351	consensus Conserved Zn-finger protein [General fun	95.78
KOG1995	351	consensus Conserved Zn-finger protein [General fun	95.78
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.77
KOG1295	376	consensus Nonsense-mediated decay protein Upf3 [RN	95.66
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.5
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.46
KOG3152	278	consensus TBP-binding protein, activator of basal	95.41
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.99
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	94.85
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.56
KOG2314	698	consensus Translation initiation factor 3, subunit	94.38
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.05
KOG2314	698	consensus Translation initiation factor 3, subunit	94.05
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	93.91
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	93.78
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	93.4
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	92.97
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	92.79
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	91.83
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.57
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	91.23
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	90.87
KOG2068	327	consensus MOT2 transcription factor [Transcription	90.04
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	89.97
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	89.79
KOG1996	378	consensus mRNA splicing factor [RNA processing and	88.74
KOG2135	526	consensus Proteins containing the RNA recognition	88.55
KOG2591	684	consensus c-Mpl binding protein, contains La domai	88.49
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	87.37
KOG2591	684	consensus c-Mpl binding protein, contains La domai	87.07
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	86.82
KOG2068	327	consensus MOT2 transcription factor [Transcription	86.38
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	86.06
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	85.76
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	85.74
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	82.51
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	82.33
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	81.88

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

Probab=100.00  E-value=6.6e-71  Score=621.73  Aligned_cols=519  Identities=50%  Similarity=0.720  Sum_probs=368.4

Q ss_pred             hhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCc
Q 001991          222 EDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD  301 (985)
Q Consensus       222 ee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~  301 (985)
                      ++++.|..++||+|+++....+....+        ....+.....+++..+  +++ ||         .+|..+|++|+ 
T Consensus         2 ~d~~lf~~~G~~el~~~~~~~~~~~~~--------~~n~~~~~~~~~P~~~--s~~-~~---------~~l~a~f~~~~-   60 (549)
T KOG4660|consen    2 EDCDLFSSGGGMELDADSFDNLSVRNS--------DRNSAGFVFPEHPPGE--SRT-FV---------SELSALFEPFN-   60 (549)
T ss_pred             CccccccCCCCCCcccccccchhhccc--------ccCCCccccCCCCCCC--CCC-Ch---------hhHHhhhhccC-
Confidence            456899999999999765433222111        1233345556777777  566 77         78888898881 


Q ss_pred             EEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHh
Q 001991          302 IRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIF  381 (985)
Q Consensus       302 I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelF  381 (985)
                                                       +.+           +++.+.+++.++++|+|.|||.+|++++|+++|
T Consensus        61 ---------------------------------~p~-----------~~~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f   96 (549)
T KOG4660|consen   61 ---------------------------------KPL-----------RPDNPSEKDMNQGTLVVFNLPRSVSNDTLLRIF   96 (549)
T ss_pred             ---------------------------------CCC-----------CcCCCCcccCccceEEEEecCCcCCHHHHHHHH
Confidence                                             111           114556678899999999999999999999999


Q ss_pred             hccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchhhhhhhhhhhccCCCcc----cCC
Q 001991          382 GIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC----QIP  457 (985)
Q Consensus       382 s~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rrl~qq~eq~q~e~nLy----kNl  457 (985)
                      +.||+|++|+..+..++.+||+|+|+.+|++|+++||+.+|.|+.|+    ++...++.+.-    +....++    ..+
T Consensus        97 ~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k----~~~~~~~~~~~----~~~~~~~~~~~~p~  168 (549)
T KOG4660|consen   97 GAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK----RPGGARRAMGL----QSGTSFLNHFGSPL  168 (549)
T ss_pred             HhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc----CCCcccccchh----cccchhhhhccchh
Confidence            99999999999999999999999999999999999999999999999    66666552211    1112222    333


Q ss_pred             CCCCCccccccccceEEEecCCCCcceeccCCCCCcccccccCCCCCCCCCCCCCCccCcCCccccccCCCCcccccccC
Q 001991          458 FDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFG  537 (985)
Q Consensus       458 p~svt~e~L~~fG~I~S~~~enG~srgf~s~~~~P~~~~~~~~~s~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  537 (985)
                      .+++++.+-              ..+.|.     +|.|..    +++++                   ++..+++.-.-+
T Consensus       169 a~s~pgg~~--------------~~~~~g-----~l~P~~----s~~~~-------------------~~~~~~~~~~~~  206 (549)
T KOG4660|consen  169 ANSPPGGWP--------------RGQLFG-----MLSPTR----SSILL-------------------EHISSVDGSSPG  206 (549)
T ss_pred             hcCCCCCCc--------------CCccee-----eeccch----hhhhh-------------------hcchhccCcccc
Confidence            444433321              111111     122211    11111                   111111111011


Q ss_pred             CC-CCCCCCCCcccccccccCCCCCCCCccccccccccCCcccCCCCCCCccccCCCCCCCCCCCCccCCCCCCCccCCC
Q 001991          538 NQ-HPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHG  616 (985)
Q Consensus       538 ~~-~~~~~~~s~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~g  616 (985)
                       + .+-++ |   .+...++.+.+|..+    ..                  . +  |.++-...++.        +++|
T Consensus       207 -~~~~~~~-h---q~~~~~~~~~s~a~~----~~------------------~-~--G~~~s~~~~v~--------t~S~  248 (549)
T KOG4660|consen  207 -RETPLLN-H---QRFVEFADNRSYAFS----EP------------------R-G--GFLISNSSGVI--------TFSG  248 (549)
T ss_pred             -ccccchh-h---hhhhhhccccchhhc----cc------------------C-C--ceecCCCCceE--------EecC
Confidence             1 11221 1   223334444433211    00                  0 0  33221112333        3333


Q ss_pred             CCccCCCCCCCCCCCCCCCcCCCCCCccCCcccCCCCCCCCCCCCCcccccCCCC-CcccccCCCCCCCCccccccccCC
Q 001991          617 NPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSP-AHHHIGSAPAVNPSLWDRQHAYAG  695 (985)
Q Consensus       617 ~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~gsap~~~~~~~~~~~~~~~  695 (985)
                      +                .++|       |++.+++..|            +.+.. .|||||+||+.             
T Consensus       249 ~----------------~g~~-------n~~~~~r~~~------------~~~~~~~~~hi~~~Ps~-------------  280 (549)
T KOG4660|consen  249 P----------------GGVW-------NPFPSRRQRQ------------NSSSSHYEHHIGSAPSM-------------  280 (549)
T ss_pred             C----------------Cccc-------CCcccccccc------------ccCcccccCccCCCccc-------------
Confidence            2                1344       3333332111            12212 38999999982             


Q ss_pred             CCCCCcccccCCCCCCCCCCCCCCcccccc--cccccccCCCCccCcC-CCCCCCCcccccCCCCCCCCCccccccccch
Q 001991          696 ESPETSNFHLGSLGSGGFLGRSPSHHVDIA--SQNILSHVGGNCMDMT-KNVGMRSPQQICHLFPGRNPMMSMQTSFDSS  772 (985)
Q Consensus       696 ~~~~~~~~~~g~~g~~g~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~~~~s~~~~~~~~~g~~~~~~~~~~~~~~  772 (985)
                             .|+..-++++|.+..+.+.|...  ....+.+..|++++.. +++++.+.++..+.|.++.-+.   ...+..
T Consensus       281 -------~~l~~~~~~~f~~~s~~~~~~~~~~~n~g~~~~t~~~~e~~s~n~~~e~~~rv~~~f~~~~~~~---~~~~~~  350 (549)
T KOG4660|consen  281 -------HHLLSRISVGFNGGSGALEMNSNGQANQGFLTKTGNVTEFNSKNVGMESSPRVPKNFEGRRSYT---SQNDYP  350 (549)
T ss_pred             -------ccccccCccccCCCCCCccccccccCCCCccccCcccccccCCCccccccCCCCcccccccccc---cccccc
Confidence                   24445566777766665555444  2345667889998888 9999999999999999887443   345555


Q ss_pred             hHHhhhccccccCCCCCcccccccccchhhhhcCCCCceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEecccccccc
Q 001991          773 NERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKC  852 (985)
Q Consensus       773 ~~~~r~~~~~~~~~~~~~~~~~~~~~d~~~i~~g~d~rTTvMirNIPnk~t~~~L~~~id~~~~g~yDF~YlpiDf~~~~  852 (985)
                      .+..+++.-||.+.+....+++++.+|+.+|++|+|.|||+||||||||||++||++. ||.++|+|||+||||||+|+|
T Consensus       351 ~~~~~~~~~~Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~-d~~~~gtYDFlYLPiDF~nkc  429 (549)
T KOG4660|consen  351 VELILNYRDRRTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAA-DEKNKGTYDFLYLPIDFKNKC  429 (549)
T ss_pred             cccccccccchhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhh-hccccCccceEEecccccccc
Confidence            6644445558888777777899999999999999999999999999999999999999 999999999999999999999


Q ss_pred             eeEEEEEecCCchhhHHHHHHhcCCcccCCCCccEEEEEeecccCHHHHHHHhccCccccCCCCccceEEecCCCCCCCC
Q 001991          853 NVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVASLAYARIQGKAALIAHFQNSSLMNEDKRCRPILFHTDGPNAGDP  932 (985)
Q Consensus       853 N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~K~~~v~yA~iQG~~ali~hf~~s~~~~~~~~~rP~~f~~~g~~~g~~  932 (985)
                      |||||||||++|++|++||++|||++|++|+|+|||+|+|||||||++|++|||||++|||++.|+|++|++  |+.|.+
T Consensus       430 NvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQGk~~Li~hFqnS~lm~E~e~y~Pvvf~p--p~dg~~  507 (549)
T KOG4660|consen  430 NVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQGKEALIEHFQNSSLMCEDEAYRPVVFSP--PEDGRE  507 (549)
T ss_pred             ccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhchHHHHHHhhcccccccchhcCceEecC--cccccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999997  899999


Q ss_pred             CCCCCCCCccCCCCCCCccCcc
Q 001991          933 EPFPMGTNIRSRLGKPRINGNE  954 (985)
Q Consensus       933 ~~fp~~~~~~~~~~~~r~~~~~  954 (985)
                      +++|...+++.+.+.++.....
T Consensus       508 ~~~p~~~~~~a~~~~s~~~~~~  529 (549)
T KOG4660|consen  508 EPEPVKLNQDAGAGHSTNASLK  529 (549)
T ss_pred             cCccccccccCCCCcccchhhh
Confidence            9999999999887777766655

>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=1.6e-45  Score=341.22  Aligned_cols=97  Identities=65%  Similarity=1.188  Sum_probs=96.3

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEecccccccceeEEEEEecCCchhhHHHHHHhcCCcccCCCCccEEE
Q 001991          810 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVAS  889 (985)
Q Consensus       810 rTTvMirNIPnk~t~~~L~~~id~~~~g~yDF~YlpiDf~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~K~~~  889 (985)
                      |||||||||||||||+||+++||+.|+|+||||||||||+++||+|||||||+++++|.+|++.|+|++|+.++|+|||+
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             EEeecccCHHHHHHHhc
Q 001991          890 LAYARIQGKAALIAHFQ  906 (985)
Q Consensus       890 v~yA~iQG~~ali~hf~  906 (985)
                      |+||||||++|||+|||
T Consensus        81 i~yAriQG~~alv~~f~   97 (97)
T PF04059_consen   81 ISYARIQGKDALVEHFR   97 (97)
T ss_pred             EehhHhhCHHHHHHhhC
Confidence            99999999999999996

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

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

Probab=100.00  E-value=8.7e-36  Score=354.78  Aligned_cols=276  Identities=22%  Similarity=0.348  Sum_probs=232.6

Q ss_pred             ccCCCCeeeecccCCCCCcccCCCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCCh-hh
Q 001991          123 NSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDE-DD  200 (985)
Q Consensus       123 ~~~~g~~i~im~s~rd~sl~sSsl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpde-dD  200 (985)
                      ..++|++|+|+|+++|++++++..++|||+||+. ++++.|++.              |        +.+|+|+..+ ..
T Consensus        65 ~~i~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~--------------F--------~~~G~i~~~~i~~  122 (562)
T TIGR01628        65 KRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDT--------------F--------SKFGNILSCKVAT  122 (562)
T ss_pred             CEECCeeEEeecccccccccccCCCceEEcCCCccCCHHHHHHH--------------H--------HhcCCcceeEeee
Confidence            4589999999999999999999999999999998 999999998              8        6677777621 00


Q ss_pred             hhccCCCCeeeeecCCChhhhhhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEE
Q 001991          201 LFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFV  280 (985)
Q Consensus       201 L~sG~SkGfGFV~ff~t~Edaee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfV  280 (985)
                      -.+|.++|||||+ |++.++++  +|+..++|+.+. +..+.++.......+              + .......++|||
T Consensus       123 ~~~g~skg~afV~-F~~~e~A~--~Ai~~lng~~~~-~~~i~v~~~~~~~~~--------------~-~~~~~~~~~l~V  183 (562)
T TIGR01628       123 DENGKSRGYGFVH-FEKEESAK--AAIQKVNGMLLN-DKEVYVGRFIKKHER--------------E-AAPLKKFTNLYV  183 (562)
T ss_pred             cCCCCcccEEEEE-ECCHHHHH--HHHHHhcccEec-CceEEEecccccccc--------------c-cccccCCCeEEE
Confidence            1267899999999 66888888  899999999998 555555443321110              0 113345689999


Q ss_pred             ecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccc----cccccccccCCCCC
Q 001991          281 RNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLR----RRKLDIHYSIPKDN  352 (985)
Q Consensus       281 gNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~----Gr~L~V~~a~pk~~  352 (985)
                      +|||.++|+++|+++|+.||+|.++++    +++++|||||+|.+.++|.+|++.|++..+.    |+.+.|.++..+.+
T Consensus       184 ~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~e  263 (562)
T TIGR01628       184 KNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAE  263 (562)
T ss_pred             eCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhh
Confidence            999999999999999999999999876    4678999999999999999999999999999    99999998877654


Q ss_pred             CCc--------------ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHH
Q 001991          353 PSE--------------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETAL  414 (985)
Q Consensus       353 ~~~--------------~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI  414 (985)
                      +..              ......+|||+||+..+|+++|+++|++||.|++|+++.+    ++|||||+|.+.++|.+|+
T Consensus       264 r~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~  343 (562)
T TIGR01628       264 REAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAV  343 (562)
T ss_pred             hHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHH
Confidence            310              1223458999999999999999999999999999998654    5799999999999999999


Q ss_pred             HHhCCceeCCceEEEEeccCcchhh
Q 001991          415 RTLNRSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       415 ~~LNG~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      ..|||+.|+|++|+|.++.+++.|+
T Consensus       344 ~~~~g~~~~gk~l~V~~a~~k~~~~  368 (562)
T TIGR01628       344 TEMHGRMLGGKPLYVALAQRKEQRR  368 (562)
T ss_pred             HHhcCCeeCCceeEEEeccCcHHHH
Confidence            9999999999999999999988776

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=100.00  E-value=5.7e-34  Score=339.21  Aligned_cols=294  Identities=19%  Similarity=0.287  Sum_probs=234.6

Q ss_pred             ccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCC--hhhhhccCCCCeeeeecCCChhhhhhh
Q 001991          148 DIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPD--EDDLFSGVTDDMGHNFQANTVDDLEDF  224 (985)
Q Consensus       148 ~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpd--edDL~sG~SkGfGFV~ff~t~Edaee~  224 (985)
                      .|||+||+. ++.+.|++.              |        +.+|.|...  ..|..++.++|||||. |.+.++|+  
T Consensus         2 sl~VgnLp~~vte~~L~~~--------------F--------~~~G~v~~v~v~~d~~t~~s~G~afV~-F~~~~~A~--   56 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDL--------------F--------KPFGPVLSVRVCRDSVTRRSLGYGYVN-FQNPADAE--   56 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHH--------------H--------HhcCCEEEEEEEecCCCCCcceEEEEE-ECCHHHHH--
Confidence            699999997 888889988              8        444544441  1233467899999999 66888888  


Q ss_pred             HHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE
Q 001991          225 DLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT  304 (985)
Q Consensus       225 ~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s  304 (985)
                      +|+..+++..+.| +.+.+..                +..  +........++|||+|||.++++++|+++|++||.|.+
T Consensus        57 ~Al~~ln~~~i~g-k~i~i~~----------------s~~--~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~  117 (562)
T TIGR01628        57 RALETMNFKRLGG-KPIRIMW----------------SQR--DPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILS  117 (562)
T ss_pred             HHHHHhCCCEECC-eeEEeec----------------ccc--cccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcce
Confidence            8999999988873 3322111                110  00112223568999999999999999999999999999


Q ss_pred             EEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCC-CcccccccceeeecCCCCCCHHHHHH
Q 001991          305 IYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP-SEKDANQGTLVVFNLDSSVSTEELHQ  379 (985)
Q Consensus       305 Vki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~-~~~~~~~~tLfV~NLp~svTeedLre  379 (985)
                      |++    +++++|||||+|.+.++|++|++.++|..+.++.|.|....++... .......++|||+||+.++|+++|++
T Consensus       118 ~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~  197 (562)
T TIGR01628       118 CKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRE  197 (562)
T ss_pred             eEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHH
Confidence            876    4678999999999999999999999999999999999877665554 22334567899999999999999999


Q ss_pred             HhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeC----CceEEEEeccCcchhh--hhhhhhhhc-
Q 001991          380 IFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVA----GKQIKLEASRPGGARR--FMVQSEQEQ-  448 (985)
Q Consensus       380 lFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~----Gr~IkV~~A~~k~~Rr--l~qq~eq~q-  448 (985)
                      +|++||+|.++++..+    .+|||||+|.+.++|.+|++.|||..|.    |+.|.|.+++.+.++.  +....++.+ 
T Consensus       198 ~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~  277 (562)
T TIGR01628       198 LFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQ  277 (562)
T ss_pred             HHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhh
Confidence            9999999999988654    5789999999999999999999999999    9999999998887663  222222221 


Q ss_pred             ------cCCCcc-cCCCCCCCcccc----ccccceEEE---ecCCCCccee
Q 001991          449 ------DDLNLC-QIPFDDLSSGQM----VSSGVITST---CMDNGSIQVL  485 (985)
Q Consensus       449 ------~e~nLy-kNlp~svt~e~L----~~fG~I~S~---~~enG~srgf  485 (985)
                            ...+|| +||+.++++++|    +.||.|+++   ..++|.++||
T Consensus       278 ~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~  328 (562)
T TIGR01628       278 ERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGF  328 (562)
T ss_pred             hhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCe
Confidence                  224788 999999999999    899999998   4467888886

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=2.1e-32  Score=306.34  Aligned_cols=247  Identities=17%  Similarity=0.287  Sum_probs=196.3

Q ss_pred             CcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCC--hhhhhccCCCCeeeeecCCChhhhh
Q 001991          146 LSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPD--EDDLFSGVTDDMGHNFQANTVDDLE  222 (985)
Q Consensus       146 l~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpd--edDL~sG~SkGfGFV~ff~t~Edae  222 (985)
                      -.+|||+||+. ++.+.|++.              |        ..+|.|...  ..|..+|.++|||||+ |.+.++|+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~--------------F--------~~~G~i~~v~i~~d~~~g~s~g~afV~-f~~~~~A~   59 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSL--------------F--------TSIGEIESCKLVRDKVTGQSLGYGFVN-YVRPEDAE   59 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHH--------------H--------HccCCEEEEEEEEcCCCCccceEEEEE-ECcHHHHH
Confidence            35899999997 888899988              8        555655441  1222368899999999 56788888


Q ss_pred             hhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcE
Q 001991          223 DFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI  302 (985)
Q Consensus       223 e~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I  302 (985)
                        +|+..++|..|. +..+.+.....                    .......++|||+|||..+++++|+++|++||.|
T Consensus        60 --~Ai~~l~g~~l~-g~~i~v~~a~~--------------------~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i  116 (352)
T TIGR01661        60 --KAVNSLNGLRLQ-NKTIKVSYARP--------------------SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQI  116 (352)
T ss_pred             --HHHhhcccEEEC-CeeEEEEeecc--------------------cccccccceEEECCccccCCHHHHHHHHhccCCE
Confidence              899999999998 44333322111                    0112345789999999999999999999999999


Q ss_pred             EEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccccCCCCCCCc----------------c---
Q 001991          303 RTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIPKDNPSE----------------K---  356 (985)
Q Consensus       303 ~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~pk~~~~~----------------~---  356 (985)
                      ..+++     ++.++|||||+|.+.++|++|++.|+|..+.|  .+|.|.++........                .   
T Consensus       117 ~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (352)
T TIGR01661       117 ITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPL  196 (352)
T ss_pred             EEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCc
Confidence            98865     45689999999999999999999999999887  5677777643321000                0   


Q ss_pred             ---------------------------------------------------------------------cccccceeeec
Q 001991          357 ---------------------------------------------------------------------DANQGTLVVFN  367 (985)
Q Consensus       357 ---------------------------------------------------------------------~~~~~tLfV~N  367 (985)
                                                                                           .....+|||+|
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~N  276 (352)
T TIGR01661       197 STILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYN  276 (352)
T ss_pred             cccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeC
Confidence                                                                                 00112599999


Q ss_pred             CCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchh
Q 001991          368 LDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGAR  438 (985)
Q Consensus       368 Lp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~R  438 (985)
                      ||.++++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|.+|++.|||..|+||+|+|.|+..++.|
T Consensus       277 L~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~~  352 (352)
T TIGR01661       277 LSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAYR  352 (352)
T ss_pred             CCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCCC
Confidence            9999999999999999999999998754     5899999999999999999999999999999999999887643

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=4.7e-31  Score=298.40  Aligned_cols=271  Identities=22%  Similarity=0.333  Sum_probs=230.3

Q ss_pred             cccCCCCeeeecccCCCCCcccCCCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChh-
Q 001991          122 INSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDED-  199 (985)
Q Consensus       122 ~~~~~g~~i~im~s~rd~sl~sSsl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpded-  199 (985)
                      ...++|++|||||++||+++       ||++||+. +|++.||++              |        +.+|+|||++- 
T Consensus        59 ~~~~~~~~~rim~s~rd~~~-------~~i~nl~~~~~~~~~~d~--------------f--------~~~g~ilS~kv~  109 (369)
T KOG0123|consen   59 FDVLKGKPIRIMWSQRDPSL-------VFIKNLDESIDNKSLYDT--------------F--------SEFGNILSCKVA  109 (369)
T ss_pred             CcccCCcEEEeehhccCCce-------eeecCCCcccCcHHHHHH--------------H--------HhhcCeeEEEEE
Confidence            46899999999999999998       99999997 999999999              9        99999999331 


Q ss_pred             hhhccCCCCeeeeecCCChhhhhhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEE
Q 001991          200 DLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLF  279 (985)
Q Consensus       200 DL~sG~SkGfGFV~ff~t~Edaee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLf  279 (985)
                      .-..| ++|| ||+ |+++++|+  .++..+||+.+. ++++.+|.......+.           ..... .....+.+|
T Consensus       110 ~~~~g-~kg~-FV~-f~~e~~a~--~ai~~~ng~ll~-~kki~vg~~~~~~er~-----------~~~~~-~~~~~t~v~  171 (369)
T KOG0123|consen  110 TDENG-SKGY-FVQ-FESEESAK--KAIEKLNGMLLN-GKKIYVGLFERKEERE-----------APLGE-YKKRFTNVY  171 (369)
T ss_pred             EcCCC-ceee-EEE-eCCHHHHH--HHHHHhcCcccC-CCeeEEeeccchhhhc-----------ccccc-hhhhhhhhh
Confidence            11145 9999 999 66888888  899999999998 7777887765532211           01111 234568999


Q ss_pred             EecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCC-
Q 001991          280 VRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS-  354 (985)
Q Consensus       280 VgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~-  354 (985)
                      |.|++.+++++.|.++|..||+|.++.+    .+++++|+||.|++.++|..|++.|++..+.+..+.|..+..+.+.. 
T Consensus       172 vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~  251 (369)
T KOG0123|consen  172 VKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREA  251 (369)
T ss_pred             eeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHH
Confidence            9999999999999999999999999875    57789999999999999999999999999999999998887644321 


Q ss_pred             -------------cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHh
Q 001991          355 -------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTL  417 (985)
Q Consensus       355 -------------~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~L  417 (985)
                                   .......+|||.||+..++++.|+++|+.||+|.+++++.+    .+||+||+|...++|.+|+..+
T Consensus       252 ~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~  331 (369)
T KOG0123|consen  252 ELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTEM  331 (369)
T ss_pred             HHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCccceEEEEcCCHHHHHHHHHhh
Confidence                         11345569999999999999999999999999999888643    6899999999999999999999


Q ss_pred             CCceeCCceEEEEeccCcchhh
Q 001991          418 NRSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       418 NG~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      |+..+.+++|.|.+++.+..|+
T Consensus       332 n~~~i~~k~l~vav~qr~~~r~  353 (369)
T KOG0123|consen  332 NGRLIGGKPLYVAVAQRKEDRR  353 (369)
T ss_pred             ChhhhcCCchhhhHHhhhccch
Confidence            9999999999999999777665

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.97  E-value=1.1e-29  Score=297.59  Aligned_cols=292  Identities=16%  Similarity=0.186  Sum_probs=212.4

Q ss_pred             ccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhHH
Q 001991          148 DIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDL  226 (985)
Q Consensus       148 ~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~a  226 (985)
                      .|||+||++ +++++|++.              |        +.+|.|....  +  -.+||||||+ |++.++|+  .|
T Consensus         4 vv~V~nLp~~~te~~L~~~--------------f--------~~fG~V~~v~--i--~~~k~~afVe-f~~~e~A~--~A   54 (481)
T TIGR01649         4 VVHVRNLPQDVVEADLVEA--------------L--------IPFGPVSYVM--M--LPGKRQALVE-FEDEESAK--AC   54 (481)
T ss_pred             EEEEcCCCCCCCHHHHHHH--------------H--------HhcCCeeEEE--E--ECCCCEEEEE-eCchHHHH--HH
Confidence            699999998 899899988              8        5566555422  1  1267899999 56788878  77


Q ss_pred             Hhc--cCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE
Q 001991          227 FSS--GGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT  304 (985)
Q Consensus       227 i~~--~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s  304 (985)
                      +..  .++..+. +..+.+......   ......  +..   ..........+|||+||+..+|+++|+++|+.||+|..
T Consensus        55 i~~~~~~~~~l~-g~~l~v~~s~~~---~~~~~~--~~~---~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~  125 (481)
T TIGR01649        55 VNFATSVPIYIR-GQPAFFNYSTSQ---EIKRDG--NSD---FDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLR  125 (481)
T ss_pred             HHHhhcCCceEc-CeEEEEEecCCc---ccccCC--CCc---ccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEE
Confidence            764  5788887 443333222110   000000  000   00111223468999999999999999999999999999


Q ss_pred             EEe-ccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccccCCCCC-------CC--------------------
Q 001991          305 IYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIPKDN-------PS--------------------  354 (985)
Q Consensus       305 Vki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~pk~~-------~~--------------------  354 (985)
                      |++ ....+++|||+|.+.++|.+|++.|||+.|.+  ..|+|.|+.+..-       ..                    
T Consensus       126 v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~  205 (481)
T TIGR01649       126 IVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTH  205 (481)
T ss_pred             EEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccc
Confidence            987 33345799999999999999999999999965  4677776654210       00                    


Q ss_pred             ----c------------------------------------------------------------ccccccceeeecCCC
Q 001991          355 ----E------------------------------------------------------------KDANQGTLVVFNLDS  370 (985)
Q Consensus       355 ----~------------------------------------------------------------~~~~~~tLfV~NLp~  370 (985)
                          .                                                            ...+.++|||+||++
T Consensus       206 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~  285 (481)
T TIGR01649       206 RQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQ  285 (481)
T ss_pred             cccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCC
Confidence                0                                                            001345899999998


Q ss_pred             -CCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchhhhh--------
Q 001991          371 -SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFM--------  441 (985)
Q Consensus       371 -svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rrl~--------  441 (985)
                       .+|+++|+++|+.||.|.+|+++.+++|||||+|.+.++|.+|++.|||..|.|++|+|.+++........        
T Consensus       286 ~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~  365 (481)
T TIGR01649       286 EKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGL  365 (481)
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCC
Confidence             69999999999999999999999888999999999999999999999999999999999998654211000        


Q ss_pred             ---hhhh---------hh--------ccCCCcc-cCCCCCCCcccc----ccccc--eEEEec
Q 001991          442 ---VQSE---------QE--------QDDLNLC-QIPFDDLSSGQM----VSSGV--ITSTCM  477 (985)
Q Consensus       442 ---qq~e---------q~--------q~e~nLy-kNlp~svt~e~L----~~fG~--I~S~~~  477 (985)
                         +...         ..        ....+|| +|||.++++++|    ..||.  |+.++.
T Consensus       366 ~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~  428 (481)
T TIGR01649       366 TSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKF  428 (481)
T ss_pred             cccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEE
Confidence               0000         00        0123677 999999999999    88997  777744

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.96  E-value=3.5e-29  Score=295.25  Aligned_cols=236  Identities=21%  Similarity=0.306  Sum_probs=190.8

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCCh--hhhhccCCCCeeeeecCCChhhhhh
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDE--DDLFSGVTDDMGHNFQANTVDDLED  223 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpde--dDL~sG~SkGfGFV~ff~t~Edaee  223 (985)
                      .+|||+||++ ++++.|.+.              |        ..+|.|...+  .| .++.++|||||+ |.+.|+|+ 
T Consensus        59 ~~lFVgnLp~~~tEd~L~~~--------------F--------~~~G~I~~vrl~~D-~sG~sRGfaFV~-F~~~e~A~-  113 (578)
T TIGR01648        59 CEVFVGKIPRDLYEDELVPL--------------F--------EKAGPIYELRLMMD-FSGQNRGYAFVT-FCGKEEAK-  113 (578)
T ss_pred             CEEEeCCCCCCCCHHHHHHH--------------H--------HhhCCEEEEEEEEC-CCCCccceEEEE-eCCHHHHH-
Confidence            5899999997 888889888              8        3444443311  12 478999999999 66888888 


Q ss_pred             hHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCc-E
Q 001991          224 FDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD-I  302 (985)
Q Consensus       224 ~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~-I  302 (985)
                       +|+..++|.++...+.+.+                .          .....++|||+|||.++++++|.+.|++++. +
T Consensus       114 -~Ai~~lng~~i~~Gr~l~V----------------~----------~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egv  166 (578)
T TIGR01648       114 -EAVKLLNNYEIRPGRLLGV----------------C----------ISVDNCRLFVGGIPKNKKREEILEEFSKVTEGV  166 (578)
T ss_pred             -HHHHHcCCCeecCCccccc----------------c----------ccccCceeEeecCCcchhhHHHHHHhhcccCCc
Confidence             8999999998862222110                0          0123589999999999999999999999974 3


Q ss_pred             EEEEe------ccccceEEEEEeCCHHHHHHHHHHccC--cccccccccccccCCCCCCCcc-cccccceeeecCCCCCC
Q 001991          303 RTIYT------ACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIHYSIPKDNPSEK-DANQGTLVVFNLDSSVS  373 (985)
Q Consensus       303 ~sVki------tgksrGfAFV~F~d~esA~kAi~~Lng--~~I~Gr~L~V~~a~pk~~~~~~-~~~~~tLfV~NLp~svT  373 (985)
                      ..+.+      .++++|||||+|.+.++|..|++.|+.  ..+.|+.|.|.|+.++....+. ....++|||+||+.+++
T Consensus       167 v~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~t  246 (578)
T TIGR01648       167 VDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTT  246 (578)
T ss_pred             eEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccccccccccEEEEeCCCCCCC
Confidence            33322      356899999999999999999998864  3578999999999887654322 23346899999999999


Q ss_pred             HHHHHHHhhcc--CCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          374 TEELHQIFGIY--GEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       374 eedLrelFs~f--G~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      +++|+++|++|  |+|++|+++   ++||||+|.+.++|++|++.|||.+|.|++|+|.|++++..
T Consensus       247 ee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       247 EEIIEKSFSEFKPGKVERVKKI---RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHHHHHHHHhcCCCceEEEEee---cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            99999999999  999999875   57999999999999999999999999999999999988653

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=99.96  E-value=3.3e-28  Score=285.31  Aligned_cols=287  Identities=18%  Similarity=0.210  Sum_probs=206.3

Q ss_pred             cccCCCCeeeecccCCCCCcc----------cCCCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeE
Q 001991          122 INSLSGNRSGINGIQSESSLF----------SSSLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQT  190 (985)
Q Consensus       122 ~~~~~g~~i~im~s~rd~sl~----------sSsl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~  190 (985)
                      ...+.|++|+|+|+.+...-+          .+....|||+||.. ++.+.|+..              |        ..
T Consensus        62 ~~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~--------------F--------~~  119 (481)
T TIGR01649        62 PIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQI--------------F--------NP  119 (481)
T ss_pred             CceEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHH--------------H--------hc
Confidence            467899999999986542111          12344699999986 888888888              8        44


Q ss_pred             ecCcCCChhhhhccCCCCeeeeecCCChhhhhhhHHHhccCCeeEcCCc-ch----------hhhccccc---ccCC-CC
Q 001991          191 IGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDD-RL----------FAVQKNSD---FVGG-VS  255 (985)
Q Consensus       191 iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~ai~~~nG~eLegd~-~~----------~vg~~ls~---l~k~-~~  255 (985)
                      +|.|+...  +..-...++|||+ |++.++|+  +|+..++|.++.+.. .+          .+.+....   ++.. .+
T Consensus       120 ~G~V~~v~--i~~~~~~~~afVe-f~~~~~A~--~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~  194 (481)
T TIGR01649       120 YGKVLRIV--TFTKNNVFQALVE-FESVNSAQ--HAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLP  194 (481)
T ss_pred             cCCEEEEE--EEecCCceEEEEE-ECCHHHHH--HHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCC
Confidence            55554411  0011124689999 56788878  899999999986431 11          11110000   0000 00


Q ss_pred             -------------CCCC----------CCC--C-------------c---------------------C--CCCCCCCCC
Q 001991          256 -------------NQGV----------SAG--S-------------V---------------------V--GEHPYGEHP  274 (985)
Q Consensus       256 -------------n~~~----------~~~--~-------------~---------------------~--~e~~~~e~~  274 (985)
                                   .+..          .++  .             .                     .  .-.+....+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (481)
T TIGR01649       195 GRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGP  274 (481)
T ss_pred             CCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCC
Confidence                         0000          000  0             0                     0  000011346


Q ss_pred             CcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCC
Q 001991          275 SRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP  353 (985)
Q Consensus       275 srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~  353 (985)
                      +++|||+|||+ .+|+++|+++|+.||.|..|++....+|||||+|.+.++|++|++.|||..|.|++|+|.++..+...
T Consensus       275 ~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~  354 (481)
T TIGR01649       275 GSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQ  354 (481)
T ss_pred             CCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccccc
Confidence            78999999998 69999999999999999999985556899999999999999999999999999999999987543110


Q ss_pred             Cc------------c---------------------cccccceeeecCCCCCCHHHHHHHhhccCC--EEEEEEcCCC--
Q 001991          354 SE------------K---------------------DANQGTLVVFNLDSSVSTEELHQIFGIYGE--IREIRDTQHK--  396 (985)
Q Consensus       354 ~~------------~---------------------~~~~~tLfV~NLp~svTeedLrelFs~fG~--I~~Vri~~~s--  396 (985)
                      ..            +                     ..+..+|||+|||.++++++|+++|+.||.  |..|++.+..  
T Consensus       355 ~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~  434 (481)
T TIGR01649       355 PPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNE  434 (481)
T ss_pred             CCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCC
Confidence            00            0                     013458999999999999999999999998  8888886543  


Q ss_pred             -CcEEEEEEcCHHHHHHHHHHhCCceeCCce------EEEEeccCc
Q 001991          397 -HNHKFIEFYDIRAAETALRTLNRSDVAGKQ------IKLEASRPG  435 (985)
Q Consensus       397 -kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~------IkV~~A~~k  435 (985)
                       +++|||+|.+.++|.+||..||+..|.++.      |+|.|++++
T Consensus       435 ~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       435 RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence             789999999999999999999999999985      999999864

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=1.7e-27  Score=266.80  Aligned_cols=159  Identities=22%  Similarity=0.408  Sum_probs=143.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      +.++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.
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            4689999999999999999999999999999876     57789999999999999999999999999999999999998


Q ss_pred             CCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       349 pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                      ++...    ....+|||+|||..+++++|+++|++||.|..+++..+     .+|||||+|.+.++|++|++.|||..+.
T Consensus        82 ~~~~~----~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661        82 PSSDS----IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             ccccc----cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccC
Confidence            76432    34568999999999999999999999999999887643     5789999999999999999999999997


Q ss_pred             C--ceEEEEeccCcc
Q 001991          424 G--KQIKLEASRPGG  436 (985)
Q Consensus       424 G--r~IkV~~A~~k~  436 (985)
                      |  .+|.|.++....
T Consensus       158 g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       158 GCTEPITVKFANNPS  172 (352)
T ss_pred             CCceeEEEEECCCCC
Confidence            7  678999986543

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=5.4e-27  Score=259.60  Aligned_cols=242  Identities=21%  Similarity=0.329  Sum_probs=193.2

Q ss_pred             CcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhh
Q 001991          146 LSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDF  224 (985)
Q Consensus       146 l~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~  224 (985)
                      .+.|||++|+. +-+++|...              |+...+|-...    |.  -|..+|.+|||+||. |.+.|+|+  
T Consensus        83 G~EVfvGkIPrD~~EdeLvpl--------------fEkiG~I~elR----LM--mD~~sG~nRGYAFVt-f~~Ke~Aq--  139 (506)
T KOG0117|consen   83 GCEVFVGKIPRDVFEDELVPL--------------FEKIGKIYELR----LM--MDPFSGDNRGYAFVT-FCTKEEAQ--  139 (506)
T ss_pred             CceEEecCCCccccchhhHHH--------------HHhccceeeEE----Ee--ecccCCCCcceEEEE-eecHHHHH--
Confidence            35799999986 666666655              74333331111    11  222489999999999 55777777  


Q ss_pred             HHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCc-EE
Q 001991          225 DLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD-IR  303 (985)
Q Consensus       225 ~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~-I~  303 (985)
                      .||+..|+.|+...+.+  +.+                        -....++|||+|||.+.++++|++.|++.++ |+
T Consensus       140 ~Aik~lnn~Eir~GK~i--gvc------------------------~Svan~RLFiG~IPK~k~keeIlee~~kVteGVv  193 (506)
T KOG0117|consen  140 EAIKELNNYEIRPGKLL--GVC------------------------VSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVV  193 (506)
T ss_pred             HHHHHhhCccccCCCEe--EEE------------------------EeeecceeEeccCCccccHHHHHHHHHhhCCCee
Confidence            79999898888733321  111                        1235689999999999999999999999986 55


Q ss_pred             EEEe------ccccceEEEEEeCCHHHHHHHHHHccC--cccccccccccccCCCCCCCccc-ccccceeeecCCCCCCH
Q 001991          304 TIYT------ACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIHYSIPKDNPSEKD-ANQGTLVVFNLDSSVST  374 (985)
Q Consensus       304 sVki------tgksrGfAFV~F~d~esA~kAi~~Lng--~~I~Gr~L~V~~a~pk~~~~~~~-~~~~tLfV~NLp~svTe  374 (985)
                      .|.+      ..++||||||+|++...|..|-+.|-.  ..+.|..+.|.|+.|+.+..+.. ..-..|||+||+.++|+
T Consensus       194 dVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTe  273 (506)
T KOG0117|consen  194 DVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTE  273 (506)
T ss_pred             EEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhH
Confidence            5543      578999999999999999999987644  46789999999999988765442 23458999999999999


Q ss_pred             HHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchhh
Q 001991          375 EELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       375 edLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      |.|+++|++||.|+.|+.++   .||||.|.+.++|.+|++.+||++|.|..|.|.+|+|...++
T Consensus       274 E~lk~~F~~~G~veRVkk~r---DYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  274 ETLKKLFNEFGKVERVKKPR---DYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             HHHHHHHHhccceEEeeccc---ceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            99999999999999998774   499999999999999999999999999999999999987665

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.94  E-value=1.8e-26  Score=271.17  Aligned_cols=267  Identities=16%  Similarity=0.189  Sum_probs=187.0

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCC--ChhhhhccCCCCeeeeecCCChhhhhh
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLP--DEDDLFSGVTDDMGHNFQANTVDDLED  223 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILp--dedDL~sG~SkGfGFV~ff~t~Edaee  223 (985)
                      -.|||+||+. ++.+.|.+.              |...  +....++...+  ...++..+..+|||||+ |.+.++|+ 
T Consensus       176 r~lyVgnLp~~~t~~~l~~~--------------F~~~--~~~~~~~~~~~~~~v~~~~~~~~kg~afVe-F~~~e~A~-  237 (509)
T TIGR01642       176 RRLYVGGIPPEFVEEAVVDF--------------FNDL--MIATGYHKAEDGKHVSSVNINKEKNFAFLE-FRTVEEAT-  237 (509)
T ss_pred             cEEEEeCCCCCCCHHHHHHH--------------HHHH--HHhcCCCCCCCCCceEEEEECCCCCEEEEE-eCCHHHHh-
Confidence            4699999998 888888877              6321  01111111111  01122244578999999 55777777 


Q ss_pred             hHHHhccCCeeEcCCcchhhhcccccccCC--CCC--C---CCCCCCc--CCCCCCCCCCCcEEEEecCCCCCCHHHHHH
Q 001991          224 FDLFSSGGGMELEGDDRLFAVQKNSDFVGG--VSN--Q---GVSAGSV--VGEHPYGEHPSRTLFVRNINSNVEDSELKA  294 (985)
Q Consensus       224 ~~ai~~~nG~eLegd~~~~vg~~ls~l~k~--~~n--~---~~~~~~~--~~e~~~~e~~srtLfVgNLP~~vTEedLre  294 (985)
                       .|+ .++|+.|.| ..+.+.+........  ...  .   .......  ...........++|||+|||..+++++|++
T Consensus       238 -~Al-~l~g~~~~g-~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~  314 (509)
T TIGR01642       238 -FAM-ALDSIIYSN-VFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKE  314 (509)
T ss_pred             -hhh-cCCCeEeeC-ceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHH
Confidence             677 589999984 444443321111000  000  0   0000000  000011234568999999999999999999


Q ss_pred             hhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCc--------------
Q 001991          295 LFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE--------------  355 (985)
Q Consensus       295 lFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~--------------  355 (985)
                      +|+.||.|..+.+     ++.++|||||+|.+.++|..|++.|+|..|.|+.|.|.++........              
T Consensus       315 ~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~  394 (509)
T TIGR01642       315 LLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLA  394 (509)
T ss_pred             HHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCcccccccccccccc
Confidence            9999999998865     577899999999999999999999999999999999998754321100              


Q ss_pred             ----------ccccccceeeecCCCC--C--------CHHHHHHHhhccCCEEEEEEcCC--------CCcEEEEEEcCH
Q 001991          356 ----------KDANQGTLVVFNLDSS--V--------STEELHQIFGIYGEIREIRDTQH--------KHNHKFIEFYDI  407 (985)
Q Consensus       356 ----------~~~~~~tLfV~NLp~s--v--------TeedLrelFs~fG~I~~Vri~~~--------skGfaFVeF~d~  407 (985)
                                ...+..+|+|.|+...  +        ..++|+++|++||.|+.|+|+..        ..|++||+|.+.
T Consensus       395 ~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~  474 (509)
T TIGR01642       395 KALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADV  474 (509)
T ss_pred             ccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCH
Confidence                      0124567899999532  1        23689999999999999998643        358999999999


Q ss_pred             HHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          408 RAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       408 edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ++|++|+..|||..|+|+.|.|.|...
T Consensus       475 e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       475 RSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            999999999999999999999999764

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.94  E-value=4.3e-26  Score=256.58  Aligned_cols=163  Identities=23%  Similarity=0.411  Sum_probs=146.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ......++|||+|||+++|+++|+++|+.||+|++|++     +++++|||||+|.+.++|++|++.|++..|.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            35567899999999999999999999999999999976     5778999999999999999999999999999999999


Q ss_pred             cccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCC
Q 001991          345 HYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNR  419 (985)
Q Consensus       345 ~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG  419 (985)
                      .++.+...    .....+|||.|||..+|+++|+++|++||+|+.|+++.+     +++||||+|.+.++|++||+.||+
T Consensus       182 ~~a~p~~~----~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng  257 (346)
T TIGR01659       182 SYARPGGE----SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN  257 (346)
T ss_pred             eccccccc----ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            99876432    234568999999999999999999999999999988754     468999999999999999999999


Q ss_pred             ceeCC--ceEEEEeccCcc
Q 001991          420 SDVAG--KQIKLEASRPGG  436 (985)
Q Consensus       420 ~~I~G--r~IkV~~A~~k~  436 (985)
                      ..+.+  ++|+|.+++...
T Consensus       258 ~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       258 VIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CccCCCceeEEEEECCccc
Confidence            98865  799999988654

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).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.94  E-value=4.5e-26  Score=264.50  Aligned_cols=257  Identities=19%  Similarity=0.294  Sum_probs=188.0

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      -.|||+||+. ++.+.|++.              |....++....+   +   .|..++.++|||||+ |.+.++|+  +
T Consensus        90 ~~l~V~nlp~~~~~~~l~~~--------------F~~~G~v~~v~i---~---~d~~~~~skg~afVe-F~~~e~A~--~  146 (457)
T TIGR01622        90 RTVFVLQLALKARERDLYEF--------------FSKVGKVRDVQC---I---KDRNSRRSKGVAYVE-FYDVESVI--K  146 (457)
T ss_pred             cEEEEeCCCCCCCHHHHHHH--------------HHhcCCeeEEEE---e---ecCCCCCcceEEEEE-ECCHHHHH--H
Confidence            3699999998 888888877              744333222111   1   122478899999999 55777777  6


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI  305 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV  305 (985)
                      |+. ++|..|.|. .+.+.....     .++......   ..........++|||+|||..+++++|+++|++||.|..|
T Consensus       147 Al~-l~g~~~~g~-~i~v~~~~~-----~~~~~~~~~---~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v  216 (457)
T TIGR01622       147 ALA-LTGQMLLGR-PIIVQSSQA-----EKNRAAKAA---THQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDV  216 (457)
T ss_pred             HHH-hCCCEECCe-eeEEeecch-----hhhhhhhcc---cccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEE
Confidence            775 788888733 332211111     001000000   0001112237999999999999999999999999999998


Q ss_pred             Ee-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCC---------------------------
Q 001991          306 YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP---------------------------  353 (985)
Q Consensus       306 ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~---------------------------  353 (985)
                      .+     +++++|||||+|.+.++|.+|++.|+|..|.|++|.|.|+......                           
T Consensus       217 ~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (457)
T TIGR01622       217 QLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQ  296 (457)
T ss_pred             EEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHH
Confidence            76     3578999999999999999999999999999999999995321000                           


Q ss_pred             --------C-------------------------------------------------c--ccccccceeeecCCCCCC-
Q 001991          354 --------S-------------------------------------------------E--KDANQGTLVVFNLDSSVS-  373 (985)
Q Consensus       354 --------~-------------------------------------------------~--~~~~~~tLfV~NLp~svT-  373 (985)
                              .                                                 .  ......+|+|.||-...+ 
T Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~  376 (457)
T TIGR01622       297 LMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATE  376 (457)
T ss_pred             HHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCccc
Confidence                    0                                                 0  012345788899854433 


Q ss_pred             ---------HHHHHHHhhccCCEEEEEEc-CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          374 ---------TEELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       374 ---------eedLrelFs~fG~I~~Vri~-~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                               .++|++.|++||.|+.|.+. +...|++||+|.+.++|.+|++.|||+.|+|+.|.|.+.....
T Consensus       377 ~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~  449 (457)
T TIGR01622       377 EEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDV  449 (457)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHH
Confidence                     37899999999999999987 6678999999999999999999999999999999999986543

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.

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=4.3e-26  Score=258.18  Aligned_cols=282  Identities=20%  Similarity=0.280  Sum_probs=231.2

Q ss_pred             ccccccCCCCCcccccccCcccccCCCCCCCCCcccccceeeEecCcCC--ChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          148 DIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLP--DEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       148 ~lFv~nL~~~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILp--dedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      .||++  +.+++..|++.              |        +.+|.+++  -..|. +  |-|||||. |.+.++++  +
T Consensus         3 sl~vg--~~v~e~~l~~~--------------f--------~~~~~v~s~rvc~d~-t--slgy~yvn-f~~~~da~--~   52 (369)
T KOG0123|consen    3 SLYVG--PDVTEAMLFDK--------------F--------SPAGPVLSIRVCRDA-T--SLGYAYVN-FQQPADAE--R   52 (369)
T ss_pred             ceecC--CcCChHHHHHH--------------h--------cccCCceeEEEeecC-C--ccceEEEe-cCCHHHHH--H
Confidence            46777  55777788888              8        88888888  23454 4  99999999 67888889  8


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI  305 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV  305 (985)
                      |+..+|...+.|.+.                 +..|+..         ....|||+||+++++.++|.++|+.||+|.+|
T Consensus        53 A~~~~n~~~~~~~~~-----------------rim~s~r---------d~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~  106 (369)
T KOG0123|consen   53 ALDTMNFDVLKGKPI-----------------RIMWSQR---------DPSLVFIKNLDESIDNKSLYDTFSEFGNILSC  106 (369)
T ss_pred             HHHHcCCcccCCcEE-----------------Eeehhcc---------CCceeeecCCCcccCcHHHHHHHHhhcCeeEE
Confidence            999999888874332                 1122211         11229999999999999999999999999999


Q ss_pred             Ee---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCcc----cccccceeeecCCCCCCHHHHH
Q 001991          306 YT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEK----DANQGTLVVFNLDSSVSTEELH  378 (985)
Q Consensus       306 ki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~----~~~~~tLfV~NLp~svTeedLr  378 (985)
                      ++   ..-++|| ||+|++.++|++|++.+||..+.+++|.|.....+..+...    .....+++|.|++.+++++.|.
T Consensus       107 kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~  185 (369)
T KOG0123|consen  107 KVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELK  185 (369)
T ss_pred             EEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHH
Confidence            87   2338999 99999999999999999999999999999888877665322    2334589999999999999999


Q ss_pred             HHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchhh--hhhhhhh------
Q 001991          379 QIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR--FMVQSEQ------  446 (985)
Q Consensus       379 elFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rr--l~qq~eq------  446 (985)
                      ..|..||.|..+.++++    .++|+||.|+++++|..|++.||+..+.++.+.|..++.+.++.  +.+..++      
T Consensus       186 ~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~  265 (369)
T KOG0123|consen  186 DLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRS  265 (369)
T ss_pred             HhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhcc
Confidence            99999999999988764    58899999999999999999999999999999999999877665  3332222      


Q ss_pred             -hccCCCcc-cCCCCCCCcccc----ccccceEEE---ecCCCCcceec
Q 001991          447 -EQDDLNLC-QIPFDDLSSGQM----VSSGVITST---CMDNGSIQVLH  486 (985)
Q Consensus       447 -~q~e~nLy-kNlp~svt~e~L----~~fG~I~S~---~~enG~srgf~  486 (985)
                       .....+|| +|++..++.+.|    ..||+|+++   .+++|.++||.
T Consensus       266 ~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~g  314 (369)
T KOG0123|consen  266 VSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFG  314 (369)
T ss_pred             ccccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCccceE
Confidence             22335888 999999999999    799999998   66789998874

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=8.9e-26  Score=235.54  Aligned_cols=246  Identities=17%  Similarity=0.278  Sum_probs=190.6

Q ss_pred             CcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhh
Q 001991          146 LSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDF  224 (985)
Q Consensus       146 l~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~  224 (985)
                      -+||.|.=|+. .+.+++...              |.|..|||....-      .|..+|.|-|||||.|. ..+|+|  
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSL--------------F~SiGeiEScKLv------RDKitGqSLGYGFVNYv-~p~DAe--   97 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSL--------------FGSIGEIESCKLV------RDKITGQSLGYGFVNYV-RPKDAE--   97 (360)
T ss_pred             cceeeeeecccccCHHHHHHH--------------hhcccceeeeeee------eccccccccccceeeec-ChHHHH--
Confidence            35666666665 555555544              7444444432211      44469999999999965 667778  


Q ss_pred             HHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE
Q 001991          225 DLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT  304 (985)
Q Consensus       225 ~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s  304 (985)
                      +|+...||..|. .+.+.|.-.                    ..........+|||.+||..+|..||..+|++||.|..
T Consensus        98 ~AintlNGLrLQ-~KTIKVSyA--------------------RPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIIt  156 (360)
T KOG0145|consen   98 KAINTLNGLRLQ-NKTIKVSYA--------------------RPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIIT  156 (360)
T ss_pred             HHHhhhcceeec-cceEEEEec--------------------cCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhh
Confidence            899999999998 443222111                    11123445689999999999999999999999999876


Q ss_pred             EE-----eccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccccCCCCCC------------------------
Q 001991          305 IY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIPKDNP------------------------  353 (985)
Q Consensus       305 Vk-----itgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~pk~~~------------------------  353 (985)
                      -+     +++.+||.+||.|...++|+.||+.|||..-.|  .+|.|+|+......                        
T Consensus       157 SRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~  236 (360)
T KOG0145|consen  157 SRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQ  236 (360)
T ss_pred             hhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccch
Confidence            54     378999999999999999999999999988766  57888877532110                        


Q ss_pred             -----------------------------------CcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---
Q 001991          354 -----------------------------------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---  395 (985)
Q Consensus       354 -----------------------------------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---  395 (985)
                                                         +.......+|||.||.++.++.-|+++|.+||.|..|+++++   
T Consensus       237 ~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~tt  316 (360)
T KOG0145|consen  237 AQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTT  316 (360)
T ss_pred             hhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCc
Confidence                                               000112358999999999999999999999999999999765   


Q ss_pred             --CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          396 --KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       396 --skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                        .+|||||.+.+.++|..||..|||..+++|.|.|.|...|
T Consensus       317 nkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  317 NKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             ccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence              6899999999999999999999999999999999997654

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

Probab=99.92  E-value=6e-25  Score=231.03  Aligned_cols=161  Identities=20%  Similarity=0.438  Sum_probs=148.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .-.|||+.|.+.++-++|++.|.+||+|.++++     ++++|||+||.|.+.++|++||..|||+.|.+|.|+..|+..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            567999999999999999999999999999875     799999999999999999999999999999999999999988


Q ss_pred             CCCCCc------------ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh
Q 001991          350 KDNPSE------------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL  417 (985)
Q Consensus       350 k~~~~~------------~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L  417 (985)
                      |.....            .....++|||+||+..+++++|++.|++||.|.+||+.++ +||+||.|++.|+|.+||..+
T Consensus       142 Kp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-qGYaFVrF~tkEaAahAIv~m  220 (321)
T KOG0148|consen  142 KPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-QGYAFVRFETKEAAAHAIVQM  220 (321)
T ss_pred             CccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-cceEEEEecchhhHHHHHHHh
Confidence            764321            1235679999999999999999999999999999999986 899999999999999999999


Q ss_pred             CCceeCCceEEEEeccCcc
Q 001991          418 NRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       418 NG~~I~Gr~IkV~~A~~k~  436 (985)
                      |+.+|+|..+++.|.+...
T Consensus       221 Nntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  221 NNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             cCceeCceEEEEeccccCC
Confidence            9999999999999987644

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.92  E-value=2.5e-24  Score=254.67  Aligned_cols=165  Identities=19%  Similarity=0.374  Sum_probs=145.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|.+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            345689999999999999999999999999999976     678999999999999999999999999999999999986


Q ss_pred             cCCCCCCC-------cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHH
Q 001991          347 SIPKDNPS-------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETAL  414 (985)
Q Consensus       347 a~pk~~~~-------~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI  414 (985)
                      ........       ......++|||+||+.++++++|+++|+.||.|++|++..+     ++|||||+|.+.++|.+|+
T Consensus       184 p~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI  263 (612)
T TIGR01645       184 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI  263 (612)
T ss_pred             cccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHH
Confidence            54322110       11223468999999999999999999999999999998753     6899999999999999999


Q ss_pred             HHhCCceeCCceEEEEeccCcc
Q 001991          415 RTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       415 ~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      +.||+..|+|+.|+|.++.++.
T Consensus       264 ~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       264 ASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             HHhCCCeeCCeEEEEEecCCCc
Confidence            9999999999999999988643

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.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.91  E-value=2.1e-23  Score=246.93  Aligned_cols=169  Identities=12%  Similarity=0.266  Sum_probs=127.7

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCC--hhhhhccCCCCeeeeecCCChhhh
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPD--EDDLFSGVTDDMGHNFQANTVDDL  221 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpd--edDL~sG~SkGfGFV~ff~t~Eda  221 (985)
                      .+..|||+||++ ++.+.|.+.              |        ..+|.|...  ..|..++.++|||||+ |++.+++
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~l--------------F--------~~fG~I~sV~I~~D~~TgkskGfAFVe-F~s~e~A  162 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRA--------------F--------DPFGPIKSINMSWDPATGKHKGFAFVE-YEVPEAA  162 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHH--------------H--------HccCCEEEEEEeecCCCCCcCCeEEEE-eCcHHHH
Confidence            456899999998 888888888              8        445544441  1233478899999999 6688888


Q ss_pred             hhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCc
Q 001991          222 EDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD  301 (985)
Q Consensus       222 ee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~  301 (985)
                      +  .|+..++|..++ ++.+.+++...     ...   . ..............++|||+||++++++++|+++|+.||+
T Consensus       163 ~--~Ai~~lnG~~i~-GR~IkV~rp~~-----~p~---a-~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~  230 (612)
T TIGR01645       163 Q--LALEQMNGQMLG-GRNIKVGRPSN-----MPQ---A-QPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGE  230 (612)
T ss_pred             H--HHHHhcCCeEEe-cceeeeccccc-----ccc---c-ccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCC
Confidence            8  899999999998 44444432111     000   0 0000011112235689999999999999999999999999


Q ss_pred             EEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          302 IRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       302 I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      |.++++     ++++||||||+|.+.++|.+|++.||+..|.|+.|+|.++.
T Consensus       231 I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       231 IVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             eeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            999976     46789999999999999999999999999999999986654

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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.91  E-value=2.8e-23  Score=245.50  Aligned_cols=191  Identities=21%  Similarity=0.285  Sum_probs=160.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccc-cccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~-Gr~L~V~~a~  348 (985)
                      ..++|||+|||.+++|++|+++|++||.|..|++    +++++|||||+|.+.++|++||+.||+..|. |+.|.|..+.
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            4589999999999999999999999999999976    5789999999999999999999999999885 7877776553


Q ss_pred             CCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCC-EEEEEEc------CCCCcEEEEEEcCHHHHHHHHHHhCC--
Q 001991          349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDT------QHKHNHKFIEFYDIRAAETALRTLNR--  419 (985)
Q Consensus       349 pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~-I~~Vri~------~~skGfaFVeF~d~edA~kAI~~LNG--  419 (985)
                                ..++|||+|||.++++++|+++|++++. ++++.+.      ..+++||||+|.+.++|.+|++.|+.  
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                      3568999999999999999999999864 4444432      13589999999999999999998864  


Q ss_pred             ceeCCceEEEEeccCcchhhhhhhhhhhccCCCcc-cCCCCCCCcccc----ccc--cceEEEecC
Q 001991          420 SDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSS--GVITSTCMD  478 (985)
Q Consensus       420 ~~I~Gr~IkV~~A~~k~~Rrl~qq~eq~q~e~nLy-kNlp~svt~e~L----~~f--G~I~S~~~e  478 (985)
                      ..+.|+.|.|.|+.++....    .+.....+.|| +||+.++++++|    +.|  |+|..+...
T Consensus       207 i~l~Gr~I~VdwA~p~~~~d----~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~  268 (578)
T TIGR01648       207 IQLWGHVIAVDWAEPEEEVD----EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI  268 (578)
T ss_pred             eEecCceEEEEeeccccccc----ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee
Confidence            36789999999998765321    12223446789 999999999999    788  999998543

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.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=6.5e-23  Score=231.27  Aligned_cols=269  Identities=19%  Similarity=0.281  Sum_probs=190.2

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      ..|||.+|+. ++++.|.+.              |.....+...+.+    +.  --++.++|||||+ |.-+||++  .
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~--------------FS~vGPik~~~vV----t~--~gs~~~RGfgfVt-Fam~ED~q--r   62 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEF--------------FSYVGPIKHAVVV----TN--KGSSEKRGFGFVT-FAMEEDVQ--R   62 (678)
T ss_pred             ceEEEecCCCccchhHHHHh--------------hhcccCcceeEEe----cC--CCcccccCcccee-eehHhHHH--H
Confidence            6799999998 666556555              7333333222222    11  1145599999999 55778877  6


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCC----CCC--CCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhccc
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGG----VSN--QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQF  299 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~----~~n--~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~f  299 (985)
                      ++....+..|+| ..+.+..........    ..+  ......+..........+.-.|.|+|||+.+.+.+|+.+|+.|
T Consensus        63 A~~e~~~~kf~G-r~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~  141 (678)
T KOG0127|consen   63 ALAETEQSKFEG-RILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNF  141 (678)
T ss_pred             HHHHhhcCcccc-eecccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhc
Confidence            776656655552 223332221111000    000  0000000000001123346789999999999999999999999


Q ss_pred             CcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCC----------------------
Q 001991          300 GDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP----------------------  353 (985)
Q Consensus       300 G~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~----------------------  353 (985)
                      |.|..|.+    .++-.|||||.|.+..+|.+|++.+|+..|.||+|-|.|+.++...                      
T Consensus       142 G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e  221 (678)
T KOG0127|consen  142 GKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKE  221 (678)
T ss_pred             ceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcc
Confidence            99999987    4556699999999999999999999999999999999998765310                      


Q ss_pred             --------------------Cc-cc-------------------------------------------ccccceeeecCC
Q 001991          354 --------------------SE-KD-------------------------------------------ANQGTLVVFNLD  369 (985)
Q Consensus       354 --------------------~~-~~-------------------------------------------~~~~tLfV~NLp  369 (985)
                                          .+ .+                                           ....+|||+|||
T Consensus       222 ~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~  301 (678)
T KOG0127|consen  222 ADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLP  301 (678)
T ss_pred             cccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCC
Confidence                                00 00                                           012589999999


Q ss_pred             CCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHh-----CC-ceeCCceEEEEeccCcchh
Q 001991          370 SSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTL-----NR-SDVAGKQIKLEASRPGGAR  438 (985)
Q Consensus       370 ~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~L-----NG-~~I~Gr~IkV~~A~~k~~R  438 (985)
                      +++|+++|+++|++||+|.++.++.     .++|.|||.|.+..+|++||...     .| ..|.||.|+|..+..+.+.
T Consensus       302 fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA  381 (678)
T KOG0127|consen  302 FDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEA  381 (678)
T ss_pred             ccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHH
Confidence            9999999999999999999987753     47899999999999999999976     23 5789999999999987755


Q ss_pred             h
Q 001991          439 R  439 (985)
Q Consensus       439 r  439 (985)
                      .
T Consensus       382 ~  382 (678)
T KOG0127|consen  382 A  382 (678)
T ss_pred             H
Confidence            4

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.89  E-value=8.4e-23  Score=237.24  Aligned_cols=163  Identities=26%  Similarity=0.455  Sum_probs=144.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .+.+.++|||+|||..+++++|+++|++||+|..|++     +++++|||||+|.+.++|++||. |+|+.+.|++|.|.
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            4556799999999999999999999999999999976     57789999999999999999995 99999999999998


Q ss_pred             ccCCCCCCCc--------ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHH
Q 001991          346 YSIPKDNPSE--------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAET  412 (985)
Q Consensus       346 ~a~pk~~~~~--------~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~k  412 (985)
                      ++........        ......+|||+|||..+++++|+++|++||.|..|.+..     ..+|||||+|.+.++|.+
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            8654332211        112357899999999999999999999999999998874     357899999999999999


Q ss_pred             HHHHhCCceeCCceEEEEeccC
Q 001991          413 ALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       413 AI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      |++.|||..|.|++|+|.|+..
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.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=3.4e-22  Score=221.77  Aligned_cols=189  Identities=21%  Similarity=0.308  Sum_probs=164.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccc-cccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHY  346 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~-Gr~L~V~~  346 (985)
                      ...+-|||+.||.++.|++|.-+|++.|+|..+++     ++.+||||||.|.+.++|++|++.||+.+|. |+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            45689999999999999999999999999999975     7899999999999999999999999999985 88898887


Q ss_pred             cCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCC-EEEEEEcC------CCCcEEEEEEcCHHHHHHHHHHhCC
Q 001991          347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDTQ------HKHNHKFIEFYDIRAAETALRTLNR  419 (985)
Q Consensus       347 a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~-I~~Vri~~------~skGfaFVeF~d~edA~kAI~~LNG  419 (985)
                      +.          ..+.|||+|||...++++|++.|.+.++ |..|.+.+      +++|||||+|++...|..|-+.|-.
T Consensus       161 Sv----------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~  230 (506)
T KOG0117|consen  161 SV----------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMP  230 (506)
T ss_pred             ee----------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccC
Confidence            64          4678999999999999999999999885 66776643      3789999999999999999987743


Q ss_pred             --ceeCCceEEEEeccCcchhhhhhhhhhhccCCCcc-cCCCCCCCcccc----ccccceEEE
Q 001991          420 --SDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITST  475 (985)
Q Consensus       420 --~~I~Gr~IkV~~A~~k~~Rrl~qq~eq~q~e~nLy-kNlp~svt~e~L----~~fG~I~S~  475 (985)
                        ..+-|..|.|+||.+.++-.    -+-...-+-|| +||+.++|+|.|    ..||.|..+
T Consensus       231 g~~klwgn~~tVdWAep~~e~d----ed~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRV  289 (506)
T KOG0117|consen  231 GKIKLWGNAITVDWAEPEEEPD----EDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERV  289 (506)
T ss_pred             CceeecCCcceeeccCcccCCC----hhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEe
Confidence              36789999999999877443    12334457899 999999999999    778888888

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.88  E-value=4.7e-22  Score=233.89  Aligned_cols=164  Identities=15%  Similarity=0.288  Sum_probs=137.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhccc------------CcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQF------------GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL  337 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~f------------G~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I  337 (985)
                      ......++|||+|||+.+|+++|+++|.+|            +.|..+.+ .+.+|||||+|.+.++|..|| +|+|..|
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-~~~kg~afVeF~~~e~A~~Al-~l~g~~~  247 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-NKEKNFAFLEFRTVEEATFAM-ALDSIIY  247 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-CCCCCEEEEEeCCHHHHhhhh-cCCCeEe
Confidence            455677999999999999999999999975            34555555 678999999999999999999 5999999


Q ss_pred             ccccccccccCCCCCCC-------------------------cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEE
Q 001991          338 RRRKLDIHYSIPKDNPS-------------------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD  392 (985)
Q Consensus       338 ~Gr~L~V~~a~pk~~~~-------------------------~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri  392 (985)
                      .|+.|.|.........+                         .......+|||+|||..+++++|+++|+.||.|..+.+
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            99999996432111000                         00122468999999999999999999999999999887


Q ss_pred             cCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          393 TQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       393 ~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      +.+     ++|||||+|.+.++|.+|++.|||..|.|++|.|.++...
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            643     6899999999999999999999999999999999998643

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.87  E-value=1.3e-21  Score=204.69  Aligned_cols=163  Identities=23%  Similarity=0.413  Sum_probs=146.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      +...++|.|.-||.++|++||+.+|...|+|++|++     ++.+.||+||.|-++++|++|+..|||..+..+.|+|.|
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            445688999999999999999999999999999974     789999999999999999999999999999999999999


Q ss_pred             cCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCce
Q 001991          347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSD  421 (985)
Q Consensus       347 a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~  421 (985)
                      +.|..+.    ....+|||.+||..+|..||.++|++||.|..-||.     +-++|.|||.|+..++|++||+.|||..
T Consensus       118 ARPSs~~----Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  118 ARPSSDS----IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             ccCChhh----hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            9886543    556799999999999999999999999998776654     3479999999999999999999999998


Q ss_pred             eCC--ceEEEEeccCcchh
Q 001991          422 VAG--KQIKLEASRPGGAR  438 (985)
Q Consensus       422 I~G--r~IkV~~A~~k~~R  438 (985)
                      -.|  .+|.|+|+.....+
T Consensus       194 P~g~tepItVKFannPsq~  212 (360)
T KOG0145|consen  194 PSGCTEPITVKFANNPSQK  212 (360)
T ss_pred             CCCCCCCeEEEecCCcccc
Confidence            765  68999999865544

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=7.1e-22  Score=218.33  Aligned_cols=165  Identities=21%  Similarity=0.416  Sum_probs=144.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCc-cccc--cccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNK-PLRR--RKLD  343 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~-~I~G--r~L~  343 (985)
                      +...-+|||+-||..++|+||+++|++||.|.+|.+     ++.++|||||.|++.++|.+|+.+|+++ .|.|  .+|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            356689999999999999999999999999999854     7889999999999999999999999885 4666  5777


Q ss_pred             ccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCC
Q 001991          344 IHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNR  419 (985)
Q Consensus       344 V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG  419 (985)
                      |+|+....++   -...++|||+-|+..++|.+++++|++||.|++|+|.++    +||||||+|.+.|.|..||++|||
T Consensus       111 vk~Ad~E~er---~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng  187 (510)
T KOG0144|consen  111 VKYADGERER---IVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNG  187 (510)
T ss_pred             ecccchhhhc---cccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhcc
Confidence            8887654333   245779999999999999999999999999999998764    799999999999999999999999


Q ss_pred             c-eeCC--ceEEEEeccCcchhh
Q 001991          420 S-DVAG--KQIKLEASRPGGARR  439 (985)
Q Consensus       420 ~-~I~G--r~IkV~~A~~k~~Rr  439 (985)
                      . .+.|  .+|.|.||.++.+|.
T Consensus       188 ~~tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  188 TQTMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             ceeeccCCCceEEEecccCCCch
Confidence            7 5655  699999998877654

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=1.1e-21  Score=216.76  Aligned_cols=274  Identities=17%  Similarity=0.280  Sum_probs=198.7

Q ss_pred             ccccCCCCeeeecccCCCCCcccCCCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCC--C
Q 001991          121 GINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLP--D  197 (985)
Q Consensus       121 ~~~~~~g~~i~im~s~rd~sl~sSsl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILp--d  197 (985)
                      .+....|..++-+.++..+.--..+.-+|||+-++. .++++|...              |        ..+|++..  -
T Consensus         9 ~~~~~~gs~~~~~~~~~~~d~~d~~~vKlfVgqIprt~sE~dlr~l--------------F--------e~yg~V~einl   66 (510)
T KOG0144|consen    9 PPSPCGGSSLADNGSLDHTDNPDGSAVKLFVGQIPRTASEKDLREL--------------F--------EKYGNVYEINL   66 (510)
T ss_pred             CCCCCCCcchhhcCCCCCCCCCCchhhhheeccCCccccHHHHHHH--------------H--------HHhCceeEEEe
Confidence            345566777777777666665556777899999887 555555555              6        33343333  0


Q ss_pred             hhhhhccCCCCeeeeecCCChhhhhhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcE
Q 001991          198 EDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRT  277 (985)
Q Consensus       198 edDL~sG~SkGfGFV~ff~t~Edaee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srt  277 (985)
                      -.|-.++.++||.||.|...+|+.+.+.|+.+  -..|.|...    .+           ....+  ++|.. .....++
T Consensus        67 ~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn--~ktlpG~~~----pv-----------qvk~A--d~E~e-r~~~e~K  126 (510)
T KOG0144|consen   67 IKDKSTGQSKGCCFVKYYTRKEADEAINALHN--QKTLPGMHH----PV-----------QVKYA--DGERE-RIVEERK  126 (510)
T ss_pred             ecccccCcccceEEEEeccHHHHHHHHHHhhc--ccccCCCCc----ce-----------eeccc--chhhh-ccccchh
Confidence            12335788999999998866666554444432  222321111    00           01101  11111 1134689


Q ss_pred             EEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCc-cccc--ccccccccCCC
Q 001991          278 LFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNK-PLRR--RKLDIHYSIPK  350 (985)
Q Consensus       278 LfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~-~I~G--r~L~V~~a~pk  350 (985)
                      |||+-|+..+||.|++++|++||.|++|++    .+.+||||||.|.+.|.|..||+.|||. .+.|  .+|.|+|+.++
T Consensus       127 LFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtq  206 (510)
T KOG0144|consen  127 LFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQ  206 (510)
T ss_pred             hhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccC
Confidence            999999999999999999999999999986    5789999999999999999999999995 4555  57888777654


Q ss_pred             CCCC----------------------------------------------------------------------------
Q 001991          351 DNPS----------------------------------------------------------------------------  354 (985)
Q Consensus       351 ~~~~----------------------------------------------------------------------------  354 (985)
                      +++.                                                                            
T Consensus       207 kdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~~~~ta  286 (510)
T KOG0144|consen  207 KDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALAAAATA  286 (510)
T ss_pred             CCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhhhhccc
Confidence            3210                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q 001991          355 --------------------------------------------------------------------------------  354 (985)
Q Consensus       355 --------------------------------------------------------------------------------  354 (985)
                                                                                                      
T Consensus       287 ~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~aa~~~~  366 (510)
T KOG0144|consen  287 AQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVAASLAN  366 (510)
T ss_pred             ccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcccccccc
Confidence                                                                                            


Q ss_pred             ----------------------------------------------------cccccccceeeecCCCCCCHHHHHHHhh
Q 001991          355 ----------------------------------------------------EKDANQGTLVVFNLDSSVSTEELHQIFG  382 (985)
Q Consensus       355 ----------------------------------------------------~~~~~~~tLfV~NLp~svTeedLrelFs  382 (985)
                                                                          .+.....+|||.+||.+.-+.+|-..|.
T Consensus       367 lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~l~~~f~  446 (510)
T KOG0144|consen  367 LQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQDLIATFQ  446 (510)
T ss_pred             cccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHHHHHHhc
Confidence                                                                0000124799999999999999999999


Q ss_pred             ccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          383 IYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       383 ~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      .||.|++.++.-+     ++.|+||.|++..+|..||..|||..|+.++++|...+.+.
T Consensus       447 pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~  505 (510)
T KOG0144|consen  447 PFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRN  505 (510)
T ss_pred             cccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccC
Confidence            9999999776433     68899999999999999999999999999999999987654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=9e-21  Score=214.11  Aligned_cols=161  Identities=20%  Similarity=0.365  Sum_probs=144.6

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      .||||++||+.++.++|.++|+.+|+|..+.+     +..+|||+||+|.-.+++++|++.+++..+.|+.|.|.++.++
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            79999999999999999999999999999875     4568999999999999999999999999999999999998765


Q ss_pred             CCCCc--------------------c--cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEE
Q 001991          351 DNPSE--------------------K--DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEF  404 (985)
Q Consensus       351 ~~~~~--------------------~--~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF  404 (985)
                      ....+                    .  +.+...|.|+|||+.+.+.+|+.+|+.||.|.+|.|+..    -.|||||+|
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            43210                    0  123568999999999999999999999999999998754    358999999


Q ss_pred             cCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          405 YDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       405 ~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      .+..+|.+|++.+|+.+|.||+|-|.||.++.
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

>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=6.6e-21  Score=202.40  Aligned_cols=148  Identities=24%  Similarity=0.410  Sum_probs=138.6

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE  355 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~  355 (985)
                      -+|||+|||..+++.+|+.+|++||+|.+|++   -|.||||+.++...|+.||..|++..|+|..|.|+-++.|.    
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            46999999999999999999999999999998   67799999999999999999999999999999999887653    


Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                        ....+|+|+||.+.++.++|+..|++||.|.+++|.   ++|+||.|+-.++|..|++.|++++|.|++++|+.+..+
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              346789999999999999999999999999999987   569999999999999999999999999999999998754

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.82  E-value=3.6e-20  Score=186.21  Aligned_cols=163  Identities=21%  Similarity=0.313  Sum_probs=142.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ....+|||+||+..++++.|.++|-+.|+|..+++     +...+|||||+|.++|+|+-|++-||...+.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            35689999999999999999999999999999975     6779999999999999999999999999999999999887


Q ss_pred             CCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEE-EEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCce
Q 001991          348 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDT-----QHKHNHKFIEFYDIRAAETALRTLNRSD  421 (985)
Q Consensus       348 ~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~V-ri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~  421 (985)
                      ...   ...-....+|||+||++.+++..|.+.|+.||.+... +++     +.+++||||.|.+.|.+.+|+..|||+.
T Consensus        87 s~~---~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~  163 (203)
T KOG0131|consen   87 SAH---QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQY  163 (203)
T ss_pred             ccc---cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccch
Confidence            621   1222334699999999999999999999999998662 322     3578899999999999999999999999


Q ss_pred             eCCceEEEEeccCcchh
Q 001991          422 VAGKQIKLEASRPGGAR  438 (985)
Q Consensus       422 I~Gr~IkV~~A~~k~~R  438 (985)
                      +..++|.|.++..++.+
T Consensus       164 l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  164 LCNRPITVSYAFKKDTK  180 (203)
T ss_pred             hcCCceEEEEEEecCCC
Confidence            99999999999866533

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

Probab=99.77  E-value=1.1e-18  Score=184.23  Aligned_cols=176  Identities=19%  Similarity=0.313  Sum_probs=142.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      ....|||||+||..+|||+-|..||.+.|.|..+++-          |+                    .|.|.++....
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i----------~~--------------------e~~v~wa~~p~   52 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVI----------FD--------------------ELKVNWATAPG   52 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceee----------hh--------------------hhccccccCcc
Confidence            3467999999999999999999999999999999871          11                    45666665544


Q ss_pred             CCCccccc-ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCc
Q 001991          352 NPSEKDAN-QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGK  425 (985)
Q Consensus       352 ~~~~~~~~-~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr  425 (985)
                      ........ .--+||+.|...++.++||+.|.+||+|.+++|+++     +||||||.|.+.++|+.||..|||..|++|
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            43333333 347999999999999999999999999999998765     799999999999999999999999999999


Q ss_pred             eEEEEeccCcchhh-hhhh-hhh-----hccCCCcc-cCCCCCCCcccc----ccccceEEEec
Q 001991          426 QIKLEASRPGGARR-FMVQ-SEQ-----EQDDLNLC-QIPFDDLSSGQM----VSSGVITSTCM  477 (985)
Q Consensus       426 ~IkV~~A~~k~~Rr-l~qq-~eq-----~q~e~nLy-kNlp~svt~e~L----~~fG~I~S~~~  477 (985)
                      .|+-.||.+|..+. ..+. .++     ..+...+| .|++.-++++.|    ++||.|..++.
T Consensus       133 ~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRv  196 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRV  196 (321)
T ss_pred             eeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEE
Confidence            99999998776443 1111 222     22345778 999998888888    89999998854

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=1e-18  Score=197.10  Aligned_cols=161  Identities=17%  Similarity=0.230  Sum_probs=125.6

Q ss_pred             CCCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCC--hhhhhccCCCCeeeeecCCChhh
Q 001991          144 SSLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPD--EDDLFSGVTDDMGHNFQANTVDD  220 (985)
Q Consensus       144 Ssl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpd--edDL~sG~SkGfGFV~ff~t~Ed  220 (985)
                      +.-.+|||++|++ ++.++|++.              |+.        +|.|...  ..|..++.++|||||+ |.+.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~l--------------F~~--------~G~V~~v~i~~d~~tg~srGyaFVe-F~~~e~  161 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYAL--------------FRT--------IGPINTCRIMRDYKTGYSFGYAFVD-FGSEAD  161 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHH--------------HHh--------cCCEEEEEEEecCCCCccCcEEEEE-EccHHH
Confidence            4567899999998 888889888              843        4444331  1234578899999999 568888


Q ss_pred             hhhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccC
Q 001991          221 LEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG  300 (985)
Q Consensus       221 aee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG  300 (985)
                      |+  +|+..++|.+|. ++.+.+.....                .    ......++|||+|||.++|+++|+++|++||
T Consensus       162 A~--~Ai~~LnG~~l~-gr~i~V~~a~p----------------~----~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG  218 (346)
T TIGR01659       162 SQ--RAIKNLNGITVR-NKRLKVSYARP----------------G----GESIKDTNLYVTNLPRTITDDQLDTIFGKYG  218 (346)
T ss_pred             HH--HHHHHcCCCccC-Cceeeeecccc----------------c----ccccccceeEEeCCCCcccHHHHHHHHHhcC
Confidence            88  899999999997 44432221110                0    1122457899999999999999999999999


Q ss_pred             cEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccccCCC
Q 001991          301 DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIPK  350 (985)
Q Consensus       301 ~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~pk  350 (985)
                      +|..|++     +++++|||||+|.+.++|++||+.||+..+.+  ++|.|.++...
T Consensus       219 ~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       219 QIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             CEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            9998865     56788999999999999999999999998876  68888887654

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).

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.75  E-value=2.5e-18  Score=186.53  Aligned_cols=161  Identities=19%  Similarity=0.397  Sum_probs=141.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      --++|||+.|...+.|+.|+..|..||+|++|.+     ++++||||||+|+-+|.|+.|++.|||..++||.|+|....
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            3588999999999999999999999999999975     79999999999999999999999999999999999997432


Q ss_pred             CCCCC-------CcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHH
Q 001991          349 PKDNP-------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRT  416 (985)
Q Consensus       349 pk~~~-------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~  416 (985)
                      .-...       .+.......|||..+.++++++||+.+|+.||+|.+|.+-+.     .+|||||+|.+..+-..||..
T Consensus       192 NmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             CCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            11111       112234568999999999999999999999999999998543     589999999999999999999


Q ss_pred             hCCceeCCceEEEEeccC
Q 001991          417 LNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       417 LNG~~I~Gr~IkV~~A~~  434 (985)
                      ||-..++|..|+|..+..
T Consensus       272 MNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  272 MNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             cchhhcccceEecccccC
Confidence            999999999999987653

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.71  E-value=1.4e-17  Score=175.17  Aligned_cols=166  Identities=21%  Similarity=0.402  Sum_probs=138.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcc-ccc--ccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKP-LRR--RKLDIHY  346 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~-I~G--r~L~V~~  346 (985)
                      ..|+|||+-|...-.|||++.+|..||+|.+|.+    .+.+||+|||.|.+..+|+.||..|+|.. +.|  ..|.|+|
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            6799999999999999999999999999999976    67899999999999999999999999843 333  2344433


Q ss_pred             cCCCCCC-------------------------------------------------------------------------
Q 001991          347 SIPKDNP-------------------------------------------------------------------------  353 (985)
Q Consensus       347 a~pk~~~-------------------------------------------------------------------------  353 (985)
                      +...+++                                                                         
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            3211100                                                                         


Q ss_pred             --------------------------------------------------------------------------------
Q 001991          354 --------------------------------------------------------------------------------  353 (985)
Q Consensus       354 --------------------------------------------------------------------------------  353 (985)
                                                                                                      
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             ---------------------CcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCH
Q 001991          354 ---------------------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDI  407 (985)
Q Consensus       354 ---------------------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~  407 (985)
                                           .......++|||..||.+..+.||.++|-+||.|.+.++.-     .+|+|+||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                                 00112457999999999999999999999999999987753     4789999999999


Q ss_pred             HHHHHHHHHhCCceeCCceEEEEeccCcchhh
Q 001991          408 RAAETALRTLNRSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       408 edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      .+|+.||.+|||..|+-|+|+|.+.+||++.|
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            99999999999999999999999999987543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.71  E-value=2.2e-17  Score=192.34  Aligned_cols=162  Identities=24%  Similarity=0.433  Sum_probs=141.6

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEecc--------ccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC--------KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitg--------ksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ++|||+||+.+.|.++|..+|...|.|.++.|..        .+.|||||+|.+.++|+.|++.|+|..|+|+.|.|+++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            3499999999999999999999999999997621        13499999999999999999999999999999999998


Q ss_pred             CCCCCC-----CcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHh
Q 001991          348 IPKDNP-----SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTL  417 (985)
Q Consensus       348 ~pk~~~-----~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~L  417 (985)
                      ..+...     .......+.|.|+|||...+..+++++|..||.|.+|+++..     .+|||||+|-++++|.+|+.+|
T Consensus       596 ~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al  675 (725)
T KOG0110|consen  596 ENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDAL  675 (725)
T ss_pred             cCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhh
Confidence            722211     011122468999999999999999999999999999999764     4789999999999999999999


Q ss_pred             CCceeCCceEEEEeccCcch
Q 001991          418 NRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       418 NG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ..+.+.||+|.++|+.....
T Consensus       676 ~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  676 GSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             cccceechhhheehhccchH
Confidence            99999999999999987664

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.71  E-value=2e-17  Score=188.71  Aligned_cols=234  Identities=19%  Similarity=0.250  Sum_probs=160.3

Q ss_pred             eEecCcCC--ChhhhhccCCCCeeeeecCCChhhhhhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCC
Q 001991          189 QTIGNLLP--DEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVG  266 (985)
Q Consensus       189 ~~iGnILp--dedDL~sG~SkGfGFV~ff~t~Edaee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~  266 (985)
                      +.+|.+-+  ---|-.++.+||.+||+|. +.+.+-  -+| ...|..|-|-+ +.+     .++...+|...+.+. .-
T Consensus       201 s~~gkVrdVriI~Dr~s~rskgi~Yvef~-D~~sVp--~ai-aLsGqrllg~p-v~v-----q~sEaeknr~a~~s~-a~  269 (549)
T KOG0147|consen  201 SIVGKVRDVRIIGDRNSRRSKGIAYVEFC-DEQSVP--LAI-ALSGQRLLGVP-VIV-----QLSEAEKNRAANASP-AL  269 (549)
T ss_pred             HhhcCcceeEeeccccchhhcceeEEEEe-cccchh--hHh-hhcCCcccCce-eEe-----cccHHHHHHHHhccc-cc
Confidence            55555444  1123357889999999966 444444  234 33444333222 111     111111221111000 00


Q ss_pred             CCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccc
Q 001991          267 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  341 (985)
Q Consensus       267 e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~  341 (985)
                      +...-..|.+.|||+||-.++++++|+.+|+.||.|..|.+     ++.++||+||+|.+.++|++|++.|||.+|.|+.
T Consensus       270 ~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~  349 (549)
T KOG0147|consen  270 QGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRL  349 (549)
T ss_pred             cccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCce
Confidence            10112234445999999999999999999999999999864     6889999999999999999999999999999999


Q ss_pred             ccccccCCCCCC--------------------------------------------------------------------
Q 001991          342 LDIHYSIPKDNP--------------------------------------------------------------------  353 (985)
Q Consensus       342 L~V~~a~pk~~~--------------------------------------------------------------------  353 (985)
                      |+|.....+...                                                                    
T Consensus       350 ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~  429 (549)
T KOG0147|consen  350 IKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRS  429 (549)
T ss_pred             EEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccc
Confidence            988432111000                                                                    


Q ss_pred             Cccc-------ccccceeeecC--CCCCC--------HHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHH
Q 001991          354 SEKD-------ANQGTLVVFNL--DSSVS--------TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT  416 (985)
Q Consensus       354 ~~~~-------~~~~tLfV~NL--p~svT--------eedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~  416 (985)
                      ..+.       ....++.++|+  |...|        .+++.+.+.+||+|..|.+.+++-|+.||.|.+.++|..|+++
T Consensus       430 ~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~a  509 (549)
T KOG0147|consen  430 VDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKA  509 (549)
T ss_pred             cCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHH
Confidence            0000       22334556665  22222        3788899999999999999999889999999999999999999


Q ss_pred             hCCceeCCceEEEEecc
Q 001991          417 LNRSDVAGKQIKLEASR  433 (985)
Q Consensus       417 LNG~~I~Gr~IkV~~A~  433 (985)
                      |||.+|.||.|++.|-.
T Consensus       510 lhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  510 LHGRWFAGRMITAKYLP  526 (549)
T ss_pred             HhhhhhccceeEEEEee
Confidence            99999999999999854

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.70  E-value=1.7e-16  Score=165.30  Aligned_cols=163  Identities=26%  Similarity=0.454  Sum_probs=144.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHH----hhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKA----LFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLre----lFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ...+..||||.||+..+..++|++    +|++||.|..|..  +.+.||.|||.|.+.+.|-.|++.|+|..+.|+.++|
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            344666999999999999999998    9999999999976  6889999999999999999999999999999999999


Q ss_pred             cccCCCCCCCcc----------------------------------------------cccccceeeecCCCCCCHHHHH
Q 001991          345 HYSIPKDNPSEK----------------------------------------------DANQGTLVVFNLDSSVSTEELH  378 (985)
Q Consensus       345 ~~a~pk~~~~~~----------------------------------------------~~~~~tLfV~NLp~svTeedLr  378 (985)
                      +||..+.+...+                                              ..+...|++.|||..++.+.|.
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~  164 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLS  164 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHH
Confidence            999765431100                                              2234589999999999999999


Q ss_pred             HHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeC-CceEEEEecc
Q 001991          379 QIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA-GKQIKLEASR  433 (985)
Q Consensus       379 elFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~-Gr~IkV~~A~  433 (985)
                      .+|.+|...++|+++...++.|||+|.+...|..|...+.+..|. ...++|.+++
T Consensus       165 ~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  165 DLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999999999988999999999999999999999999987 8888888775

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=3e-16  Score=170.59  Aligned_cols=254  Identities=14%  Similarity=0.279  Sum_probs=184.4

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCC--ChhhhhccCCCCeeeeecCCChhhh
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLP--DEDDLFSGVTDDMGHNFQANTVDDL  221 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILp--dedDL~sG~SkGfGFV~ff~t~Eda  221 (985)
                      -+..|+|+.+.. +-++.+...              |        ..||-|-+  --=|..++..|||+||+ ++-.|++
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~A--------------F--------~PFGPIKSInMSWDp~T~kHKgFAFVE-YEvPEaA  168 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRA--------------F--------DPFGPIKSINMSWDPATGKHKGFAFVE-YEVPEAA  168 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhh--------------c--------cCCCCcceeecccccccccccceEEEE-EeCcHHH
Confidence            345677877776 555455544              4        34454444  11344689999999999 5688888


Q ss_pred             hhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCc
Q 001991          222 EDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD  301 (985)
Q Consensus       222 ee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~  301 (985)
                      .  -+.+.+||..|. .+.+.+++-..        .... -.+-.+...+.+...+|||..+-++.+|+||+..|+.||+
T Consensus       169 q--LAlEqMNg~mlG-GRNiKVgrPsN--------mpQA-QpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~  236 (544)
T KOG0124|consen  169 Q--LALEQMNGQMLG-GRNIKVGRPSN--------MPQA-QPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGE  236 (544)
T ss_pred             H--HHHHHhcccccc-CccccccCCCC--------Cccc-chHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcc
Confidence            8  899999999996 66665554211        0000 0000011123456789999999999999999999999999


Q ss_pred             EEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC------------------------
Q 001991          302 IRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN------------------------  352 (985)
Q Consensus       302 I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~------------------------  352 (985)
                      |..|++     .+.+|||+||+|.+..+-..|+..||-..++|.-|+|..+.....                        
T Consensus       237 I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTA  316 (544)
T KOG0124|consen  237 IVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATA  316 (544)
T ss_pred             eeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHH
Confidence            999986     467999999999999999999999999999999888843211000                        


Q ss_pred             --------------------------------------------------------C-----------------------
Q 001991          353 --------------------------------------------------------P-----------------------  353 (985)
Q Consensus       353 --------------------------------------------------------~-----------------------  353 (985)
                                                                              +                       
T Consensus       317 Ki~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g  396 (544)
T KOG0124|consen  317 KIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLG  396 (544)
T ss_pred             HHHHHHHhccCCcccccCCccccCccccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchh
Confidence                                                                    0                       


Q ss_pred             -----Cc--------------------------------------ccccccceeeecC--CCCCC---HHHHHHHhhccC
Q 001991          354 -----SE--------------------------------------KDANQGTLVVFNL--DSSVS---TEELHQIFGIYG  385 (985)
Q Consensus       354 -----~~--------------------------------------~~~~~~tLfV~NL--p~svT---eedLrelFs~fG  385 (985)
                           .+                                      +....+.+.++|+  |.+++   +.+|.+.|++||
T Consensus       397 ~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG  476 (544)
T KOG0124|consen  397 LLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFG  476 (544)
T ss_pred             hcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhccc
Confidence                 00                                      0012356788887  55665   578999999999


Q ss_pred             CEEEEEEcCCCCc---------EEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          386 EIREIRDTQHKHN---------HKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       386 ~I~~Vri~~~skG---------faFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      .|.+|.|.....+         .-||+|....++.+|+++|+|+.|+|+++..+...
T Consensus       477 ~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~VvAE~YD  533 (544)
T KOG0124|consen  477 AVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKVVAEVYD  533 (544)
T ss_pred             ceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCceeehhhhh
Confidence            9999887654322         36999999999999999999999999999887654

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.61  E-value=1.2e-15  Score=168.66  Aligned_cols=163  Identities=15%  Similarity=0.342  Sum_probs=144.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..++|||++|+++++++.|++.|.+||+|..|.+     +++++||+||+|++.+...+++. .....|.|+.|.+..+.
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 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            6789999999999999999999999999999875     68899999999999999999984 56678999999999998


Q ss_pred             CCCCCCcccc--cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCce
Q 001991          349 PKDNPSEKDA--NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSD  421 (985)
Q Consensus       349 pk~~~~~~~~--~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~  421 (985)
                      ++....+...  ...+|||+.||.+++++++++.|.+||.|..+.++-     +.++|+||.|++++++.+++. ..-..
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            8876644332  356899999999999999999999999998876653     368999999999999999987 78889


Q ss_pred             eCCceEEEEeccCcchh
Q 001991          422 VAGKQIKLEASRPGGAR  438 (985)
Q Consensus       422 I~Gr~IkV~~A~~k~~R  438 (985)
                      |.|+.+.|..|.|++..
T Consensus       163 ~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             ecCceeeEeeccchhhc
Confidence            99999999999997744

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.59  E-value=7.6e-13  Score=147.18  Aligned_cols=160  Identities=21%  Similarity=0.375  Sum_probs=132.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhc-ccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFE-QFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs-~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..|.+||.|||+++...+|+++|. +.|+|..|.+    .+|.||+|.|+|+++|.+++|++.||...+.||+|.|+-..
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            457799999999999999999997 7899999975    79999999999999999999999999999999999984221


Q ss_pred             CC----------------------------------------------C-CCCc--------------------------
Q 001991          349 PK----------------------------------------------D-NPSE--------------------------  355 (985)
Q Consensus       349 pk----------------------------------------------~-~~~~--------------------------  355 (985)
                      ..                                              + ++..                          
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~  202 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSAS  202 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhh
Confidence            10                                              0 0000                          


Q ss_pred             --------ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEE----cCCCCcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          356 --------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       356 --------~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri----~~~skGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                              ..+....+||.||+..+..+.|++.|.-.|+|..|.+    ...++|++.++|..+-+|-.||..|++.-+.
T Consensus       203 Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~  282 (608)
T KOG4212|consen  203 FLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLF  282 (608)
T ss_pred             hhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCc
Confidence                    0012347899999999999999999999999988754    3457899999999999999999999988888


Q ss_pred             CceEEEEecc
Q 001991          424 GKQIKLEASR  433 (985)
Q Consensus       424 Gr~IkV~~A~  433 (985)
                      .++..+.+.+
T Consensus       283 ~~~~~~Rl~~  292 (608)
T KOG4212|consen  283 DRRMTVRLDR  292 (608)
T ss_pred             cccceeeccc
Confidence            8887777643

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.59  E-value=5.7e-15  Score=172.53  Aligned_cols=208  Identities=20%  Similarity=0.330  Sum_probs=161.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC-
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP-  349 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p-  349 (985)
                      .+...+.++|+|||..+..++|..+|..||+|..+.+. ..---|+|+|.+..+|++|++.|....+...++++.++.. 
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp-~~G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~d  459 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP-PGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPED  459 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecC-cccceeeeeecCccchHHHHHHhchhhhccCccccccChhh
Confidence            45566899999999999999999999999999999663 2223599999999999999999999999888888866521 


Q ss_pred             ------CCC-------------CC------------ccc-------------c-cccceeeecCCCCCCHHHHHHHhhcc
Q 001991          350 ------KDN-------------PS------------EKD-------------A-NQGTLVVFNLDSSVSTEELHQIFGIY  384 (985)
Q Consensus       350 ------k~~-------------~~------------~~~-------------~-~~~tLfV~NLp~svTeedLrelFs~f  384 (985)
                            +..             +.            ..+             . ..++|||+||+.+++.++|..+|..+
T Consensus       460 vf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~  539 (725)
T KOG0110|consen  460 VFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQ  539 (725)
T ss_pred             hccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhc
Confidence                  100             00            000             0 12249999999999999999999999


Q ss_pred             CCEEEEEEcCC--------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchhhhhhhhhhhccCCCcc-c
Q 001991          385 GEIREIRDTQH--------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC-Q  455 (985)
Q Consensus       385 G~I~~Vri~~~--------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rrl~qq~eq~q~e~nLy-k  455 (985)
                      |.|.++.|...        +.|||||+|.+.++|+.|++.|+|+.|.|+.|.|.++..+..-..-.+....+.-..|. +
T Consensus       540 G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVR  619 (725)
T KOG0110|consen  540 GTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVR  619 (725)
T ss_pred             CeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeee
Confidence            99999977543        34999999999999999999999999999999999998333222111111111123444 9


Q ss_pred             CCCCCCCcccc----ccccceEEEecCC
Q 001991          456 IPFDDLSSGQM----VSSGVITSTCMDN  479 (985)
Q Consensus       456 Nlp~svt~e~L----~~fG~I~S~~~en  479 (985)
                      |+|...+-..+    .+||+|.+++...
T Consensus       620 NipFeAt~rEVr~LF~aFGqlksvRlPK  647 (725)
T KOG0110|consen  620 NIPFEATKREVRKLFTAFGQLKSVRLPK  647 (725)
T ss_pred             ccchHHHHHHHHHHHhcccceeeeccch
Confidence            99999887776    8999999995543

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.59  E-value=8.1e-16  Score=175.65  Aligned_cols=164  Identities=23%  Similarity=0.362  Sum_probs=142.0

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      .++...++||+--|...++..+|.++|+.+|+|..|.+     ++.++|.|||+|.|.+....|| .|.|+.+.|.+|.|
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~v  252 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIV  252 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEe
Confidence            46677899999999999999999999999999999965     6779999999999999999999 69999999999999


Q ss_pred             cccCCCCCCCc----------ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHH
Q 001991          345 HYSIPKDNPSE----------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRA  409 (985)
Q Consensus       345 ~~a~pk~~~~~----------~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~ed  409 (985)
                      +......+...          -..+-..|||+||...+++++|+.+|++||.|..|.++.+     .+|||||+|.+.++
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            87654332210          0112223999999999999999999999999999988655     68999999999999


Q ss_pred             HHHHHHHhCCceeCCceEEEEeccC
Q 001991          410 AETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       410 A~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      |.+|+..|||.+|.|+.|+|..-..
T Consensus       333 ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  333 ARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             HHHHHHHhccceecCceEEEEEeee
Confidence            9999999999999999999987543

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=1.8e-14  Score=145.32  Aligned_cols=149  Identities=19%  Similarity=0.296  Sum_probs=127.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccc--cceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--HRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgk--srGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ..+++|||+|||.++-+.+|.++|-+||.|..|.+...  .-.||||+|++..+|+.||..-+|..+.|..|+|+++..-
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            35689999999999999999999999999999987433  3469999999999999999999999999999999987543


Q ss_pred             CCC----------------------CcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHH
Q 001991          351 DNP----------------------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR  408 (985)
Q Consensus       351 ~~~----------------------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~e  408 (985)
                      ...                      +.....+..|.|.+||++-++++|+++..+-|.|....+.++  +++.|+|...|
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD--g~GvV~~~r~e  161 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD--GVGVVEYLRKE  161 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc--cceeeeeeehh
Confidence            210                      111224458999999999999999999999999998887764  69999999999


Q ss_pred             HHHHHHHHhCCceeC
Q 001991          409 AAETALRTLNRSDVA  423 (985)
Q Consensus       409 dA~kAI~~LNG~~I~  423 (985)
                      +.+-|++.|....+.
T Consensus       162 DMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  162 DMKYAVRKLDDQKFR  176 (241)
T ss_pred             hHHHHHHhhcccccc
Confidence            999999988776553

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.55  E-value=2.4e-15  Score=160.45  Aligned_cols=149  Identities=18%  Similarity=0.326  Sum_probs=123.4

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      .+|||+||+. .+..+|...              |        +.+|.+|-++      +-|.||||+ -++.++++  +
T Consensus         3 ~KLFIGNLp~~~~~~elr~l--------------F--------e~ygkVlECD------IvKNYgFVH-iEdktaae--d   51 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSL--------------F--------EQYGKVLECD------IVKNYGFVH-IEDKTAAE--D   51 (346)
T ss_pred             cchhccCCCcccchHHHHHH--------------H--------HhhCceEeee------eecccceEE-eecccccH--H
Confidence            4799999987 777666655              7        7788887754      367899999 56677767  8


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI  305 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV  305 (985)
                      +|.+++|+.|+ ...+.|+..++                      ..+.+++|+|+||.+.++.+||++.|++||+|..|
T Consensus        52 airNLhgYtLh-g~nInVeaSks----------------------Ksk~stkl~vgNis~tctn~ElRa~fe~ygpviec  108 (346)
T KOG0109|consen   52 AIRNLHGYTLH-GVNINVEASKS----------------------KSKASTKLHVGNISPTCTNQELRAKFEKYGPVIEC  108 (346)
T ss_pred             HHhhcccceec-ceEEEEEeccc----------------------cCCCccccccCCCCccccCHHHhhhhcccCCceee
Confidence            99999999998 43433332211                      23578999999999999999999999999999999


Q ss_pred             EeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          306 YTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       306 kitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      ++   -++|+||.|.-.++|..|++.|++.++.|+++.|+.+..+-.
T Consensus       109 di---vkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen  109 DI---VKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             ee---ecceeEEEEeeccchHHHHhcccccccccceeeeeeeccccc
Confidence            98   788999999999999999999999999999999999876543

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.43  E-value=9.2e-14  Score=146.01  Aligned_cols=150  Identities=23%  Similarity=0.400  Sum_probs=130.5

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCC--
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP--  353 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~--  353 (985)
                      ..|||++||+.+.+.+|.++|..||.|..+.+   ..||+||+|.+..+|..|+..+++++|.|..+.|.++......  
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            46899999999999999999999999999988   5679999999999999999999999999999999888743110  


Q ss_pred             --------------CcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCC
Q 001991          354 --------------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR  419 (985)
Q Consensus       354 --------------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG  419 (985)
                                    .......+.|.|.|+...+.+.+|.+.|.++|.+.....   ..+++||+|...++|.+|+..|++
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                          011234557899999999999999999999999965544   578999999999999999999999


Q ss_pred             ceeCCceEEEEe
Q 001991          420 SDVAGKQIKLEA  431 (985)
Q Consensus       420 ~~I~Gr~IkV~~  431 (985)
                      ..+.++.|.+..
T Consensus       156 ~~~~~~~l~~~~  167 (216)
T KOG0106|consen  156 KKLNGRRISVEK  167 (216)
T ss_pred             hhhcCceeeecc
Confidence            999999999943

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.41  E-value=3.6e-12  Score=141.85  Aligned_cols=73  Identities=19%  Similarity=0.258  Sum_probs=67.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .++|+|+|||.++|+..|++-|..||.|.++.|+...+..+.|.|.++++|++|++.|||..+.|+.|+|.+.
T Consensus       536 a~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  536 ACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            3689999999999999999999999999999987666666799999999999999999999999999999874

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.41  E-value=3.1e-12  Score=139.77  Aligned_cols=165  Identities=16%  Similarity=0.248  Sum_probs=135.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE--------EEe----ccccceEEEEEeCCHHHHHHHHHHccCcccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--------IYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLR  338 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s--------Vki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~  338 (985)
                      .....+.|||.|||.++|.+++.++|++||-|..        |++    .|+.+|=|.+.|-..+++..|++.|++..|.
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            4556788999999999999999999999998864        232    5888999999999999999999999999999


Q ss_pred             cccccccccCCCCC----------------------------------CCcccccccceeeecCC----CCCC-------
Q 001991          339 RRKLDIHYSIPKDN----------------------------------PSEKDANQGTLVVFNLD----SSVS-------  373 (985)
Q Consensus       339 Gr~L~V~~a~pk~~----------------------------------~~~~~~~~~tLfV~NLp----~svT-------  373 (985)
                      |++|+|+.|+-...                                  ...+....++|.++|+=    ...+       
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            99999976632100                                  01112345689999982    1222       


Q ss_pred             HHHHHHHhhccCCEEEEEEc-CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          374 TEELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       374 eedLrelFs~fG~I~~Vri~-~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      +++|++-+++||.|..|.+. .++.|.+-|.|.+.++|..+|+.|+|+.|+||.|..+...-+
T Consensus       290 kedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            57888999999999998876 457899999999999999999999999999999999887543

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.39  E-value=1.4e-12  Score=130.56  Aligned_cols=82  Identities=23%  Similarity=0.416  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ....+++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999876     56789999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 001991          346 YSIPKDN  352 (985)
Q Consensus       346 ~a~pk~~  352 (985)
                      ++.++..
T Consensus       110 ~a~~~~~  116 (144)
T PLN03134        110 PANDRPS  116 (144)
T ss_pred             eCCcCCC
Confidence            9876544

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.38  E-value=1.8e-12  Score=129.68  Aligned_cols=78  Identities=17%  Similarity=0.350  Sum_probs=71.9

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+++++|+++|++||.|.+|+++.+     +++||||+|.+.++|++|++.||+..|.|++|+|+++.
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            4568999999999999999999999999999988643     58999999999999999999999999999999999997


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ++.
T Consensus       113 ~~~  115 (144)
T PLN03134        113 DRP  115 (144)
T ss_pred             cCC
Confidence            644

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.36  E-value=3.1e-13  Score=136.64  Aligned_cols=164  Identities=18%  Similarity=0.280  Sum_probs=125.2

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCC---ChhhhhccCCCCeeeeecCCChhh
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLP---DEDDLFSGVTDDMGHNFQANTVDD  220 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILp---dedDL~sG~SkGfGFV~ff~t~Ed  220 (985)
                      +-..||++||+. ++..-||+.              |        -..|-++.   .+ |..+...+|||||+ |.++|+
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL--------------~--------iqagpVv~i~iPk-Drv~~~~qGygF~E-f~~eed   63 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYEL--------------F--------IQAGPVVNLHIPK-DRVTQKHQGYGFAE-FRTEED   63 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHH--------------H--------HhcCceeeeecch-hhhcccccceeEEE-Eechhh
Confidence            445799999986 776677776              6        33443333   23 33355689999999 668899


Q ss_pred             hhhhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccC
Q 001991          221 LEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG  300 (985)
Q Consensus       221 aee~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG  300 (985)
                      ++  .++.-+|+..|. ++.+.+.++-                   .....-....+|||+||.+.++|..|.+.|+.||
T Consensus        64 ad--YAikiln~VkLY-grpIrv~kas-------------------~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG  121 (203)
T KOG0131|consen   64 AD--YAIKILNMVKLY-GRPIRVNKAS-------------------AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFG  121 (203)
T ss_pred             hH--HHHHHHHHHHhc-CceeEEEecc-------------------cccccccccccccccccCcchhHHHHHHHHHhcc
Confidence            89  899999988888 4333222211                   1112223448999999999999999999999999


Q ss_pred             cEEEE------EeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCC
Q 001991          301 DIRTI------YTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS  354 (985)
Q Consensus       301 ~I~sV------kitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~  354 (985)
                      .|...      ..++..+|||||.|.+.|.+.+|++.+||+.+..+++.|.|+..+....
T Consensus       122 ~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  122 VLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             ccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            88763      1368999999999999999999999999999999999999998766543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.30  E-value=1.9e-11  Score=135.71  Aligned_cols=160  Identities=23%  Similarity=0.303  Sum_probs=136.6

Q ss_pred             CcEEEEecCCCC-CCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCC
Q 001991          275 SRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP  353 (985)
Q Consensus       275 srtLfVgNLP~~-vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~  353 (985)
                      +..|.|.||.+. ||.+.|..+|..||+|..|++-.+.+.-|.|+|.|...|+-|++.|+|..+.|++|+|.+++...-.
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            578999999765 8999999999999999999986666789999999999999999999999999999999887643210


Q ss_pred             ------Cc-------------------------ccccccceeeecCCCCCCHHHHHHHhhccCCE-EEEEEcCCCCcEEE
Q 001991          354 ------SE-------------------------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQHKHNHKF  401 (985)
Q Consensus       354 ------~~-------------------------~~~~~~tLfV~NLp~svTeedLrelFs~fG~I-~~Vri~~~skGfaF  401 (985)
                            ..                         -..+..+|.+.|+|.++++|+|+++|..-|.. +-.+..++.+.+++
T Consensus       377 lp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal  456 (492)
T KOG1190|consen  377 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMAL  456 (492)
T ss_pred             CCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceee
Confidence                  00                         01234589999999999999999999998865 44566666788999


Q ss_pred             EEEcCHHHHHHHHHHhCCceeCC-ceEEEEeccC
Q 001991          402 IEFYDIRAAETALRTLNRSDVAG-KQIKLEASRP  434 (985)
Q Consensus       402 VeF~d~edA~kAI~~LNG~~I~G-r~IkV~~A~~  434 (985)
                      +.+.++|+|..|+..++...+++ ..|+|.|++.
T Consensus       457 ~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  457 PQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             cccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            99999999999999999999975 5999999875

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.30  E-value=1.1e-11  Score=128.53  Aligned_cols=150  Identities=23%  Similarity=0.321  Sum_probs=117.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE--Eecccc----ceEEEEEeCCHHHHHHHHHHccCcccc---ccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTI--YTACKH----RGFVMISYYDIRAARNAMKALQNKPLR---RRKLD  343 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV--kitgks----rGfAFV~F~d~esA~kAi~~Lng~~I~---Gr~L~  343 (985)
                      ..-|||||.+||.++...||+.+|..|--.+.+  +.+.+.    +-+|||+|.+...|..|+.+|||..|+   +..|.
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            346999999999999999999999998766554  444433    369999999999999999999999886   55666


Q ss_pred             ccccCCCCCC---------------------------------------------------Cccc---------------
Q 001991          344 IHYSIPKDNP---------------------------------------------------SEKD---------------  357 (985)
Q Consensus       344 V~~a~pk~~~---------------------------------------------------~~~~---------------  357 (985)
                      |++++.....                                                   .+.+               
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            6655321100                                                   0000               


Q ss_pred             ----------------ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-CCcEEEEEEcCHHHHHHHHHHhCCc
Q 001991          358 ----------------ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-KHNHKFIEFYDIRAAETALRTLNRS  420 (985)
Q Consensus       358 ----------------~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-skGfaFVeF~d~edA~kAI~~LNG~  420 (985)
                                      ....||||.||...+++++|+++|+.|-....++|..+ ....|||+|++.+.|..|+..|.|.
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~  271 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGN  271 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcc
Confidence                            01238999999999999999999999987776666433 3457999999999999999999998


Q ss_pred             ee
Q 001991          421 DV  422 (985)
Q Consensus       421 ~I  422 (985)
                      .|
T Consensus       272 ~~  273 (284)
T KOG1457|consen  272 LL  273 (284)
T ss_pred             ee
Confidence            76

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.29  E-value=5.1e-11  Score=132.36  Aligned_cols=163  Identities=25%  Similarity=0.405  Sum_probs=132.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccce-EEEEEeCCHHHHHHHHHHccCccccc--ccccccccC--
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-FVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSI--  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrG-fAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~--  348 (985)
                      +--.++|.|+-.-|+-+-|..+|++||.|..|.+-.|..| .|.|+|.+.+.|+.|...|+|+-|..  ..|+|.|++  
T Consensus       149 ~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt  228 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLT  228 (492)
T ss_pred             eeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcc
Confidence            3456788999999999999999999999999876455555 59999999999999999999988754  355554432  


Q ss_pred             --------CCCCC-------Cc----------------------------------------cccc--ccceeeecCC-C
Q 001991          349 --------PKDNP-------SE----------------------------------------KDAN--QGTLVVFNLD-S  370 (985)
Q Consensus       349 --------pk~~~-------~~----------------------------------------~~~~--~~tLfV~NLp-~  370 (985)
                              .|...       ..                                        ....  ...|.|.||. .
T Consensus       229 ~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~  308 (492)
T KOG1190|consen  229 DLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEE  308 (492)
T ss_pred             cceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchh
Confidence                    11110       00                                        0001  3578888885 5


Q ss_pred             CCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          371 SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       371 svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      .+|.+.|..+|+.||+|.+|+|..+++..|.|+|.|...|+-|+..|+|..+.||+|+|.+++...
T Consensus       309 ~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  309 AVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             ccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            789999999999999999999998888999999999999999999999999999999999997543

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=2.6e-11  Score=140.72  Aligned_cols=164  Identities=17%  Similarity=0.330  Sum_probs=132.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .......+||++||..+++.+++++...||++....+     ++.++||||.+|.+......|+..|||+.+.+++|.|+
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            3445689999999999999999999999999987653     57899999999999999999999999999999999998


Q ss_pred             ccCCCCCCCc--------------------ccccccceeeecC--CCCC-C-------HHHHHHHhhccCCEEEEEEcCC
Q 001991          346 YSIPKDNPSE--------------------KDANQGTLVVFNL--DSSV-S-------TEELHQIFGIYGEIREIRDTQH  395 (985)
Q Consensus       346 ~a~pk~~~~~--------------------~~~~~~tLfV~NL--p~sv-T-------eedLrelFs~fG~I~~Vri~~~  395 (985)
                      .+.+......                    .......|.+.|+  +.++ +       -|+++..|.+||.|..|.+...
T Consensus       365 ~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~  444 (500)
T KOG0120|consen  365 RAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRP  444 (500)
T ss_pred             hhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCC
Confidence            8765432211                    1122334555554  1111 1       1567788899999999988654


Q ss_pred             --------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          396 --------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       396 --------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                              ..|..||+|.+.+++++|.++|+|.+|.|++|...|...
T Consensus       445 ~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  445 YPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             CCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence                    356789999999999999999999999999999999864

>PF00076 RRM_1: RNA recognition motif

Probab=99.28  E-value=9.4e-12  Score=106.63  Aligned_cols=66  Identities=35%  Similarity=0.563  Sum_probs=62.1

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEE
Q 001991          363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  428 (985)
Q Consensus       363 LfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~Ik  428 (985)
                      |||+|||.++++++|+++|++||.|..+.+..+    .+++|||+|.+.++|++|++.|+|..++|++|+
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            799999999999999999999999999988763    578999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>PF00076 RRM_1: RNA recognition motif

Probab=99.25  E-value=1.4e-11  Score=105.56  Aligned_cols=66  Identities=30%  Similarity=0.616  Sum_probs=61.7

Q ss_pred             EEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          278 LFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       278 LfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      |||+|||+++++++|+++|++||.|..+++    .+..+++|||+|.+.++|++|++.|+|..+.|++|+
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            799999999999999999999999998876    356899999999999999999999999999998874

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.23  E-value=5.1e-11  Score=124.44  Aligned_cols=121  Identities=28%  Similarity=0.447  Sum_probs=103.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .++|||+|||.++++++|+++|.+||.|..+.+     +++.+|||||+|.+.++|..|++.+++..|.|++|.|.+..+
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            799999999999999999999999999988764     578999999999999999999999999999999999999542


Q ss_pred             ----CCCCC----------------cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC
Q 001991          350 ----KDNPS----------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH  395 (985)
Q Consensus       350 ----k~~~~----------------~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~  395 (985)
                          +....                ........+++.+++..++..++...|..+|.+..+.+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence                22211                01123458999999999999999999999999977766543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.23  E-value=1.1e-11  Score=137.49  Aligned_cols=204  Identities=16%  Similarity=0.259  Sum_probs=130.4

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhh
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLED  223 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee  223 (985)
                      ...+||+++|+| ++.+.|.+.              |.++.|+...++      ..|..++.++|||||.|. +.+.+. 
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~y--------------f~~~Gev~d~~v------m~d~~t~rsrgFgfv~f~-~~~~v~-   62 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREY--------------FSQFGEVTDCVV------MRDPSTGRSRGFGFVTFA-TPEGVD-   62 (311)
T ss_pred             CCcceeecCcCccccHHHHHHH--------------hcccCceeeEEE------eccCCCCCcccccceecC-CCcchh-
Confidence            456899999999 888889988              744443322222      245567999999999965 333333 


Q ss_pred             hHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEE
Q 001991          224 FDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIR  303 (985)
Q Consensus       224 ~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~  303 (985)
                       .++. ..-..|+ .+.+.+.++.+              ..............+|||++||.+++++++++.|++||.|.
T Consensus        63 -~vl~-~~~h~~d-gr~ve~k~av~--------------r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~  125 (311)
T KOG4205|consen   63 -AVLN-ARTHKLD-GRSVEPKRAVS--------------REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVA  125 (311)
T ss_pred             -eeec-ccccccC-CccccceeccC--------------cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeE
Confidence             1111 1111222 11111111111              11111122233678999999999999999999999999888


Q ss_pred             EEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCcccccc-cceeeecCCCCCCHHHH
Q 001991          304 TIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ-GTLVVFNLDSSVSTEEL  377 (985)
Q Consensus       304 sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~~~~~-~tLfV~NLp~svTeedL  377 (985)
                      .+.+     +.+.+||+||.|.+.+++++++. .....|.++.+.|..|.|+.......... ...+..|+....+.-.|
T Consensus       126 ~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~~~~~~~~~~~~~~~~g~~~~~~~l  204 (311)
T KOG4205|consen  126 DVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQSTKSSVSTRGKGNNLGNGRTGFFL  204 (311)
T ss_pred             eeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhcccccccccccccccccccccccccc
Confidence            7643     67789999999999999999984 77889999999999999987653222111 12222244444444445


Q ss_pred             HHHhhccCCEE
Q 001991          378 HQIFGIYGEIR  388 (985)
Q Consensus       378 relFs~fG~I~  388 (985)
                      ...|.-|+.+.
T Consensus       205 ~~~~~g~~~~~  215 (311)
T KOG4205|consen  205 KKYFKGYGPVG  215 (311)
T ss_pred             chhccccCccc
Confidence            55565555443

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.22  E-value=5.9e-11  Score=134.90  Aligned_cols=163  Identities=17%  Similarity=0.270  Sum_probs=127.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE---eccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk---itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...-|-+++||+++|++||.++|+.|+ |+.+.   .+++..|=|||+|.+.+++++|++ .+-..+..+-|.|--+.++
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCc
Confidence            345677899999999999999999998 44443   468899999999999999999996 7777788888888655443


Q ss_pred             CCC-------CcccccccceeeecCCCCCCHHHHHHHhhccCCEEE-EEEcC----CCCcEEEEEEcCHHHHHHHHHHhC
Q 001991          351 DNP-------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRDTQ----HKHNHKFIEFYDIRAAETALRTLN  418 (985)
Q Consensus       351 ~~~-------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~-Vri~~----~skGfaFVeF~d~edA~kAI~~LN  418 (985)
                      +..       .....+...|.+++||..||++||.++|+..-.|.. |.++.    .+.|-|||+|++.+.|++|+. -|
T Consensus        87 e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rh  165 (510)
T KOG4211|consen   87 EADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RH  165 (510)
T ss_pred             cccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HH
Confidence            321       111235668999999999999999999998655544 33332    256789999999999999998 78


Q ss_pred             CceeCCceEEEEeccCcchhh
Q 001991          419 RSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       419 G~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      ...|+-+-|.|-.+...+.++
T Consensus       166 re~iGhRYIEvF~Ss~~e~~~  186 (510)
T KOG4211|consen  166 RENIGHRYIEVFRSSRAEVKR  186 (510)
T ss_pred             HHhhccceEEeehhHHHHHHh
Confidence            889999999998776544433

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.20  E-value=2.5e-11  Score=122.41  Aligned_cols=76  Identities=33%  Similarity=0.509  Sum_probs=72.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      .+.|||+||+..+++.||..+|..||.|..|-|.....|||||+|+++.+|+.|+..|+|+.|.|..|+|+++.-.
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            5689999999999999999999999999999998888999999999999999999999999999999999998753

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.12  E-value=5.7e-11  Score=119.83  Aligned_cols=78  Identities=23%  Similarity=0.493  Sum_probs=73.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      -.++|||+||+..+++.||..+|..||+|.+|.+.....|||||+|++..+|+.|+..|+|+.|.|..|.|+.+.-..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            368999999999999999999999999999999988999999999999999999999999999999999999886443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.10  E-value=2.6e-10  Score=123.11  Aligned_cols=74  Identities=19%  Similarity=0.368  Sum_probs=69.2

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC--CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~--skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .++|||+||++.+++++|+++|+.||+|.+|++..+  .++||||+|.+.++|+.|+. |||..|.|+.|.|.++..
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            468999999999999999999999999999999765  47999999999999999996 999999999999999864

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.10  E-value=1.6e-10  Score=125.86  Aligned_cols=99  Identities=16%  Similarity=0.261  Sum_probs=80.5

Q ss_pred             cCcccccccccccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC---CCCcEEEEEEcCHHH
Q 001991          333 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ---HKHNHKFIEFYDIRA  409 (985)
Q Consensus       333 ng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~---~skGfaFVeF~d~ed  409 (985)
                      ++-...|..+.++.+..    .+.....+.|+|.|||...-+-||+.+|++||+|.+|.|+-   .+||||||+|++.+|
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            34445555555443321    12223456899999999999999999999999999998863   479999999999999


Q ss_pred             HHHHHHHhCCceeCCceEEEEeccCc
Q 001991          410 AETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       410 A~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      |++|-++|||..|.||+|.|..+..+
T Consensus       149 adRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  149 ADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHHhhcceeeceEEEEeccchh
Confidence            99999999999999999999998764

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.09  E-value=2.5e-10  Score=124.25  Aligned_cols=85  Identities=21%  Similarity=0.388  Sum_probs=76.2

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .......++|+|.|||...-|-||+.+|++||+|.+|.|   ..-+|||+||+|++.++|++|-++|+|..+.||+|.|.
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn  169 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVN  169 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEe
Confidence            344556689999999999999999999999999999976   56689999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      .+.++-..
T Consensus       170 ~ATarV~n  177 (376)
T KOG0125|consen  170 NATARVHN  177 (376)
T ss_pred             ccchhhcc
Confidence            98776443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.08  E-value=3.6e-10  Score=97.96  Aligned_cols=66  Identities=27%  Similarity=0.554  Sum_probs=59.9

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCC----CcEEEEEEcCHHHHHHHHHHhCCceeCCceEE
Q 001991          363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK----HNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  428 (985)
Q Consensus       363 LfV~NLp~svTeedLrelFs~fG~I~~Vri~~~s----kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~Ik  428 (985)
                      |||+|||..+++++|+++|+.||.|..+++..+.    +++|||+|.+.++|.+|++.+++..++|+.|+
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            7999999999999999999999999999987653    68999999999999999999999999999985

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 ....

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.08  E-value=8.5e-10  Score=121.49  Aligned_cols=167  Identities=20%  Similarity=0.319  Sum_probs=135.1

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHH--ccCcccccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA--LQNKPLRRRKLDIHY  346 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~--Lng~~I~Gr~L~V~~  346 (985)
                      +....++-.|.|++|-..++|.+|.+.++.||.|..+.. ...+..|.|+|+|.+.|+.|+.-  -+...+.|..--+.|
T Consensus        25 phk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~-~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~Ny  103 (494)
T KOG1456|consen   25 PHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTC-MPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNY  103 (494)
T ss_pred             CCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEe-ccccceeeeeeccccchhhheehhccCcccccCchhhccc
Confidence            445667889999999999999999999999999998876 56677899999999999999863  233457788888888


Q ss_pred             cCCCCCCCc---cccccccee--eecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCce
Q 001991          347 SIPKDNPSE---KDANQGTLV--VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD  421 (985)
Q Consensus       347 a~pk~~~~~---~~~~~~tLf--V~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~  421 (985)
                      +..+.....   .......|.  |-|--..+|.|-|..++...|+|.+|-|+++..=.|.|||++.+.|++|..+|||..
T Consensus       104 Stsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGAD  183 (494)
T KOG1456|consen  104 STSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGAD  183 (494)
T ss_pred             chhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhccccc
Confidence            855433211   112223344  345556889999999999999999999988755579999999999999999999998


Q ss_pred             e--CCceEEEEeccCcc
Q 001991          422 V--AGKQIKLEASRPGG  436 (985)
Q Consensus       422 I--~Gr~IkV~~A~~k~  436 (985)
                      |  +..+|+|+||+|..
T Consensus       184 IYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  184 IYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             ccccceeEEEEecCcce
Confidence            8  56899999999864

>smart00362 RRM_2 RNA recognition motif

Probab=99.08  E-value=5.7e-10  Score=93.99  Aligned_cols=69  Identities=30%  Similarity=0.571  Sum_probs=64.2

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCC---CcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK---HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~s---kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      +|+|.|||..+++++|+++|.+||.|..+++..+.   +++|||+|.+.++|++|++.+++..+.|++|+|+
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            58999999999999999999999999999887654   6899999999999999999999999999999873

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.06  E-value=4.1e-10  Score=105.02  Aligned_cols=81  Identities=30%  Similarity=0.488  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ....++.|||+|||.++|.++..++|.+||.|+.|++  +...+|.|||.|++..+|++|++.|.|..+.++.|.|.|-+
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            4456799999999999999999999999999999998  56789999999999999999999999999999999999887


Q ss_pred             CCC
Q 001991          349 PKD  351 (985)
Q Consensus       349 pk~  351 (985)
                      +.+
T Consensus        94 ~~~   96 (124)
T KOG0114|consen   94 PED   96 (124)
T ss_pred             HHH
Confidence            643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.05  E-value=4.5e-10  Score=121.28  Aligned_cols=75  Identities=19%  Similarity=0.291  Sum_probs=68.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      .++|||+|||+.+++++|+++|+.||+|.+|.+  .+..+|||||+|++.++|+.|+. |+|..|.|+.|.|..+..-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            579999999999999999999999999999987  33468999999999999999995 9999999999999887643

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.05  E-value=5.6e-10  Score=96.80  Aligned_cols=66  Identities=23%  Similarity=0.560  Sum_probs=58.5

Q ss_pred             EEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          278 LFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       278 LfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      |||+|||+++++++|+++|+.||.|..+++    .+..+++|||+|.+.++|++|++.+++..+.|++|+
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            799999999999999999999999999876    244689999999999999999999998999999874

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=99.04  E-value=8.8e-10  Score=92.18  Aligned_cols=56  Identities=27%  Similarity=0.569  Sum_probs=52.2

Q ss_pred             HHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          377 LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       377 LrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      |+++|++||+|..|.+.++.+++|||+|.+.++|++|++.|||..+.|++|+|+||
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            68999999999999998776799999999999999999999999999999999986

(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 ....

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.03  E-value=1.2e-09  Score=101.92  Aligned_cols=83  Identities=28%  Similarity=0.423  Sum_probs=74.7

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc--CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~--~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      -.+.|||+|||.++|.|+..++|.+||.|..|++-  +.-+|-|||-|++..+|.+|+..|+|..+.++.|.|-+.++..
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            35689999999999999999999999999999984  4468999999999999999999999999999999999998876


Q ss_pred             hhhhh
Q 001991          437 ARRFM  441 (985)
Q Consensus       437 ~Rrl~  441 (985)
                      ..+++
T Consensus        97 ~~~~~  101 (124)
T KOG0114|consen   97 AFKLM  101 (124)
T ss_pred             HHHHH
Confidence            55433

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.03  E-value=5.4e-09  Score=115.32  Aligned_cols=164  Identities=21%  Similarity=0.350  Sum_probs=136.6

Q ss_pred             CCCCCcEEEEecCCC--CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccc
Q 001991          271 GEHPSRTLFVRNINS--NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~--~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~  346 (985)
                      ...+...|.+.=|++  .+|-+.|..+....|+|..|.+-.+.--.|+|+|++.+.|++|.+.|||..|..  ..|+|+|
T Consensus       116 s~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIey  195 (494)
T KOG1456|consen  116 SATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEY  195 (494)
T ss_pred             CCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEe
Confidence            445667777776665  589999999999999999998866666689999999999999999999988753  6788888


Q ss_pred             cCCCCCC--------------------------------------------------------------Cc------c--
Q 001991          347 SIPKDNP--------------------------------------------------------------SE------K--  356 (985)
Q Consensus       347 a~pk~~~--------------------------------------------------------------~~------~--  356 (985)
                      ++|..-.                                                              +.      .  
T Consensus       196 AkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~  275 (494)
T KOG1456|consen  196 AKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDG  275 (494)
T ss_pred             cCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccC
Confidence            8764200                                                              00      0  


Q ss_pred             --------cccccceeeecCCCC-CCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          357 --------DANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       357 --------~~~~~tLfV~NLp~s-vTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                              ......+.|.+|+.. +.-+.|..+|..||.|..|++++.+.|-|.|++.|..+.++|+..||+..+-|.+|
T Consensus       276 ~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl  355 (494)
T KOG1456|consen  276 RGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKL  355 (494)
T ss_pred             CCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceE
Confidence                    012346889999864 56789999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccC
Q 001991          428 KLEASRP  434 (985)
Q Consensus       428 kV~~A~~  434 (985)
                      .|.+++.
T Consensus       356 ~v~~SkQ  362 (494)
T KOG1456|consen  356 NVCVSKQ  362 (494)
T ss_pred             EEeeccc
Confidence            9999864

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.02  E-value=3.2e-10  Score=109.25  Aligned_cols=78  Identities=26%  Similarity=0.467  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ....+++|||+||+..++|++|.++|+++|+|+.|.+     +...-|||||+|.+.++|..|++.+++..+..+.|.|.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            3457899999999999999999999999999999975     56678999999999999999999999999999999998


Q ss_pred             ccC
Q 001991          346 YSI  348 (985)
Q Consensus       346 ~a~  348 (985)
                      |..
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            753

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.01  E-value=6.5e-10  Score=117.23  Aligned_cols=77  Identities=22%  Similarity=0.393  Sum_probs=72.2

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...+|.|.||+.++++++|+++|.+||.|.+|.+..+     ++|||||.|.+.++|++||+.|||.-+..-.|+|+|++
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            4568999999999999999999999999999987544     78999999999999999999999999999999999999


Q ss_pred             Cc
Q 001991          434 PG  435 (985)
Q Consensus       434 ~k  435 (985)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            85

>PLN03213 repressor of silencing 3; Provisional

Probab=99.00  E-value=1e-09  Score=123.98  Aligned_cols=90  Identities=20%  Similarity=0.260  Sum_probs=78.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-CCcEEEEEEcCH--HHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-KHNHKFIEFYDI--RAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-skGfaFVeF~d~--edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ....+|||+||++.+++++|+.+|..||.|.+|.|++. .||||||+|.+.  .++.+||..|||.++.|+.|+|..|++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            34568999999999999999999999999999998754 489999999987  789999999999999999999999998


Q ss_pred             cchhhhhhhhhhh
Q 001991          435 GGARRFMVQSEQE  447 (985)
Q Consensus       435 k~~Rrl~qq~eq~  447 (985)
                      .-.-||.+.+++.
T Consensus        88 ~YLeRLkrEReea  100 (759)
T PLN03213         88 HYLARLKREWEAA  100 (759)
T ss_pred             HHHHHHHHHHHHh
Confidence            7766666554443

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

Probab=98.98  E-value=4.3e-10  Score=129.70  Aligned_cols=162  Identities=24%  Similarity=0.356  Sum_probs=130.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|+|-|||..|++++|+++|+.||+|+.|+.+...+|.+||+|+|..+|++|+++|++.++.|+.|........
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            35678999999999999999999999999999999999999999999999999999999999999999998884222111


Q ss_pred             CC------------------CCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHH
Q 001991          351 DN------------------PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET  412 (985)
Q Consensus       351 ~~------------------~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~k  412 (985)
                      ..                  .....-+...++.- |++..+..-++.+|+.+|.+.. +.++.....-|++|.+..++..
T Consensus       151 ~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~  228 (549)
T KOG4660|consen  151 AMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAF  228 (549)
T ss_pred             cchhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhh
Confidence            10                  01111223455544 9999988888889999999988 7777666789999999999977


Q ss_pred             HHHHhCCceeCCceEEEEeccCc
Q 001991          413 ALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       413 AI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      +...+ |..+.++...++++.+.
T Consensus       229 ~~~~~-G~~~s~~~~v~t~S~~~  250 (549)
T KOG4660|consen  229 SEPRG-GFLISNSSGVITFSGPG  250 (549)
T ss_pred             cccCC-ceecCCCCceEEecCCC
Confidence            77644 67777777777777763

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=98.97  E-value=1e-09  Score=115.80  Aligned_cols=79  Identities=23%  Similarity=0.447  Sum_probs=74.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .....+|-|.||+.+++|++|+++|.+||.|..|++     ++.+||||||+|.+.++|.+||+.|||.-+..--|+|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            346789999999999999999999999999999975     799999999999999999999999999999999999999


Q ss_pred             cCCC
Q 001991          347 SIPK  350 (985)
Q Consensus       347 a~pk  350 (985)
                      +.|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9886

>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=98.95  E-value=4.6e-09  Score=88.94  Aligned_cols=70  Identities=34%  Similarity=0.609  Sum_probs=65.3

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCC----CcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK----HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~s----kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      +|+|+|||..+++++|+++|+.||.|..+.+....    +++|||+|.+.++|..|++.+++..+.|++|.|.+
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            58999999999999999999999999999887654    78999999999999999999999999999999874

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).

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=98.94  E-value=1.4e-09  Score=104.96  Aligned_cols=76  Identities=25%  Similarity=0.385  Sum_probs=68.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..+||||+||...+++|+|.++|+++|+|+.|.+-     ....|||||+|...++|+.|++.++|..+..++|.|.|--
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            56899999999999999999999999999998542     2357899999999999999999999999999999999864


Q ss_pred             C
Q 001991          434 P  434 (985)
Q Consensus       434 ~  434 (985)
                      -
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            3

>smart00362 RRM_2 RNA recognition motif

Probab=98.93  E-value=2.5e-09  Score=90.12  Aligned_cols=68  Identities=34%  Similarity=0.612  Sum_probs=62.2

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEec---cccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTA---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVkit---gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      +|||+|||..+++++|+++|++||+|..+.+.   +..+|+|||+|.+.++|++|++.+++..+.|+++.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            58999999999999999999999999998763   345799999999999999999999999999998876

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.92  E-value=1.6e-09  Score=114.06  Aligned_cols=77  Identities=25%  Similarity=0.439  Sum_probs=67.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .+...++|||++|++.+..++|+++|++||+|++..+     ++++|||+||+|.|.++|.+|++. -+-.|+||+-.|.
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            4456789999999999999999999999999998754     799999999999999999999963 4456899988887


Q ss_pred             ccC
Q 001991          346 YSI  348 (985)
Q Consensus       346 ~a~  348 (985)
                      .+.
T Consensus        87 lA~   89 (247)
T KOG0149|consen   87 LAS   89 (247)
T ss_pred             hhh
Confidence            664

>smart00360 RRM RNA recognition motif

Probab=98.92  E-value=4e-09  Score=88.35  Aligned_cols=66  Identities=35%  Similarity=0.597  Sum_probs=60.5

Q ss_pred             eecCCCCCCHHHHHHHhhccCCEEEEEEcCCC-----CcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          365 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       365 V~NLp~svTeedLrelFs~fG~I~~Vri~~~s-----kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      |+|||..+++++|+++|++||.|..+.+..+.     +++|||+|.+.++|.+|++.|++..+.|++|+|+
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            67999999999999999999999999886543     5899999999999999999999999999999873

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.91  E-value=3.9e-09  Score=112.57  Aligned_cols=74  Identities=19%  Similarity=0.254  Sum_probs=68.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC--CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~--skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ..+|||+||++.+|+++|+++|+.||+|.+|++..+  .+++|||+|.++++|+.|+. |||..|.+++|.|.....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            469999999999999999999999999999999865  45799999999999999996 999999999999998654

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.91  E-value=1.3e-09  Score=112.37  Aligned_cols=80  Identities=25%  Similarity=0.500  Sum_probs=73.8

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      +.......+|.|-||..-++.++|+.+|++||.|-+|+|     ++.++|||||.|.+..+|+.|+++|+|.+|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            334456789999999999999999999999999999987     788999999999999999999999999999999999


Q ss_pred             ccccC
Q 001991          344 IHYSI  348 (985)
Q Consensus       344 V~~a~  348 (985)
                      |+++.
T Consensus        87 Vq~ar   91 (256)
T KOG4207|consen   87 VQMAR   91 (256)
T ss_pred             ehhhh
Confidence            98774

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.91  E-value=1.4e-09  Score=112.22  Aligned_cols=76  Identities=26%  Similarity=0.502  Sum_probs=70.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      -.+|.|.||-.-++.++|+.+|++||.|-+|.|..+     ++|||||.|.+..+|+.|+++|+|..|+|+.|.|++|+-
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            458999999999999999999999999999998654     789999999999999999999999999999999999874


Q ss_pred             c
Q 001991          435 G  435 (985)
Q Consensus       435 k  435 (985)
                      .
T Consensus        93 g   93 (256)
T KOG4207|consen   93 G   93 (256)
T ss_pred             C
Confidence            3

>PLN03213 repressor of silencing 3; Provisional

Probab=98.91  E-value=2.3e-09  Score=121.28  Aligned_cols=119  Identities=13%  Similarity=0.177  Sum_probs=86.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-ccccceEEEEEeCCH--HHHHHHHHHccCcccccccccccccC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDI--RAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-tgksrGfAFV~F~d~--esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      .....+|||+||++.+++++|+.+|..||.|..|.+ ....||||||+|...  .++.+||..|||..+.|+.|+|..++
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            345689999999999999999999999999999976 222399999999987  78999999999999999999998887


Q ss_pred             CCCCC------Cc-ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEE
Q 001991          349 PKDNP------SE-KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD  392 (985)
Q Consensus       349 pk~~~------~~-~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri  392 (985)
                      |.-..      .. ......++-+--.  ......|+-+|-+.++|+.+-+
T Consensus        87 P~YLeRLkrEReea~s~~~~~~kl~k~--~~e~~qLnifFPrLrKvKslPf  135 (759)
T PLN03213         87 EHYLARLKREWEAASSTSDNTIKAPSD--SPPATHLNIFFPRLRKVKAMPL  135 (759)
T ss_pred             HHHHHHHHHHHHHhhcccccccccccc--CCccceeeEecccccccccccc
Confidence            64110      00 0001112111111  1234566777777887776544

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.89  E-value=8.1e-09  Score=107.87  Aligned_cols=75  Identities=28%  Similarity=0.568  Sum_probs=69.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ..+|||+|||.++++++|+++|.+||.|..|++..     ..+|||||+|.+.++|..|+..++|..|.|++|.|.++..
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            58999999999999999999999999998887754     4689999999999999999999999999999999999653

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.86  E-value=4.7e-09  Score=113.44  Aligned_cols=78  Identities=27%  Similarity=0.464  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...|-+||||+-|+.+++|.+|++.|+.||+|+.|.+     +++++|||||+|++..+...|.+..+|..|+|+.|.|.
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            3478899999999999999999999999999999854     89999999999999999999999999999999999998


Q ss_pred             ccC
Q 001991          346 YSI  348 (985)
Q Consensus       346 ~a~  348 (985)
                      +..
T Consensus       177 vER  179 (335)
T KOG0113|consen  177 VER  179 (335)
T ss_pred             ecc
Confidence            764

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.86  E-value=5.3e-09  Score=111.63  Aligned_cols=74  Identities=15%  Similarity=0.184  Sum_probs=67.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ...+|||+||++.+|+++|+++|+.||+|..|++  .++.++||||+|+++++|+.|+ .|+|..|.+++|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            3579999999999999999999999999999987  5567789999999999999999 699999999999996543

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.85  E-value=3.5e-09  Score=107.63  Aligned_cols=78  Identities=32%  Similarity=0.456  Sum_probs=70.8

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC--CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~--~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ...++|||+|||.++-+.+|.++|.+||.|..|.+..  ....||||+|+++.+|+.||..-+|..++|.+|+|++++..
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            3567999999999999999999999999999987643  34679999999999999999999999999999999998764

>smart00360 RRM RNA recognition motif

Probab=98.83  E-value=7.2e-09  Score=86.80  Aligned_cols=65  Identities=32%  Similarity=0.604  Sum_probs=59.3

Q ss_pred             EecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          280 VRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       280 VgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      |+|||..+++++|+++|++||.|..+.+     +++++|+|||+|.+.++|.+|++.+++..+.|++|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            5799999999999999999999998876     3456899999999999999999999999999998876

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.82  E-value=1.8e-09  Score=112.12  Aligned_cols=80  Identities=29%  Similarity=0.520  Sum_probs=75.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ...|+|||++|..+|+|.-|...|-+||+|..|.+     +.++||||||+|...|+|..||..||+.+|.||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            35689999999999999999999999999999976     7899999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 001991          348 IPKDN  352 (985)
Q Consensus       348 ~pk~~  352 (985)
                      .|...
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            88654

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.82  E-value=1.4e-08  Score=109.78  Aligned_cols=90  Identities=24%  Similarity=0.385  Sum_probs=78.4

Q ss_pred             cCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCce
Q 001991          347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSD  421 (985)
Q Consensus       347 a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~  421 (985)
                      ..|..++.....+-+||||.-|+.++++.+|+..|+.||.|+.|+++.     .++|||||+|+++.+...|.+..+|.+
T Consensus        88 wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~  167 (335)
T KOG0113|consen   88 WDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIK  167 (335)
T ss_pred             cCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCce
Confidence            345555544556778999999999999999999999999999998764     479999999999999999999999999


Q ss_pred             eCCceEEEEeccCcc
Q 001991          422 VAGKQIKLEASRPGG  436 (985)
Q Consensus       422 I~Gr~IkV~~A~~k~  436 (985)
                      |+|+.|.|.+-+...
T Consensus       168 Idgrri~VDvERgRT  182 (335)
T KOG0113|consen  168 IDGRRILVDVERGRT  182 (335)
T ss_pred             ecCcEEEEEeccccc
Confidence            999999999876543

>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=98.80  E-value=1.4e-08  Score=86.03  Aligned_cols=70  Identities=33%  Similarity=0.656  Sum_probs=63.4

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEecc----ccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVkitg----ksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      +|+|+|||..+++++|+++|+.||.|..+.+..    ..+|+|||+|.+.++|+.|++.+++..+.|+++.|.+
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            489999999999999999999999999987632    3489999999999999999999999999999988754

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).

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.75  E-value=5.1e-09  Score=108.77  Aligned_cols=80  Identities=26%  Similarity=0.485  Sum_probs=73.9

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||++|..++++.-|...|-+||.|+.|.++-+     .+|||||+|.-.|+|.+||..||+.++.||.|+|.+|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            4579999999999999999999999999999988643     68999999999999999999999999999999999999


Q ss_pred             Ccchh
Q 001991          434 PGGAR  438 (985)
Q Consensus       434 ~k~~R  438 (985)
                      |...+
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            86544

>PF13893 RRM_5: RNA recognition motif

Probab=98.75  E-value=1.4e-08  Score=84.91  Aligned_cols=56  Identities=29%  Similarity=0.632  Sum_probs=50.6

Q ss_pred             HHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          292 LKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       292 LrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      |+++|++||+|..+.+..+.+++|||+|.+.++|++|++.|||..+.|++|+|.|+
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            68999999999999985544799999999999999999999999999999999885

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.74  E-value=1.4e-08  Score=98.92  Aligned_cols=81  Identities=20%  Similarity=0.407  Sum_probs=73.0

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      +......|||.++....++++|.+.|..||+|+.|.+.-+     .+|||+|+|++.++|++|+.+|||..|-|.+|.|.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VD  147 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVD  147 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEE
Confidence            4456678999999999999999999999999999987543     57899999999999999999999999999999999


Q ss_pred             eccCcc
Q 001991          431 ASRPGG  436 (985)
Q Consensus       431 ~A~~k~  436 (985)
                      |+--++
T Consensus       148 w~Fv~g  153 (170)
T KOG0130|consen  148 WCFVKG  153 (170)
T ss_pred             EEEecC
Confidence            986544

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.73  E-value=1.5e-08  Score=106.88  Aligned_cols=79  Identities=24%  Similarity=0.319  Sum_probs=68.2

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      +...++|||++|++.+..|.|++.|++||+|+++.|+     .++||||||+|.|.++|.+|++.- .-.|+||+..|.+
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccch
Confidence            4456789999999999999999999999999997765     347999999999999999999833 3578999999998


Q ss_pred             ccCcc
Q 001991          432 SRPGG  436 (985)
Q Consensus       432 A~~k~  436 (985)
                      |--+.
T Consensus        88 A~lg~   92 (247)
T KOG0149|consen   88 ASLGG   92 (247)
T ss_pred             hhhcC
Confidence            87644

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.70  E-value=1.6e-07  Score=108.18  Aligned_cols=142  Identities=19%  Similarity=0.321  Sum_probs=108.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-------ccccce---EEEEEeCCHHHHHHHHHHccCcccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-------ACKHRG---FVMISYYDIRAARNAMKALQNKPLRRR  340 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-------tgksrG---fAFV~F~d~esA~kAi~~Lng~~I~Gr  340 (985)
                      ...-+++|||++||++++|++|...|..||.+..-.-       ....+|   |+|+.|+++..++.-+.+..-   ...
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~  331 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEG  331 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---ccc
Confidence            4556899999999999999999999999998764321       122456   999999999998887765332   333


Q ss_pred             cccccccCCCCCC-------------------CcccccccceeeecCCCCCCHHHHHHHhh-ccCCEEEEEEcCC-----
Q 001991          341 KLDIHYSIPKDNP-------------------SEKDANQGTLVVFNLDSSVSTEELHQIFG-IYGEIREIRDTQH-----  395 (985)
Q Consensus       341 ~L~V~~a~pk~~~-------------------~~~~~~~~tLfV~NLp~svTeedLrelFs-~fG~I~~Vri~~~-----  395 (985)
                      +++++.+.+....                   ...-.+.+||||++||--++.++|..+|+ -||.|..+-|..|     
T Consensus       332 ~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KY  411 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKY  411 (520)
T ss_pred             ceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCC
Confidence            3444333332211                   11223567999999999999999999999 6999999887655     


Q ss_pred             CCcEEEEEEcCHHHHHHHHH
Q 001991          396 KHNHKFIEFYDIRAAETALR  415 (985)
Q Consensus       396 skGfaFVeF~d~edA~kAI~  415 (985)
                      .+|-|-|.|.+..+-.+||.
T Consensus       412 PkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  412 PKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             CCCcceeeecccHHHHHHHh
Confidence            57889999999999999998

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.67  E-value=3.3e-09  Score=107.74  Aligned_cols=75  Identities=20%  Similarity=0.420  Sum_probs=70.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..+.-|||+|||.+.||.||.-+|++||+|+.|.+     +|+++||||+.|++..+...|+..|||..|.||.|+|...
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            46788999999999999999999999999999864     8999999999999999999999999999999999999643

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.66  E-value=2.7e-08  Score=115.22  Aligned_cols=77  Identities=25%  Similarity=0.450  Sum_probs=72.9

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      +.|||||||++++|++|.++|+..|.|.++++     +++.+||||++|.+.++|.+|++.|||.++.|++|+|.|+...
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            89999999999999999999999999999975     7999999999999999999999999999999999999998755


Q ss_pred             CC
Q 001991          351 DN  352 (985)
Q Consensus       351 ~~  352 (985)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.65  E-value=6.3e-08  Score=112.25  Aligned_cols=79  Identities=25%  Similarity=0.354  Sum_probs=73.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      +.+||+|+|.++++++|..+|+..|.|.++++.-|     .+||||++|.+.++|++|++.|||.++.|++|+|.|+...
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            78999999999999999999999999999988643     6899999999999999999999999999999999999866


Q ss_pred             chhh
Q 001991          436 GARR  439 (985)
Q Consensus       436 ~~Rr  439 (985)
                      ..+.
T Consensus        99 ~~~~  102 (435)
T KOG0108|consen   99 KNAE  102 (435)
T ss_pred             chhH
Confidence            6544

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.63  E-value=3.6e-08  Score=96.02  Aligned_cols=81  Identities=17%  Similarity=0.442  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .....-.|||.++-+.++|++|.+.|..||+|..+.+     ++-.+|||+|+|++.++|++|+..+||..|.|.+|.|.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VD  147 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVD  147 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEE
Confidence            4445678999999999999999999999999999865     68889999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 001991          346 YSIPKD  351 (985)
Q Consensus       346 ~a~pk~  351 (985)
                      |+.-+.
T Consensus       148 w~Fv~g  153 (170)
T KOG0130|consen  148 WCFVKG  153 (170)
T ss_pred             EEEecC
Confidence            986543

>smart00361 RRM_1 RNA recognition motif

Probab=98.61  E-value=1e-07  Score=83.74  Aligned_cols=56  Identities=27%  Similarity=0.464  Sum_probs=49.2

Q ss_pred             HHHHHHHhh----ccCCEEEEE-E-c------CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEE
Q 001991          374 TEELHQIFG----IYGEIREIR-D-T------QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL  429 (985)
Q Consensus       374 eedLrelFs----~fG~I~~Vr-i-~------~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV  429 (985)
                      +++|+++|+    +||.|.+|. + +      +.++|||||+|.+.++|.+|++.|||+.+.|+.|++
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            577888888    999999884 2 2      346899999999999999999999999999999987

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.60  E-value=7.2e-08  Score=112.52  Aligned_cols=164  Identities=18%  Similarity=0.344  Sum_probs=134.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhccc-----------C-cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQF-----------G-DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR  338 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~f-----------G-~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~  338 (985)
                      .....+.+||+++|..++++.+-.+|..-           | .|..+.+ ...+.|||++|.+.+.|..|+ .+++..+.
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~-n~~~nfa~ie~~s~~~at~~~-~~~~~~f~  248 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL-NLEKNFAFIEFRSISEATEAM-ALDGIIFE  248 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee-cccccceeEEecCCCchhhhh-cccchhhC
Confidence            34556899999999999999999988754           3 3777777 778899999999999999999 58998888


Q ss_pred             cccccccccCCCCC-------------------CCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----
Q 001991          339 RRKLDIHYSIPKDN-------------------PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----  394 (985)
Q Consensus       339 Gr~L~V~~a~pk~~-------------------~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----  394 (985)
                      |..+.+........                   ..........++|++||..+++++++++...||.+...++..     
T Consensus       249 g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g  328 (500)
T KOG0120|consen  249 GRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATG  328 (500)
T ss_pred             CCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccc
Confidence            88877732211100                   011123456899999999999999999999999998866643     


Q ss_pred             CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          395 HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       395 ~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      .++||||.+|.+......|+..|||..+++++|.|..|....
T Consensus       329 ~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  329 NSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             cccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            478999999999999999999999999999999999987654

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.60  E-value=2.5e-08  Score=120.00  Aligned_cols=159  Identities=19%  Similarity=0.337  Sum_probs=138.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEec----cccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA----CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkit----gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....+++||++||+..+++.+|+..|..+|.|..|.+.    +...-||||.|.+...+-.|.-++.+..|....+++.+
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            45568999999999999999999999999999999872    23345999999999999999999999999888888888


Q ss_pred             cCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCC--
Q 001991          347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG--  424 (985)
Q Consensus       347 a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~G--  424 (985)
                      ..++      ....+.++|++|...+....|...|..||.|..|.+. +..-|+||.|.+...|+.|+..|-|..|+|  
T Consensus       448 G~~k------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~-hgq~yayi~yes~~~aq~a~~~~rgap~G~P~  520 (975)
T KOG0112|consen  448 GQPK------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR-HGQPYAYIQYESPPAAQAATHDMRGAPLGGPP  520 (975)
T ss_pred             cccc------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc-cCCcceeeecccCccchhhHHHHhcCcCCCCC
Confidence            7653      3446689999999999999999999999999998764 346699999999999999999999999986  


Q ss_pred             ceEEEEeccCcc
Q 001991          425 KQIKLEASRPGG  436 (985)
Q Consensus       425 r~IkV~~A~~k~  436 (985)
                      ++|.|.|+.+..
T Consensus       521 ~r~rvdla~~~~  532 (975)
T KOG0112|consen  521 RRLRVDLASPPG  532 (975)
T ss_pred             cccccccccCCC
Confidence            789999998654

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.57  E-value=7.4e-08  Score=114.50  Aligned_cols=76  Identities=33%  Similarity=0.558  Sum_probs=72.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      +|||||+.|+.+++|.||.++|+.||+|.+|.+ ...+|||||......+|.+|+.+|.+..+.++.|+|.|+..+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~l-i~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G  496 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIIL-IPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKG  496 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEee-ccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCC
Confidence            699999999999999999999999999999998 6789999999999999999999999999999999999997554

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.54  E-value=9.9e-09  Score=104.29  Aligned_cols=75  Identities=20%  Similarity=0.376  Sum_probs=69.4

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...-|||+|||..+|+.+|..+|++||+|..|.++++     ++||||++|+|.++..-|+..|||..|.||.|+|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            4567999999999999999999999999999988654     78999999999999999999999999999999998754

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.52  E-value=1.8e-07  Score=98.46  Aligned_cols=75  Identities=27%  Similarity=0.499  Sum_probs=70.2

Q ss_pred             ceeeecCCCCCCHHHHHH----HhhccCCEEEEEEc--CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          362 TLVVFNLDSSVSTEELHQ----IFGIYGEIREIRDT--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       362 tLfV~NLp~svTeedLre----lFs~fG~I~~Vri~--~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ||||.||.+.+..++|+.    +|++||+|.+|...  +.-+|.|||.|.+.+.|..|++.|+|..+-||.++|.||+.+
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~   90 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSD   90 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCc
Confidence            999999999999999988    99999999998875  446899999999999999999999999999999999999876


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      .
T Consensus        91 s   91 (221)
T KOG4206|consen   91 S   91 (221)
T ss_pred             c
Confidence            5

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.49  E-value=2.4e-07  Score=110.24  Aligned_cols=81  Identities=28%  Similarity=0.373  Sum_probs=76.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ...+||||+.|+..+++.||..+|+.||+|.+|.++. .+++|||++....+|.+|+.+|+...+.++.|+|.|+..++.
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~-~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~  497 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP-PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGP  497 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc-CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCc
Confidence            4578999999999999999999999999999998876 589999999999999999999999999999999999999887


Q ss_pred             hh
Q 001991          438 RR  439 (985)
Q Consensus       438 Rr  439 (985)
                      +.
T Consensus       498 ks  499 (894)
T KOG0132|consen  498 KS  499 (894)
T ss_pred             ch
Confidence            65

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.46  E-value=2.2e-07  Score=99.12  Aligned_cols=81  Identities=22%  Similarity=0.406  Sum_probs=75.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      -.+.++|||-.||.+..+.||...|-.||.|.+.++     ++.+|+|+||.|.++.+|+.||..|||..|+-++|+|+.
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            345799999999999999999999999999999865     789999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 001991          347 SIPKDN  352 (985)
Q Consensus       347 a~pk~~  352 (985)
                      ..||+.
T Consensus       362 KRPkda  367 (371)
T KOG0146|consen  362 KRPKDA  367 (371)
T ss_pred             cCcccc
Confidence            888764

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.44  E-value=1.5e-07  Score=99.55  Aligned_cols=162  Identities=19%  Similarity=0.322  Sum_probs=111.6

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      ..+|+++|.+ ...+.|...              |        +-+|.|.-.+      ...|||||+ |++.-|++  |
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~--------------f--------~~yg~~~d~~------mk~gf~fv~-fed~rda~--D   50 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERF--------------F--------KGYGKIPDAD------MKNGFGFVE-FEDPRDAD--D   50 (216)
T ss_pred             CceeecccCCccchhHHHHH--------------H--------hhccccccce------eecccceec-cCchhhhh--c
Confidence            4678888887 545455444              6        5566443321      145699998 66777778  8


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCC----cCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCc
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGS----VVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD  301 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~----~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~  301 (985)
                      |+...+|.+|.+.. +.+......    ....+..-+.    ............+.+.|.+++..+.+.+|.+.|.++|.
T Consensus        51 av~~l~~~~l~~e~-~vve~~r~~----~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~  125 (216)
T KOG0106|consen   51 AVHDLDGKELCGER-LVVEHARGK----RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGE  125 (216)
T ss_pred             ccchhcCceeccee-eeeeccccc----ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCC
Confidence            99999999998544 222221110    0000110000    01111223455688999999999999999999999999


Q ss_pred             EEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          302 IRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       302 I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +.....   ..+++||+|...++|.+|+..|++..+.++.|.+.+.
T Consensus       126 ~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  126 VTYVDA---RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             Cchhhh---hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            954444   7889999999999999999999999999999999544

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.44  E-value=5.3e-08  Score=101.52  Aligned_cols=131  Identities=22%  Similarity=0.296  Sum_probs=103.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ...+||||.|+...|+|+-|.++|-+.|+|..|.+    .++.+ ||||.|+++-.+.-|++.+||..+.++.+.|++-.
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            45699999999999999999999999999999987    33444 99999999999999999999999999988886543


Q ss_pred             CCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHh
Q 001991          349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTL  417 (985)
Q Consensus       349 pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~L  417 (985)
                      -....             -|+..++.+.+.+.|+.-|.+..+++...    .+.++|+.+...-+.-.|+...
T Consensus        86 G~sha-------------pld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y  145 (267)
T KOG4454|consen   86 GNSHA-------------PLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLY  145 (267)
T ss_pred             CCCcc-------------hhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhh
Confidence            21110             16677899999999999999998887543    4567777765555544555433

>smart00361 RRM_1 RNA recognition motif

Probab=98.43  E-value=3.6e-07  Score=80.25  Aligned_cols=56  Identities=23%  Similarity=0.402  Sum_probs=50.3

Q ss_pred             HHHHHHhhc----ccCcEEEEE---e---c--cccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          289 DSELKALFE----QFGDIRTIY---T---A--CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       289 EedLrelFs----~fG~I~sVk---i---t--gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      +++|+++|+    +||.|.++.   +   +  +.++|||||+|.+.++|.+|++.|||..+.|+.|.+
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            678999998    999999884   2   2  678999999999999999999999999999999875

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.41  E-value=5.2e-07  Score=99.62  Aligned_cols=79  Identities=30%  Similarity=0.435  Sum_probs=70.5

Q ss_pred             cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh-CCceeCCceEEEEecc
Q 001991          355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL-NRSDVAGKQIKLEASR  433 (985)
Q Consensus       355 ~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L-NG~~I~Gr~IkV~~A~  433 (985)
                      ..+..-.+|||++|-+.+++.+|+++|.+||+|++|++... +++|||+|.+.++|++|.+++ |...|.|++|+|.|++
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            34566779999999999999999999999999999998875 669999999999999998765 5567899999999999


Q ss_pred             C
Q 001991          434 P  434 (985)
Q Consensus       434 ~  434 (985)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            8

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.41  E-value=4.1e-07  Score=100.39  Aligned_cols=83  Identities=23%  Similarity=0.467  Sum_probs=73.4

Q ss_pred             CCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHH-ccCccccccccccc
Q 001991          267 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA-LQNKPLRRRKLDIH  345 (985)
Q Consensus       267 e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~-Lng~~I~Gr~L~V~  345 (985)
                      ..+.++...++|||++|...++|.+|+++|.+||+|+++.+ -..+++|||+|.+.++|+.|.++ ++...|.|++|.|.
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~-~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRI-LPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEe-ecccccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            45567778899999999999999999999999999999988 45567999999999999999876 45567899999999


Q ss_pred             ccCCC
Q 001991          346 YSIPK  350 (985)
Q Consensus       346 ~a~pk  350 (985)
                      |..++
T Consensus       299 Wg~~~  303 (377)
T KOG0153|consen  299 WGRPK  303 (377)
T ss_pred             eCCCc
Confidence            99883

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.32  E-value=6.4e-07  Score=98.73  Aligned_cols=79  Identities=22%  Similarity=0.360  Sum_probs=72.4

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCC-----CcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~s-----kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      .++.+.|||..|.+-+++++|.-+|+.||+|.+|.++.+.     -.||||+|++.+++++|.-.|++..|..++|.|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            3567899999999999999999999999999999988663     45999999999999999999999999999999999


Q ss_pred             ccCc
Q 001991          432 SRPG  435 (985)
Q Consensus       432 A~~k  435 (985)
                      ++.-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8753

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.31  E-value=6.7e-07  Score=99.22  Aligned_cols=162  Identities=20%  Similarity=0.276  Sum_probs=130.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ....++|++++...+.+.+...++..+|.+....+     ...++|+++|.|...+.+..|+.......+.++.+.....
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            45789999999999999999999999997776643     4678999999999999999999754445666665555444


Q ss_pred             CCCCCC-------Cccccccccee-eecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHH
Q 001991          348 IPKDNP-------SEKDANQGTLV-VFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETAL  414 (985)
Q Consensus       348 ~pk~~~-------~~~~~~~~tLf-V~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI  414 (985)
                      ......       ..... ..++| |.+|+..+++++|+..|..+|.|..+++...     .++||||+|.+...+..|+
T Consensus       166 ~~~~~~~~n~~~~~~~~~-s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~  244 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGP-SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLAL  244 (285)
T ss_pred             ccccccccchhcccccCc-cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHh
Confidence            332211       11122 23455 9999999999999999999999999998654     5789999999999999999


Q ss_pred             HHhCCceeCCceEEEEeccCcc
Q 001991          415 RTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       415 ~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      .. ....+.++++.+.+..+..
T Consensus       245 ~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  245 ND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             hc-ccCcccCcccccccCCCCc
Confidence            97 8889999999999987754

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.28  E-value=4e-06  Score=93.45  Aligned_cols=162  Identities=12%  Similarity=0.177  Sum_probs=118.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhccc-----Cc--EEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQF-----GD--IRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~f-----G~--I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ..-.|-+++||.++++.++.++|..-     |.  |.-|+- +++..|-|||.|..+++|+.|+. .+...|+.|-|.+-
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIElF  238 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIELF  238 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHHH
Confidence            34567789999999999999999732     22  233332 68889999999999999999996 44445554544442


Q ss_pred             ccCC--------------CCC-------C------CcccccccceeeecCCCCCCHHHHHHHhhccCC-EEE--EEEc--
Q 001991          346 YSIP--------------KDN-------P------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE-IRE--IRDT--  393 (985)
Q Consensus       346 ~a~p--------------k~~-------~------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~-I~~--Vri~--  393 (985)
                      .+..              -..       .      ........+|.+++||...+.|+|..+|..|-. |..  |.++  
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N  318 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN  318 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc
Confidence            1110              000       0      011223568999999999999999999999874 332  4443  


Q ss_pred             --CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          394 --QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       394 --~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                        +...|-|||+|.+.|+|..|....+++..+.|.|.|-.+.-.+
T Consensus       319 ~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~ee  363 (508)
T KOG1365|consen  319 GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEE  363 (508)
T ss_pred             CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHH
Confidence              3356789999999999999999999998889999998776544

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.25  E-value=1.5e-05  Score=91.76  Aligned_cols=151  Identities=11%  Similarity=0.160  Sum_probs=102.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEE-EE----eccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRT-IY----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~s-Vk----itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .....|-+++||..||++||.++|+-.-.|.. +.    -.++..|-|||+|++.+.|++|+. -+...|..|-|.|-.+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            45678999999999999999999997655444 21    246678899999999999999995 4444454444433110


Q ss_pred             -----------------------C------------CCC------C------------------C--------Ccc----
Q 001991          348 -----------------------I------------PKD------N------------------P--------SEK----  356 (985)
Q Consensus       348 -----------------------~------------pk~------~------------------~--------~~~----  356 (985)
                                             .            .+.      .                  .        ..+    
T Consensus       180 s~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~  259 (510)
T KOG4211|consen  180 SRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNY  259 (510)
T ss_pred             HHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccccccc
Confidence                                   0            000      0                  0        000    


Q ss_pred             -----------------cccc-cceeeecCCCCCCHHHHHHHhhccCCE-EEEEEcC--CCCcEEEEEEcCHHHHHHHHH
Q 001991          357 -----------------DANQ-GTLVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQ--HKHNHKFIEFYDIRAAETALR  415 (985)
Q Consensus       357 -----------------~~~~-~tLfV~NLp~svTeedLrelFs~fG~I-~~Vri~~--~skGfaFVeF~d~edA~kAI~  415 (985)
                                       .... ..++.++||...++.++..+|+..-.+ ..|.+-+  ...|-|+|+|.+.++|..|+.
T Consensus       260 ~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~t~edav~Ams  339 (510)
T KOG4211|consen  260 PVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFATGEDAVGAMG  339 (510)
T ss_pred             CCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecccchhhHhhhc
Confidence                             0011 357778999999999999999986554 3344433  356789999999999999986


Q ss_pred             HhCCceeCCc
Q 001991          416 TLNRSDVAGK  425 (985)
Q Consensus       416 ~LNG~~I~Gr  425 (985)
                       -++..+..+
T Consensus       340 -kd~anm~hr  348 (510)
T KOG4211|consen  340 -KDGANMGHR  348 (510)
T ss_pred             -cCCcccCcc
Confidence             333344433

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.22  E-value=1.7e-07  Score=112.66  Aligned_cols=139  Identities=14%  Similarity=0.218  Sum_probs=120.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ..++||+||++.+.+++|...|..+|.|..+++     .++.||+|||.|...+++.+|+.......+ |          
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~-g----------  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF-G----------  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh-h----------
Confidence            468999999999999999999999998887753     678899999999999999999964333332 2          


Q ss_pred             CCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCc
Q 001991          350 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGK  425 (985)
Q Consensus       350 k~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr  425 (985)
                                ...|+|.|.|...|.++|+.+|..+|.+++++++.    ..+|.+||.|.+..+|.++...+.+..+.-+
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                      23689999999999999999999999999987653    3678999999999999999999998888888


Q ss_pred             eEEEEeccC
Q 001991          426 QIKLEASRP  434 (985)
Q Consensus       426 ~IkV~~A~~  434 (985)
                      .+.|..+.|
T Consensus       806 ~~~v~vsnp  814 (881)
T KOG0128|consen  806 NGEVQVSNP  814 (881)
T ss_pred             CccccccCC
Confidence            888888776

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.21  E-value=1.2e-06  Score=96.57  Aligned_cols=81  Identities=20%  Similarity=0.393  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...|...|||.-|++-+|+++|.-+|+.||.|.+|.+     ++.+..||||+|++.+++++|.-.|++..|..++|.|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            3457789999999999999999999999999999965     67888899999999999999999999999999999999


Q ss_pred             ccCCCC
Q 001991          346 YSIPKD  351 (985)
Q Consensus       346 ~a~pk~  351 (985)
                      |++...
T Consensus       315 FSQSVs  320 (479)
T KOG0415|consen  315 FSQSVS  320 (479)
T ss_pred             hhhhhh
Confidence            987543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.15  E-value=4.1e-06  Score=87.30  Aligned_cols=81  Identities=19%  Similarity=0.341  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhccc-CcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQF-GDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~f-G~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      ........+||..+|.-+.+.++..+|.+| |.|+.+++     +|.++|||||+|++.+.|.-|-+.||+..+.++.|.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            345567889999999999999999999999 77777765     799999999999999999999999999999999999


Q ss_pred             ccccCCC
Q 001991          344 IHYSIPK  350 (985)
Q Consensus       344 V~~a~pk  350 (985)
                      |++-.|.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9987654

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.13  E-value=1.8e-06  Score=92.11  Aligned_cols=160  Identities=18%  Similarity=0.218  Sum_probs=118.6

Q ss_pred             EEEEecCCCCCCHHH-H--HHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          277 TLFVRNINSNVEDSE-L--KALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       277 tLfVgNLP~~vTEed-L--relFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .+++.++-..+..+- |  ...|+.|-.+...++    .+..++++|+.|.....-.++-..-+++++.-.++++.-...
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            344555555554443 2  455555554443322    466788999999988888888877788888877777655544


Q ss_pred             CCCCC--cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCcee
Q 001991          350 KDNPS--EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDV  422 (985)
Q Consensus       350 k~~~~--~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I  422 (985)
                      -.++.  +.+...-.||.+.|..+++++.|-..|.+|-.....+++     .+++||+||.|.+..++..|+++|||+.+
T Consensus       178 wedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyV  257 (290)
T KOG0226|consen  178 WEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYV  257 (290)
T ss_pred             cCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccccc
Confidence            44432  344566799999999999999999999998765554444     44789999999999999999999999999


Q ss_pred             CCceEEEEeccCcc
Q 001991          423 AGKQIKLEASRPGG  436 (985)
Q Consensus       423 ~Gr~IkV~~A~~k~  436 (985)
                      +.++|++..+.-++
T Consensus       258 gsrpiklRkS~wke  271 (290)
T KOG0226|consen  258 GSRPIKLRKSEWKE  271 (290)
T ss_pred             ccchhHhhhhhHHh
Confidence            99999987665544

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.04  E-value=6.3e-06  Score=95.17  Aligned_cols=75  Identities=20%  Similarity=0.380  Sum_probs=69.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .++|+|.+|...+-..+|+.+|++||+|+-.+++.+     -++|+||++.+.++|.++|..|+.++|.|+.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            468999999999999999999999999999888644     478999999999999999999999999999999999875

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=98.01  E-value=5.6e-06  Score=85.89  Aligned_cols=91  Identities=19%  Similarity=0.356  Sum_probs=60.3

Q ss_pred             CCceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEec--cc--ccccceeEEEEEecCCchhhHHHHHHhcCCcccCCC
Q 001991          808 DSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLP--ID--FKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFN  883 (985)
Q Consensus       808 d~rTTvMirNIPnk~t~~~L~~~id~~~~g~yDF~Ylp--iD--f~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~  883 (985)
                      ..++.|.||++|..+|++.+++.|+......++|-|.+  .+  --..+-...|||||.+.+++..|.+.|+|+.|..-.
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            46889999999999999999998887666665555544  22  223445788999999999999999999999998665


Q ss_pred             Cc-cEEEEEeecccCH
Q 001991          884 SE-KVASLAYARIQGK  898 (985)
Q Consensus       884 s~-K~~~v~yA~iQG~  898 (985)
                      .. -++.|.||-.|-.
T Consensus        85 g~~~~~~VE~Apyqk~  100 (176)
T PF03467_consen   85 GNEYPAVVEFAPYQKV  100 (176)
T ss_dssp             S-EEEEEEEE-SS---
T ss_pred             CCCcceeEEEcchhcc
Confidence            54 5899999998754

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.98  E-value=1.2e-05  Score=95.21  Aligned_cols=85  Identities=20%  Similarity=0.383  Sum_probs=75.1

Q ss_pred             CCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--------ccccceEEEEEeCCHHHHHHHHHHccCccc
Q 001991          266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--------ACKHRGFVMISYYDIRAARNAMKALQNKPL  337 (985)
Q Consensus       266 ~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--------tgksrGfAFV~F~d~esA~kAi~~Lng~~I  337 (985)
                      +....++..+++|||+||++.++++.|...|..||+|.++++        ....+.++||.|.+..+|++|++.|+|..+
T Consensus       165 gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv  244 (877)
T KOG0151|consen  165 GSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV  244 (877)
T ss_pred             CcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee
Confidence            444456677899999999999999999999999999999986        244567999999999999999999999999


Q ss_pred             ccccccccccCCC
Q 001991          338 RRRKLDIHYSIPK  350 (985)
Q Consensus       338 ~Gr~L~V~~a~pk  350 (985)
                      .+..+++.|+++.
T Consensus       245 ~~~e~K~gWgk~V  257 (877)
T KOG0151|consen  245 MEYEMKLGWGKAV  257 (877)
T ss_pred             eeeeeeecccccc
Confidence            9999999998543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=97.97  E-value=1.9e-05  Score=82.40  Aligned_cols=79  Identities=19%  Similarity=0.273  Sum_probs=71.1

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhcc-CCEEEEEE-----cCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIY-GEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~f-G~I~~Vri-----~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ....+.++|..+|..+.+.++...|.+| |.|..+++     +++++|||||+|++.+.|.-|-+.||+..+.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3456789999999999999999999998 77888877     35689999999999999999999999999999999999


Q ss_pred             eccCc
Q 001991          431 ASRPG  435 (985)
Q Consensus       431 ~A~~k  435 (985)
                      +-.+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            98775

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.90  E-value=1.8e-06  Score=97.03  Aligned_cols=149  Identities=17%  Similarity=0.337  Sum_probs=123.0

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccC--cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCc-ccccccccccccCCCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFG--DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK-PLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG--~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~-~I~Gr~L~V~~a~pk~~  352 (985)
                      .++|++||.+.++.++|..+|...-  --..+-   ...||+||.+.+...|.+|++.++|+ ++.|+++.|.++.++..
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            4689999999999999999997541  000011   24589999999999999999999995 68999999999887765


Q ss_pred             CCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-C-CcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-K-HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       353 ~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-s-kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      +      .+.+-|.|+|+..-++.|..+..+||.+..|..+.- + .-..-|+|...+.+..||..|+|..+....++|.
T Consensus        79 r------srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~  152 (584)
T KOG2193|consen   79 R------SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVG  152 (584)
T ss_pred             H------hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcc
Confidence            4      445999999999999999999999999998865432 2 1234578999999999999999999999999999


Q ss_pred             ecc
Q 001991          431 ASR  433 (985)
Q Consensus       431 ~A~  433 (985)
                      |--
T Consensus       153 YiP  155 (584)
T KOG2193|consen  153 YIP  155 (584)
T ss_pred             cCc
Confidence            853

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.90  E-value=1.7e-05  Score=91.67  Aligned_cols=76  Identities=18%  Similarity=0.344  Sum_probs=68.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .-.++|||.+|...+-..+|+++|++||+|+-.++     +.--++|+||++.+.++|.+||+.|+-.+|.|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34699999999999999999999999999998765     2335789999999999999999999999999999999776


Q ss_pred             C
Q 001991          348 I  348 (985)
Q Consensus       348 ~  348 (985)
                      +
T Consensus       483 K  483 (940)
T KOG4661|consen  483 K  483 (940)
T ss_pred             c
Confidence            4

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.86  E-value=2e-05  Score=93.60  Aligned_cols=78  Identities=28%  Similarity=0.381  Sum_probs=71.3

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC--------CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEE
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--------HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  428 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~--------~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~Ik  428 (985)
                      +...++|||.||++.++++.|...|+.||.|..|+++-        ..+.+|||-|-+..+|++|++.|+|..+.+..++
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            45677999999999999999999999999999999862        2467899999999999999999999999999999


Q ss_pred             EEeccC
Q 001991          429 LEASRP  434 (985)
Q Consensus       429 V~~A~~  434 (985)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999964

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.77  E-value=4.3e-05  Score=82.77  Aligned_cols=80  Identities=26%  Similarity=0.377  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .+....+|+|.|||..|+++||+++|+.||.+..+-+    .+.+.|.|-|.|...++|.+|++.+++..+.|+.|.+..
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445588999999999999999999999998887755    688899999999999999999999999999999998876


Q ss_pred             cCCC
Q 001991          347 SIPK  350 (985)
Q Consensus       347 a~pk  350 (985)
                      ..+.
T Consensus       159 i~~~  162 (243)
T KOG0533|consen  159 ISSP  162 (243)
T ss_pred             ecCc
Confidence            6543

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.72  E-value=3.6e-05  Score=80.87  Aligned_cols=76  Identities=20%  Similarity=0.187  Sum_probs=68.3

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ..+||||.|+...++++-|.++|-+.|.|..|.|...   ...||||.|.++-...-|++.|||..+.+..|+|.+-.-
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            4579999999999999999999999999999988653   223999999999999999999999999999999988543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.68  E-value=0.00011  Score=77.35  Aligned_cols=78  Identities=21%  Similarity=0.272  Sum_probs=65.3

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEE--EEcCCC----CcEEEEEEcCHHHHHHHHHHhCCceeC---CceEEE
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHK----HNHKFIEFYDIRAAETALRTLNRSDVA---GKQIKL  429 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~V--ri~~~s----kGfaFVeF~d~edA~kAI~~LNG~~I~---Gr~IkV  429 (985)
                      .-+||||.+||.++...+|+.+|..|-..+..  +...+.    +-+|||.|.+..+|.+|+.+|||..|+   +..|++
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            35799999999999999999999998655553  333322    358999999999999999999999985   899999


Q ss_pred             EeccCcc
Q 001991          430 EASRPGG  436 (985)
Q Consensus       430 ~~A~~k~  436 (985)
                      ++++...
T Consensus       113 ElAKSNt  119 (284)
T KOG1457|consen  113 ELAKSNT  119 (284)
T ss_pred             eehhcCc
Confidence            9998654

>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=97.66  E-value=0.00019  Score=65.58  Aligned_cols=69  Identities=23%  Similarity=0.308  Sum_probs=49.1

Q ss_pred             cceeeecCCCCCCHH----HHHHHhhccC-CEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          361 GTLVVFNLDSSVSTE----ELHQIFGIYG-EIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       361 ~tLfV~NLp~svTee----dLrelFs~fG-~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ..|+|.|||.+.+..    .|++++.-+| +|.+|.     .+.|+|.|.+.+.|++|.+.|+|..+-|.+|.|.+...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-----~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-----GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-----CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            469999999998864    4677777776 677763     68999999999999999999999999999999999743

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=4.8e-05  Score=88.26  Aligned_cols=74  Identities=26%  Similarity=0.414  Sum_probs=62.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---c--cccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---A--CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---t--gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ...+|||+|||.++++++|+++|.+||+|+...+   .  ++..+||||+|++.++++.|+.+ +-..|++++|.|+--.
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            3456999999999999999999999999998765   2  34448999999999999999974 4778889999986443

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.62  E-value=0.00016  Score=78.48  Aligned_cols=78  Identities=21%  Similarity=0.322  Sum_probs=69.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ...+|+|.|||..|++++|+++|..||.++.+-+..+    +.|.|-|.|...++|.+|++.+||..++|+.+++....+
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            3468999999999999999999999998888776533    568999999999999999999999999999999988765


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            43

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.61  E-value=7.8e-05  Score=86.52  Aligned_cols=74  Identities=26%  Similarity=0.464  Sum_probs=63.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC----C-CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ----H-KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~----~-skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      .+|||+|||.+++.++|+++|..||.|+..+|..    . ..+||||+|.+.++++.||.+ +-..|++++|.|+-.++.
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            4699999999999999999999999999866542    1 237999999999999999994 477899999999876553

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.59  E-value=0.00012  Score=81.45  Aligned_cols=74  Identities=15%  Similarity=0.344  Sum_probs=65.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEE--------EEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~--------Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                      ...|||.|||.++|.+++.++|+++|.|..        |++..+    -+|-|.|+|...++..-|++.|++..+.|++|
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~  213 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKL  213 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEE
Confidence            346999999999999999999999999865        555443    46779999999999999999999999999999


Q ss_pred             EEEecc
Q 001991          428 KLEASR  433 (985)
Q Consensus       428 kV~~A~  433 (985)
                      +|+.|+
T Consensus       214 rVerAk  219 (382)
T KOG1548|consen  214 RVERAK  219 (382)
T ss_pred             EEehhh
Confidence            999884

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.48  E-value=0.0003  Score=78.91  Aligned_cols=159  Identities=16%  Similarity=0.221  Sum_probs=112.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhccc-----CcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQF-----GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~f-----G~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..+..|-.++||+.-++.+|..+|+-.     |.+......+...|.|.|.|.+.|.-+.|++ -+...+.++.|.|-.+
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka  136 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKA  136 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeecc
Confidence            345566778999999999999999733     3334444467888999999999999999995 5667777888877544


Q ss_pred             CCCCC---------CC---cccccccceeeecCCCCCCHHHHHHHhhcc----CCEEEEEEc----CCCCcEEEEEEcCH
Q 001991          348 IPKDN---------PS---EKDANQGTLVVFNLDSSVSTEELHQIFGIY----GEIREIRDT----QHKHNHKFIEFYDI  407 (985)
Q Consensus       348 ~pk~~---------~~---~~~~~~~tLfV~NLp~svTeedLrelFs~f----G~I~~Vri~----~~skGfaFVeF~d~  407 (985)
                      ...+-         ..   ....++-.|.+++||.++++.++.++|.+-    |..+.|-++    ++..|-|||.|..+
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            43221         00   111234578889999999999999999732    222333222    33567899999999


Q ss_pred             HHHHHHHHHhCCceeCCceEEEEecc
Q 001991          408 RAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       408 edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ++|+.|+. -|...|+-|-|.+-.+.
T Consensus       217 e~aq~aL~-khrq~iGqRYIElFRST  241 (508)
T KOG1365|consen  217 EDAQFALR-KHRQNIGQRYIELFRST  241 (508)
T ss_pred             HHHHHHHH-HHHHHHhHHHHHHHHHh
Confidence            99999998 56666666666554443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.44  E-value=0.00014  Score=78.73  Aligned_cols=79  Identities=23%  Similarity=0.388  Sum_probs=69.9

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      +......+||+|++..+|.+++..+|+.||.|..|.+..     +.++|+||+|.+.+.+++|++ |||..|.|+.|.|.
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            345667899999999999999999999999998766543     468999999999999999999 99999999999999


Q ss_pred             eccCc
Q 001991          431 ASRPG  435 (985)
Q Consensus       431 ~A~~k  435 (985)
                      +.+-.
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            97653

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

Probab=97.43  E-value=0.00058  Score=64.43  Aligned_cols=81  Identities=19%  Similarity=0.194  Sum_probs=65.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhhcc--CCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeC----CceEEE
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIY--GEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVA----GKQIKL  429 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~f--G~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~----Gr~IkV  429 (985)
                      +||.|+|||...|.++|.+++...  |...-+.++-+     +.|||||.|.+++.|.+-.+.++|+...    .|...|
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            589999999999999999998763  55544554432     5799999999999999999999999774    688899


Q ss_pred             EeccCcchhhhh
Q 001991          430 EASRPGGARRFM  441 (985)
Q Consensus       430 ~~A~~k~~Rrl~  441 (985)
                      .||+-.+...++
T Consensus        82 ~yAriQG~~alv   93 (97)
T PF04059_consen   82 SYARIQGKDALV   93 (97)
T ss_pred             ehhHhhCHHHHH
Confidence            999876644444

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

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.35  E-value=8.6e-05  Score=83.38  Aligned_cols=157  Identities=18%  Similarity=0.195  Sum_probs=116.2

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEec--------cccceEEEEEeCCHHHHHHHHHHccCccccccccccc-c
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTA--------CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH-Y  346 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkit--------gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~-~  346 (985)
                      ..|-|.||.+.+|.++++.+|...|+|..+.+-        ......|||.|.|...+..|-. |.+.++-++.|.|- |
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            489999999999999999999999999998751        2345689999999999998874 77766666655552 2


Q ss_pred             cCCCCC----------------------------CC--cc---------------------cccccceeeecCCCCCCHH
Q 001991          347 SIPKDN----------------------------PS--EK---------------------DANQGTLVVFNLDSSVSTE  375 (985)
Q Consensus       347 a~pk~~----------------------------~~--~~---------------------~~~~~tLfV~NLp~svTee  375 (985)
                      ..+...                            +.  ..                     ..-.++++|.+|+..+...
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            111000                            00  00                     0012589999999999999


Q ss_pred             HHHHHhhccCCEEEEEEcC-CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          376 ELHQIFGIYGEIREIRDTQ-HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       376 dLrelFs~fG~I~~Vri~~-~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ++-+.|..+|+|...++-. ....+|-|+|........|++ ++|.++.-....+....|
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            9999999999999877643 345688899999999999998 788877644444443333

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.35  E-value=0.00023  Score=76.96  Aligned_cols=78  Identities=17%  Similarity=0.308  Sum_probs=69.1

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ..+...+.+||+|+...+|.+++...|+.||.|..+.+     .+..+||+||+|.+.+.+++|+. |++..|.|+.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            45667899999999999999999999999999975533     56689999999999999999997 9999999999999


Q ss_pred             cccC
Q 001991          345 HYSI  348 (985)
Q Consensus       345 ~~a~  348 (985)
                      .+..
T Consensus       175 t~~r  178 (231)
T KOG4209|consen  175 TLKR  178 (231)
T ss_pred             eeee
Confidence            7654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.30  E-value=0.00068  Score=75.60  Aligned_cols=78  Identities=22%  Similarity=0.440  Sum_probs=69.0

Q ss_pred             CCcEEE-EecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          274 PSRTLF-VRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       274 ~srtLf-VgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +..++| |++|+.++++++|+..|..+|.|..+++     ++..+|||||.|.+...+..|+.. +...+.++.+.+.+.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            445555 9999999999999999999999999976     678899999999999999999976 889999999999988


Q ss_pred             CCCCC
Q 001991          348 IPKDN  352 (985)
Q Consensus       348 ~pk~~  352 (985)
                      .+...
T Consensus       262 ~~~~~  266 (285)
T KOG4210|consen  262 EPRPK  266 (285)
T ss_pred             CCCcc
Confidence            76643

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.26  E-value=0.00045  Score=82.23  Aligned_cols=166  Identities=13%  Similarity=0.020  Sum_probs=118.9

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhccc-Cc---EEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQF-GD---IRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~f-G~---I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .-....+.+-+++.+.+.++.+++++|... -.   |..-.+.+...|-++|.|....++++|++ -|...+..|.+.|.
T Consensus       306 qvv~d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~  384 (944)
T KOG4307|consen  306 QVVSDKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTG  384 (944)
T ss_pred             cccchhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeec
Confidence            334455667778999999999999999732 22   22223344557999999999999999985 55555555555552


Q ss_pred             ccCCC------------C-----------------CC------CcccccccceeeecCCCCCCHHHHHHHhhccCCEEE-
Q 001991          346 YSIPK------------D-----------------NP------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-  389 (985)
Q Consensus       346 ~a~pk------------~-----------------~~------~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~-  389 (985)
                      .....            .                 ..      .-.......|||..||..+++.++.++|...-.|++ 
T Consensus       385 P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~  464 (944)
T KOG4307|consen  385 PPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDF  464 (944)
T ss_pred             CCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhhe
Confidence            21100            0                 00      000112458999999999999999999998777766 


Q ss_pred             EEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          390 IRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       390 Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      |.+.+-    .++-|||+|..++++.+|...-+...++.+.|+|.-...+.
T Consensus       465 I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~  515 (944)
T KOG4307|consen  465 IELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYA  515 (944)
T ss_pred             eEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhHH
Confidence            666533    35679999999999999998888888899999998765443

>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=97.18  E-value=0.0011  Score=60.76  Aligned_cols=69  Identities=20%  Similarity=0.385  Sum_probs=48.7

Q ss_pred             cEEEEecCCCCCCHHHHH----HhhcccC-cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          276 RTLFVRNINSNVEDSELK----ALFEQFG-DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLr----elFs~fG-~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ..|||.|||.+.+...|+    .++..|| .|..|     ..+.|+|.|.+.+.|.+|.+.|+|..+.|++|.|.|...
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            469999999999877655    6666886 66655     247899999999999999999999999999999998743

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.17  E-value=0.0004  Score=74.66  Aligned_cols=77  Identities=19%  Similarity=0.358  Sum_probs=66.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE-----EeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV-----kitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....-+||.+.|.-+++++-|...|.+|-.....     +-+++++||+||.|.+.+++..|+++|+|+.++.+.|.+.-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            3456789999999999999999999988654332     23799999999999999999999999999999999998865


Q ss_pred             cC
Q 001991          347 SI  348 (985)
Q Consensus       347 a~  348 (985)
                      +.
T Consensus       267 S~  268 (290)
T KOG0226|consen  267 SE  268 (290)
T ss_pred             hh
Confidence            53

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.16  E-value=0.0018  Score=75.67  Aligned_cols=159  Identities=15%  Similarity=0.177  Sum_probs=96.0

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCC----hhhhhccCCCC---eeeeecCC
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPD----EDDLFSGVTDD---MGHNFQAN  216 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpd----edDL~sG~SkG---fGFV~ff~  216 (985)
                      ...+||++.|++ ++++.+...              |        ..||.+.-|    ....-....+|   |-|..| +
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~--------------F--------~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvF-e  314 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINAS--------------F--------GQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVF-E  314 (520)
T ss_pred             cccceeecCCCccccHHHHHhh--------------c--------ccccceEeecCCCccccccCCCCCcccEEEEEe-c
Confidence            345799999999 888888877              7        445544431    11111223555   888884 4


Q ss_pred             Chhhhh-hhHHHhccCC-eeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHH
Q 001991          217 TVDDLE-DFDLFSSGGG-MELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKA  294 (985)
Q Consensus       217 t~Edae-e~~ai~~~nG-~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLre  294 (985)
                      .+..+. -+++.....+ ..|.    ++......... .+......++....+....-.+.+||||++||.-++.++|..
T Consensus       315 ~E~sV~~Ll~aC~~~~~~~yf~----vss~~~k~k~V-QIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~  389 (520)
T KOG0129|consen  315 DERSVQSLLSACSEGEGNYYFK----VSSPTIKDKEV-QIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAM  389 (520)
T ss_pred             chHHHHHHHHHHhhcccceEEE----EecCcccccce-eEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHH
Confidence            444444 2233332222 1221    11111111000 000011111222223445667889999999999999999999


Q ss_pred             hhc-ccCcEEEEEe--c---cccceEEEEEeCCHHHHHHHHHH
Q 001991          295 LFE-QFGDIRTIYT--A---CKHRGFVMISYYDIRAARNAMKA  331 (985)
Q Consensus       295 lFs-~fG~I~sVki--t---gksrGfAFV~F~d~esA~kAi~~  331 (985)
                      +|+ -||.|..+-|  +   +-.+|-|=|+|.+..+-.+||.+
T Consensus       390 imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  390 IMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             HHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            999 8999998755  2   45789999999999999999963

>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=97.09  E-value=0.001  Score=63.67  Aligned_cols=78  Identities=22%  Similarity=0.379  Sum_probs=49.1

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCc-----eeCCceEEEEeccCc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS-----DVAGKQIKLEASRPG  435 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~-----~I~Gr~IkV~~A~~k  435 (985)
                      ..|+|.+++..++.++|++.|++||.|..|.+.. ....|||.|.+.++|++|+..+...     .|.+..+.++.-.-.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~-G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLeGe   80 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR-GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLEGE   80 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T-T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---HH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC-CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECCCH
Confidence            3588999999999999999999999999998765 3558999999999999999887543     677888877765544


Q ss_pred             chhh
Q 001991          436 GARR  439 (985)
Q Consensus       436 ~~Rr  439 (985)
                      ++..
T Consensus        81 eE~~   84 (105)
T PF08777_consen   81 EEEE   84 (105)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.93  E-value=0.00083  Score=74.36  Aligned_cols=86  Identities=26%  Similarity=0.324  Sum_probs=68.1

Q ss_pred             CcEEEEecCCCCCCHHHH------HHhhcccCcEEEEEecccc------ce--EEEEEeCCHHHHHHHHHHccCcccccc
Q 001991          275 SRTLFVRNINSNVEDSEL------KALFEQFGDIRTIYTACKH------RG--FVMISYYDIRAARNAMKALQNKPLRRR  340 (985)
Q Consensus       275 srtLfVgNLP~~vTEedL------relFs~fG~I~sVkitgks------rG--fAFV~F~d~esA~kAi~~Lng~~I~Gr  340 (985)
                      ..-+||-+||+.+..+++      .++|.+||.|..|.+.++-      .+  =.||+|.+.|+|.+||.+.+|..++||
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            467899999999888773      2799999999998763321      12  249999999999999999999999999


Q ss_pred             cccccccCCCCCCCcccccccceeeecCC
Q 001991          341 KLDIHYSIPKDNPSEKDANQGTLVVFNLD  369 (985)
Q Consensus       341 ~L~V~~a~pk~~~~~~~~~~~tLfV~NLp  369 (985)
                      .|+..|...|         -++-|++|++
T Consensus       194 ~lkatYGTTK---------YCtsYLRn~~  213 (480)
T COG5175         194 VLKATYGTTK---------YCTSYLRNAV  213 (480)
T ss_pred             eEeeecCchH---------HHHHHHcCCC
Confidence            9999887543         3456666653

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.90  E-value=0.0012  Score=80.59  Aligned_cols=75  Identities=17%  Similarity=0.217  Sum_probs=66.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ...|+|+|.|...|.++|+.++..+|.+.++.+    .++.+|.|+|.|.+..+|.+++.......+..+.+.|..+.|
T Consensus       736 K~~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  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            356899999999999999999999999998864    688999999999999999999988888888888888877655

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.78  E-value=0.0043  Score=68.90  Aligned_cols=94  Identities=18%  Similarity=0.301  Sum_probs=71.2

Q ss_pred             cccceeeecCCCCCCHHH----H--HHHhhccCCEEEEEEcCCC------Cc-E-EEEEEcCHHHHHHHHHHhCCceeCC
Q 001991          359 NQGTLVVFNLDSSVSTEE----L--HQIFGIYGEIREIRDTQHK------HN-H-KFIEFYDIRAAETALRTLNRSDVAG  424 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeed----L--relFs~fG~I~~Vri~~~s------kG-f-aFVeF~d~edA~kAI~~LNG~~I~G  424 (985)
                      ..+-+||-+|++.+-.|+    |  .++|.+||+|..|.+.++-      .+ + .||+|.+.|+|.+||.+.+|..++|
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            455789999999887776    2  5799999999998875431      12 3 4999999999999999999999999


Q ss_pred             ceEEEEeccCcchhh-hhhhhhhhccCCCcc
Q 001991          425 KQIKLEASRPGGARR-FMVQSEQEQDDLNLC  454 (985)
Q Consensus       425 r~IkV~~A~~k~~Rr-l~qq~eq~q~e~nLy  454 (985)
                      |.|+..|...|---. |+  -.+++...-+|
T Consensus       193 r~lkatYGTTKYCtsYLR--n~~CpNp~CMy  221 (480)
T COG5175         193 RVLKATYGTTKYCTSYLR--NAVCPNPDCMY  221 (480)
T ss_pred             ceEeeecCchHHHHHHHc--CCCCCCCCeee
Confidence            999999987755333 22  23444444444

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.54  E-value=0.0029  Score=72.29  Aligned_cols=73  Identities=30%  Similarity=0.411  Sum_probs=59.5

Q ss_pred             CCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC------------------CCcEEEEEEcCHHHH
Q 001991          349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------------------KHNHKFIEFYDIRAA  410 (985)
Q Consensus       349 pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~------------------skGfaFVeF~d~edA  410 (985)
                      |-.+........++|.+.|||.+-.-+.|.++|+.+|.|+.|+|..-                  .+-+|+|+|+..+.|
T Consensus       220 Plp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A  299 (484)
T KOG1855|consen  220 PLPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAA  299 (484)
T ss_pred             CCCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHH
Confidence            33333444567889999999999999999999999999999998532                  134699999999999


Q ss_pred             HHHHHHhCCce
Q 001991          411 ETALRTLNRSD  421 (985)
Q Consensus       411 ~kAI~~LNG~~  421 (985)
                      .+|.+.||...
T Consensus       300 ~KA~e~~~~e~  310 (484)
T KOG1855|consen  300 RKARELLNPEQ  310 (484)
T ss_pred             HHHHHhhchhh
Confidence            99999886543

>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=96.43  E-value=0.0064  Score=58.21  Aligned_cols=59  Identities=17%  Similarity=0.276  Sum_probs=39.6

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK  335 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~  335 (985)
                      ..|.|.+++..++.++|++.|++||+|..|.. .+...-|||.|.+.++|++|++.+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~-~~G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDF-SRGDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEe-cCCCCEEEEEECCcchHHHHHHHHHhc
Confidence            46899999999999999999999999999988 334458999999999999999876544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>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=96.40  E-value=0.0082  Score=57.07  Aligned_cols=73  Identities=19%  Similarity=0.274  Sum_probs=54.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEE------------EcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCc-
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR------------DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGK-  425 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vr------------i~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr-  425 (985)
                      ....|.|.+.|+. ....+.+.|++||+|.+..            -.+...++..|+|+++.+|.+||+ .||..|.|. 
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            3456899999998 4567788999999998875            223457799999999999999999 899999885 


Q ss_pred             eEEEEecc
Q 001991          426 QIKLEASR  433 (985)
Q Consensus       426 ~IkV~~A~  433 (985)
                      .+-|.+.+
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            55577764

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.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.18  E-value=0.011  Score=49.86  Aligned_cols=52  Identities=23%  Similarity=0.374  Sum_probs=43.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHH
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL  414 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI  414 (985)
                      +.|-|.+.+.+..+ .+...|..||+|..+.+. ....+.||+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            46788888877664 455588899999999876 34779999999999999995

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.14  E-value=0.0099  Score=50.04  Aligned_cols=52  Identities=21%  Similarity=0.451  Sum_probs=43.5

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHH
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAM  329 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi  329 (985)
                      +.|-|.+.+++..+ .+...|..||+|..+.++ ....+.+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            57889999986664 455589999999999984 55779999999999999985

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.11  E-value=0.005  Score=70.45  Aligned_cols=78  Identities=26%  Similarity=0.384  Sum_probs=61.4

Q ss_pred             CCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccc------------------cceEEEEEeCCHHHHHHH
Q 001991          267 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK------------------HRGFVMISYYDIRAARNA  328 (985)
Q Consensus       267 e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgk------------------srGfAFV~F~d~esA~kA  328 (985)
                      +...++.++++|.+-|||.+-.-+.|.++|+.+|.|..|++...                  .+-+|+|+|+..+.|.+|
T Consensus       223 ~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA  302 (484)
T KOG1855|consen  223 EFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKA  302 (484)
T ss_pred             CccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHH
Confidence            33446679999999999999999999999999999999987111                  245899999999999999


Q ss_pred             HHHccCcccccccccc
Q 001991          329 MKALQNKPLRRRKLDI  344 (985)
Q Consensus       329 i~~Lng~~I~Gr~L~V  344 (985)
                      .+.|+...-...-|+|
T Consensus       303 ~e~~~~e~~wr~glkv  318 (484)
T KOG1855|consen  303 RELLNPEQNWRMGLKV  318 (484)
T ss_pred             HHhhchhhhhhhcchh
Confidence            9877654433333333

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.03  E-value=0.0041  Score=67.18  Aligned_cols=68  Identities=22%  Similarity=0.393  Sum_probs=60.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCC---------------CcE--EEEEEcCHHHHHHHHHHhCCce
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK---------------HNH--KFIEFYDIRAAETALRTLNRSD  421 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~s---------------kGf--aFVeF~d~edA~kAI~~LNG~~  421 (985)
                      ..+.||+++||+.+....|+++|+.||.|-.|.+.+..               ..|  |+|+|.+...|.+....||+..
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            56799999999999999999999999999999886431               112  8999999999999999999999


Q ss_pred             eCCce
Q 001991          422 VAGKQ  426 (985)
Q Consensus       422 I~Gr~  426 (985)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99865

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.84  E-value=0.011  Score=64.12  Aligned_cols=89  Identities=22%  Similarity=0.299  Sum_probs=73.7

Q ss_pred             HHHHHHHHHccCcccccccccccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC----CCCc
Q 001991          323 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ----HKHN  398 (985)
Q Consensus       323 esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~----~skG  398 (985)
                      .-|..|..+|++....++.++|.|+..           ..|||.||..-++.|.|.+.|+.||.|....+.-    ...+
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            347777788999999999999999853           4799999999999999999999999997733322    2445


Q ss_pred             EEEEEEcCHHHHHHHHHHhCCcee
Q 001991          399 HKFIEFYDIRAAETALRTLNRSDV  422 (985)
Q Consensus       399 faFVeF~d~edA~kAI~~LNG~~I  422 (985)
                      -++|+|...-.|.+|++.++-.-+
T Consensus        74 eg~v~~~~k~~a~~a~rr~~~~g~   97 (275)
T KOG0115|consen   74 EGIVEFAKKPNARKAARRCREGGF   97 (275)
T ss_pred             cchhhhhcchhHHHHHHHhccCcc
Confidence            789999999999999998754433

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=95.78  E-value=0.0082  Score=67.65  Aligned_cols=78  Identities=21%  Similarity=0.282  Sum_probs=67.5

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEE--------EEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGK  425 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~--------Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr  425 (985)
                      ...+|||.+|+..+++++|.++|.++|.|..        |.+.     ...|+-|.|.|.|...|+.|+.-++++.+.|.
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            4459999999999999999999999999865        2222     23678899999999999999999999999999


Q ss_pred             eEEEEeccCcc
Q 001991          426 QIKLEASRPGG  436 (985)
Q Consensus       426 ~IkV~~A~~k~  436 (985)
                      +|+|.++..+.
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99999987654

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=95.78  E-value=0.0087  Score=67.46  Aligned_cols=79  Identities=20%  Similarity=0.278  Sum_probs=69.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE-------------eccccceEEEEEeCCHHHHHHHHHHccCcccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-------------TACKHRGFVMISYYDIRAARNAMKALQNKPLR  338 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk-------------itgksrGfAFV~F~d~esA~kAi~~Lng~~I~  338 (985)
                      ....-+|||-+||..+++.+|.++|.+||.|..=+             .+.+.|+-|.|+|.+...|+.|+..++++.+.
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            44567999999999999999999999999886431             26789999999999999999999999999999


Q ss_pred             cccccccccCCC
Q 001991          339 RRKLDIHYSIPK  350 (985)
Q Consensus       339 Gr~L~V~~a~pk  350 (985)
                      +..|+|..+..+
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            999999877544

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.77  E-value=0.011  Score=72.87  Aligned_cols=81  Identities=25%  Similarity=0.369  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~  348 (985)
                      ...+.+.+||++|.+.+....|...|..||.|..|.+ ....-||||.|++...|+.|++.|.|..|.+  +.+.|.|+.
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            4457899999999999999999999999999999988 4556699999999999999999999999986  678888886


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      +...
T Consensus       530 ~~~~  533 (975)
T KOG0112|consen  530 PPGA  533 (975)
T ss_pred             CCCC
Confidence            5543

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]

Probab=95.66  E-value=0.0057  Score=69.52  Aligned_cols=74  Identities=19%  Similarity=0.406  Sum_probs=61.6

Q ss_pred             CceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEe-cccccccce-eEEEEEecCCchhhHHHHHHhcCCcccCCC
Q 001991          809 SRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYL-PIDFKNKCN-VGYAFINMIDPRQIIPFHQAFNGKKWEKFN  883 (985)
Q Consensus       809 ~rTTvMirNIPnk~t~~~L~~~id~~~~g~yDF~Yl-piDf~~~~N-~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~  883 (985)
                      ....|.||++|+++|.+.|++.||- +...+.|-|. |-|+....+ .+.|||||..+.++..|.+.|.|+.+-.-.
T Consensus         6 ~~~Kvv~rrlpp~l~~~~~~eqi~p-~~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~ifld~K   81 (376)
T KOG1295|consen    6 AKVKVVVRRLPPKLTEEQLLEQINP-FPEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYIFLDNK   81 (376)
T ss_pred             cceeeeeecCCCcccHHHHhhhcCC-CccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceEEecCC
Confidence            4567999999999999999999998 7788888754 466654444 677999999999999999999999876443

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.50  E-value=0.0069  Score=65.59  Aligned_cols=62  Identities=27%  Similarity=0.370  Sum_probs=51.5

Q ss_pred             HHHHHHhh-ccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          375 EELHQIFG-IYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       375 edLrelFs-~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ++|...|+ +||+|+++.|..+    -.|-+||.|...++|++|++.||+..+.|++|..++..-..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCc
Confidence            45555666 8999999876543    35679999999999999999999999999999999976433

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.46  E-value=0.03  Score=61.61  Aligned_cols=62  Identities=18%  Similarity=0.210  Sum_probs=52.1

Q ss_pred             HHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          374 TEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       374 eedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ++++++.+++||+|..|.|...      ..--.||+|...++|.+|+-.|||+.|+|+.++..|..-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~e  367 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLE  367 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHH
Confidence            5788999999999998766432      1123799999999999999999999999999999987643

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.41  E-value=0.0092  Score=64.57  Aligned_cols=69  Identities=17%  Similarity=0.401  Sum_probs=59.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEec-------------cccce----EEEEEeCCHHHHHHHHHHccCc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-------------CKHRG----FVMISYYDIRAARNAMKALQNK  335 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkit-------------gksrG----fAFV~F~d~esA~kAi~~Lng~  335 (985)
                      .....||+++||+.++-.-|+++|+.||.|-.|++.             +.++.    -|+|+|.+...|+++...||+.
T Consensus        72 rk~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~  151 (278)
T KOG3152|consen   72 RKTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT  151 (278)
T ss_pred             ccceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC
Confidence            367899999999999999999999999999999762             11221    3889999999999999999999


Q ss_pred             cccccc
Q 001991          336 PLRRRK  341 (985)
Q Consensus       336 ~I~Gr~  341 (985)
                      .|.|++
T Consensus       152 ~Iggkk  157 (278)
T KOG3152|consen  152 PIGGKK  157 (278)
T ss_pred             ccCCCC
Confidence            999875

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.99  E-value=0.069  Score=53.98  Aligned_cols=77  Identities=29%  Similarity=0.366  Sum_probs=54.4

Q ss_pred             cccccceeeecCC-----CCCCH----HHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          357 DANQGTLVVFNLD-----SSVST----EELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       357 ~~~~~tLfV~NLp-----~svTe----edLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                      .++..||.|.=+.     ...-+    ++|.+.|..||+|.=||+..   +.-+|+|.+-+.|.+|+. |+|.+++|+.|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l   99 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTL   99 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEE
Confidence            3456677777555     11222    36888899999998888775   478999999999999999 99999999999


Q ss_pred             EEEeccCcch
Q 001991          428 KLEASRPGGA  437 (985)
Q Consensus       428 kV~~A~~k~~  437 (985)
                      +|.+..+.-.
T Consensus       100 ~i~LKtpdW~  109 (146)
T PF08952_consen  100 KIRLKTPDWL  109 (146)
T ss_dssp             EEEE------
T ss_pred             EEEeCCccHH
Confidence            9998776543

; PDB: 1UFW_A 2DNR_A.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=94.85  E-value=0.056  Score=65.19  Aligned_cols=71  Identities=18%  Similarity=0.227  Sum_probs=60.6

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEE-EEEEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIR-EIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~-~Vri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      +.|-+.|+|.+++-+||.++|..|-.+- +|++-.    ...|-|.|.|++.++|.+|...|+++.|..++|++..
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3788999999999999999999997653 344422    2467899999999999999999999999999999864

>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=94.56  E-value=0.062  Score=51.18  Aligned_cols=72  Identities=13%  Similarity=0.199  Sum_probs=51.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE------------eccccceEEEEEeCCHHHHHHHHHHccCccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY------------TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  341 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk------------itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~  341 (985)
                      ..+-|.|=+.|+. ....|.+.|++||+|.+..            -......+..|.|.++.+|++||. .||..|.|.-
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            4567899999987 6677888999999998875            112345699999999999999994 8999998854


Q ss_pred             c-ccccc
Q 001991          342 L-DIHYS  347 (985)
Q Consensus       342 L-~V~~a  347 (985)
                      | -|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4 35554

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.38  E-value=0.11  Score=61.61  Aligned_cols=75  Identities=17%  Similarity=0.226  Sum_probs=59.8

Q ss_pred             ccccceeeecCCCCCC------HHHHHHHhhccCCEEEEEEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeC-Cce
Q 001991          358 ANQGTLVVFNLDSSVS------TEELHQIFGIYGEIREIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVA-GKQ  426 (985)
Q Consensus       358 ~~~~tLfV~NLp~svT------eedLrelFs~fG~I~~Vri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~-Gr~  426 (985)
                      .....|+|.|+|.--.      ..-|.++|+++|+|..+.++.    ..+||.|++|.+..+|+.|++.|||+.|. .++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3455788999885332      345778999999999987763    36789999999999999999999999885 677


Q ss_pred             EEEEec
Q 001991          427 IKLEAS  432 (985)
Q Consensus       427 IkV~~A  432 (985)
                      ..|...
T Consensus       136 f~v~~f  141 (698)
T KOG2314|consen  136 FFVRLF  141 (698)
T ss_pred             EEeehh
Confidence            777554

>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=94.05  E-value=0.31  Score=47.29  Aligned_cols=85  Identities=20%  Similarity=0.278  Sum_probs=65.9

Q ss_pred             CceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEecccccccceeEEEEEecCCchhhHHHHHHhcCCcccCCCCccEE
Q 001991          809 SRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVA  888 (985)
Q Consensus       809 ~rTTvMirNIPnk~t~~~L~~~id~~~~g~yDF~YlpiDf~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~K~~  888 (985)
                      .+|+|-+=-+|+.++...++..+-+.+.....-+.+--|..  -|.-=+-|-|.++++|..||+.|||+++...-. .+|
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            45666666889999988777667677777777666655644  466678999999999999999999999886655 459


Q ss_pred             EEEe-eccc
Q 001991          889 SLAY-ARIQ  896 (985)
Q Consensus       889 ~v~y-A~iQ  896 (985)
                      .|.| .+||
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.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.05  E-value=0.11  Score=61.61  Aligned_cols=66  Identities=24%  Similarity=0.438  Sum_probs=54.5

Q ss_pred             CCCcEEEEecCCCCCCH-------HHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccc
Q 001991          273 HPSRTLFVRNINSNVED-------SELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR  339 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTE-------edLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G  339 (985)
                      .-...|+|-|+|- |..       .-|..+|+++|+|..+.+    .+..+||.|++|.+..+|+.|++.|||+.|.-
T Consensus        56 g~D~vVvv~g~Pv-V~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   56 GFDSVVVVDGAPV-VGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             CcceEEEECCCcc-cChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecc
Confidence            4557899999985 322       235578999999998875    56799999999999999999999999988764

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=93.91  E-value=0.055  Score=61.59  Aligned_cols=72  Identities=19%  Similarity=0.391  Sum_probs=60.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC--------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~--------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      +.|.|.||.+.++.++++.+|.-.|+|.++++++.        ....|||.|.|...+..|.. |.++.+=++.|.|-++
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            47999999999999999999999999999999874        23479999999999998877 7777777777776655


Q ss_pred             c
Q 001991          433 R  433 (985)
Q Consensus       433 ~  433 (985)
                      -
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            3

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=93.78  E-value=0.048  Score=62.51  Aligned_cols=76  Identities=26%  Similarity=0.363  Sum_probs=62.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccC--CEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCc-eeCCceEEEEeccCcch
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS-DVAGKQIKLEASRPGGA  437 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG--~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~-~I~Gr~IkV~~A~~k~~  437 (985)
                      ..||++||.+.++..+|..+|...-  .-..+.   -..||+||.+.+..-|.+|++.++|+ ++.|+++.|..+.++..
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            3689999999999999999998641  111111   14689999999999999999999997 78999999999998876


Q ss_pred             hh
Q 001991          438 RR  439 (985)
Q Consensus       438 Rr  439 (985)
                      |.
T Consensus        79 rs   80 (584)
T KOG2193|consen   79 RS   80 (584)
T ss_pred             Hh
Confidence            54

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=93.40  E-value=0.25  Score=57.43  Aligned_cols=81  Identities=26%  Similarity=0.317  Sum_probs=70.5

Q ss_pred             ceeEEeecCCCCCCHHHHHHHHHhhCCCcceEEEecccccccceeEEEEEecCCchhhHHHHHHhcCCcccCCCCccEEE
Q 001991          810 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEKVAS  889 (985)
Q Consensus       810 rTTvMirNIPnk~t~~~L~~~id~~~~g~yDF~YlpiDf~~~~N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~K~~~  889 (985)
                      -|+|-|=-+|+.+|..+|+..+...+.-=-|+-.++   ..--|---+-|-|.+..+|..||+.|||+.+...-.+ +|.
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---DGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPE-VCH  149 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEee---cCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCcc-cee
Confidence            788899999999999999999998887777888888   3455666689999999999999999999998877666 999


Q ss_pred             EEeec
Q 001991          890 LAYAR  894 (985)
Q Consensus       890 v~yA~  894 (985)
                      |-|+.
T Consensus       150 ll~V~  154 (493)
T KOG0804|consen  150 LLYVD  154 (493)
T ss_pred             EEEEE
Confidence            99964

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=92.97  E-value=0.074  Score=59.66  Aligned_cols=73  Identities=16%  Similarity=0.262  Sum_probs=60.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCc--EEEE-----EeccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGD--IRTI-----YTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~--I~sV-----kitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      +...-.+||+||-+.+|++||.+.....|-  |.++     +..+.+||||+|...+..+.++-++.|-.+.|.|..-.|
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            344578999999999999999998887773  3333     247899999999999999999999999989998876554

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=92.79  E-value=0.042  Score=59.73  Aligned_cols=57  Identities=19%  Similarity=0.320  Sum_probs=47.3

Q ss_pred             HHHHhhc-ccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          291 ELKALFE-QFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       291 dLrelFs-~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +|...|+ +||+|+.+++    ...-.|-+||.|...++|++|+..||+..+.|++|...+.
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            3444444 9999999865    2235789999999999999999999999999999998775

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=91.83  E-value=0.11  Score=61.82  Aligned_cols=77  Identities=21%  Similarity=0.315  Sum_probs=63.0

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhc-ccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc---ccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFE-QFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR---RRKLDIH  345 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs-~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~---Gr~L~V~  345 (985)
                      .....+..|||.||-.-.|.-+|++++. .+|.|....| .+-+..|||.|.+.++|.....+|+|..+-   .+.|.+.
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            3566789999999999999999999999 6777777766 567789999999999999999999997653   3444444


Q ss_pred             cc
Q 001991          346 YS  347 (985)
Q Consensus       346 ~a  347 (985)
                      |.
T Consensus       518 f~  519 (718)
T KOG2416|consen  518 FV  519 (718)
T ss_pred             ec
Confidence            43

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.57  E-value=0.62  Score=46.99  Aligned_cols=75  Identities=17%  Similarity=0.275  Sum_probs=57.6

Q ss_pred             cccccceeeecCCCCC----CHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          357 DANQGTLVVFNLDSSV----STEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       357 ~~~~~tLfV~NLp~sv----TeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      +.+-.||.|+=|..++    +-..+.+..+.||+|.+|...+  +.-|.|.|.|..+|-+|+.++.. ...|..+++.|-
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            4456688887665544    3344555667899999998775  67899999999999999998876 667888888886


Q ss_pred             cC
Q 001991          433 RP  434 (985)
Q Consensus       433 ~~  434 (985)
                      ++
T Consensus       160 qr  161 (166)
T PF15023_consen  160 QR  161 (166)
T ss_pred             cc
Confidence            53

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=91.23  E-value=0.17  Score=60.36  Aligned_cols=79  Identities=15%  Similarity=0.250  Sum_probs=66.2

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhc-cCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCcee---CCceEEEEec
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGI-YGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV---AGKQIKLEAS  432 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~-fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I---~Gr~IkV~~A  432 (985)
                      ....+.|+|.||-.-+|.-+|++++++ .|.|.+. +|-+-+..|||.|.+.++|.+.+.+|||...   +++.|.+.|.
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~  519 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFV  519 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHH-HHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeec
Confidence            445679999999999999999999995 5566665 5545578999999999999999999999865   6799999998


Q ss_pred             cCcc
Q 001991          433 RPGG  436 (985)
Q Consensus       433 ~~k~  436 (985)
                      ...+
T Consensus       520 ~~de  523 (718)
T KOG2416|consen  520 RADE  523 (718)
T ss_pred             chhH
Confidence            7544

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=90.87  E-value=0.39  Score=48.72  Aligned_cols=73  Identities=23%  Similarity=0.385  Sum_probs=52.3

Q ss_pred             CCCcEEEEecCCC------CCCH---HHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          273 HPSRTLFVRNINS------NVED---SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       273 ~~srtLfVgNLP~------~vTE---edLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      .+..||.|.=+.+      ..++   .+|.+.|..||+|.-++..   .+.-+|+|.+.+.|-+|+ .++|..+.|+.|.
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv---~~~mwVTF~dg~sALaal-s~dg~~v~g~~l~  100 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFV---GDTMWVTFRDGQSALAAL-SLDGIQVNGRTLK  100 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEE---TTCEEEEESSCHHHHHHH-HGCCSEETTEEEE
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEe---CCeEEEEECccHHHHHHH-ccCCcEECCEEEE
Confidence            4567777776651      2222   3677889999999888762   357899999999999999 5999999999999


Q ss_pred             ccccCC
Q 001991          344 IHYSIP  349 (985)
Q Consensus       344 V~~a~p  349 (985)
                      |....|
T Consensus       101 i~LKtp  106 (146)
T PF08952_consen  101 IRLKTP  106 (146)
T ss_dssp             EEE---
T ss_pred             EEeCCc
Confidence            976554

; PDB: 1UFW_A 2DNR_A.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=90.04  E-value=0.19  Score=56.72  Aligned_cols=95  Identities=15%  Similarity=0.246  Sum_probs=72.9

Q ss_pred             cccceeeecCCCCCCHHHHH---HHhhccCCEEEEEEcCCC--------CcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          359 NQGTLVVFNLDSSVSTEELH---QIFGIYGEIREIRDTQHK--------HNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLr---elFs~fG~I~~Vri~~~s--------kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                      ...-+||-+|+..+.++.+.   +.|.+||.|..|.+..+.        ..-++|+|...++|..||...+|..+.|+.|
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            34567888888877655553   488999999998876532        1138999999999999999999999999999


Q ss_pred             EEEeccCcchhhhhhhhhhhccCCCcc
Q 001991          428 KLEASRPGGARRFMVQSEQEQDDLNLC  454 (985)
Q Consensus       428 kV~~A~~k~~Rrl~qq~eq~q~e~nLy  454 (985)
                      +..+..++-.-. ..+.+.++....+|
T Consensus       156 ka~~gttkycs~-~l~~~~c~~~~cmy  181 (327)
T KOG2068|consen  156 KASLGTTKYCSF-YLRNDICQNPDCMY  181 (327)
T ss_pred             HHhhCCCcchhH-HhhhhcccCccccc
Confidence            999988776443 22355666666777

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=89.97  E-value=0.81  Score=46.22  Aligned_cols=76  Identities=21%  Similarity=0.298  Sum_probs=57.6

Q ss_pred             CCCCCCcEEEEecCCCCCC----HHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVE----DSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vT----EedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ..+.+-.+|.|+=|..++.    ...+...++.||+|.+|...|  +-.|.|.|+|..+|-+|+.+++. ...|..+++.
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            3566788999977666543    344556788999999998854  45799999999999999998876 5566666666


Q ss_pred             ccC
Q 001991          346 YSI  348 (985)
Q Consensus       346 ~a~  348 (985)
                      |..
T Consensus       158 Wqq  160 (166)
T PF15023_consen  158 WQQ  160 (166)
T ss_pred             ccc
Confidence            543

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=89.79  E-value=1.2  Score=41.37  Aligned_cols=56  Identities=16%  Similarity=0.323  Sum_probs=43.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN  334 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng  334 (985)
                      ....+|. +|..+...||.++|+.||.|.--.+   ...-|||...+.+.|..|+..+..
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi---~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI---NDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEEE---CTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEEE---cCCcEEEEeecHHHHHHHHHHhcc
Confidence            3456666 9999999999999999999987777   345799999999999999987753

; 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.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=88.74  E-value=0.61  Score=51.70  Aligned_cols=75  Identities=17%  Similarity=0.381  Sum_probs=55.7

Q ss_pred             CCcEEEEecC--CCCCC---HHHHHHhhcccCcEEEEEe---ccc---cceEEEEEeCCHHHHHHHHHHccCcccccccc
Q 001991          274 PSRTLFVRNI--NSNVE---DSELKALFEQFGDIRTIYT---ACK---HRGFVMISYYDIRAARNAMKALQNKPLRRRKL  342 (985)
Q Consensus       274 ~srtLfVgNL--P~~vT---EedLrelFs~fG~I~sVki---tgk---srGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L  342 (985)
                      +++.|.++|.  +-.++   ++++++-.++||.|..|.+   .+.   ..--.||+|...++|.+|+-.|||..|+|+.+
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            3445555554  22344   3577889999999998865   111   12258999999999999999999999999999


Q ss_pred             cccccC
Q 001991          343 DIHYSI  348 (985)
Q Consensus       343 ~V~~a~  348 (985)
                      ...|..
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=88.55  E-value=0.47  Score=55.60  Aligned_cols=72  Identities=21%  Similarity=0.242  Sum_probs=58.3

Q ss_pred             eeeecCCCCC-CHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          363 LVVFNLDSSV-STEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       363 LfV~NLp~sv-TeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      |-+.-.+... +-++|...|.+||+|..|.+.-. .-.|.|+|.+..+|-+|.. .++..|+++.|+|.|-.+..
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc-hhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            3344444444 56889999999999999876433 4579999999999988887 89999999999999998755

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=88.49  E-value=0.75  Score=54.82  Aligned_cols=74  Identities=20%  Similarity=0.232  Sum_probs=58.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhc--ccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccC--ccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFE--QFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIH  345 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs--~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng--~~I~Gr~L~V~  345 (985)
                      ......+.|.++-||..+.+|+++.+|+  .|-++.+|...  ...--||+|++..+|++|.+.|..  +.|.|++|...
T Consensus       170 rp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa--~N~nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  170 RPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFA--HNDNWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             ccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeee--ecCceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            3445567788899999999999999997  47788888762  223468999999999999998866  56777777653

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=87.37  E-value=2.1  Score=47.91  Aligned_cols=73  Identities=19%  Similarity=0.239  Sum_probs=57.6

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCc-eEEEEeccCc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGK-QIKLEASRPG  435 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr-~IkV~~A~~k  435 (985)
                      ..-|-|.++++.-. .-|..+|++||+|.+.. +.....+-+|.|.+.-+|+|||. .||+.|+|. .|-|..+..|
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv-~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHV-TPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeee-cCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCH
Confidence            45677888888654 45778999999998864 34667799999999999999999 899999875 4557665543

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=87.07  E-value=1.1  Score=53.36  Aligned_cols=98  Identities=12%  Similarity=0.203  Sum_probs=70.5

Q ss_pred             CHHHHHHHHHHccCcccccccccccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhc--cCCEEEEEEcCCCCc
Q 001991          321 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGI--YGEIREIRDTQHKHN  398 (985)
Q Consensus       321 d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~--fG~I~~Vri~~~skG  398 (985)
                      |.+-..+++++.-+..++.+-++|..          ....+.|.++-||..+-.|+++.+|..  +-++.+|.+--+  .
T Consensus       146 DvdLI~Evlresp~VqvDekgekVrp----------~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N--~  213 (684)
T KOG2591|consen  146 DVDLIVEVLRESPNVQVDEKGEKVRP----------NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN--D  213 (684)
T ss_pred             chHHHHHHHhcCCCceeccCcccccc----------CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec--C
Confidence            34445556666666666655555532          234568889999999999999999985  667777765322  2


Q ss_pred             EEEEEEcCHHHHHHHHHHhCC--ceeCCceEEEE
Q 001991          399 HKFIEFYDIRAAETALRTLNR--SDVAGKQIKLE  430 (985)
Q Consensus       399 faFVeF~d~edA~kAI~~LNG--~~I~Gr~IkV~  430 (985)
                      --||+|++..||+.|.+.|..  ++|.||+|...
T Consensus       214 nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  214 NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            359999999999999998854  46788877654

>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=86.82  E-value=1.3  Score=46.88  Aligned_cols=63  Identities=17%  Similarity=0.290  Sum_probs=46.2

Q ss_pred             CHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhC--CceeCCceEEEEeccCcc
Q 001991          373 STEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN--RSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       373 TeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LN--G~~I~Gr~IkV~~A~~k~  436 (985)
                      ..+.|+++|..|+.+..+...+. =+-..|.|.+.++|.+|...|+  +..+.|+.++|.|++...
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            35789999999999888766653 3357899999999999999999  999999999999996543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=86.38  E-value=0.44  Score=53.88  Aligned_cols=76  Identities=18%  Similarity=0.262  Sum_probs=61.1

Q ss_pred             CcEEEEecCCCCCCHHHHH---HhhcccCcEEEEEecccc--------ceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          275 SRTLFVRNINSNVEDSELK---ALFEQFGDIRTIYTACKH--------RGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLr---elFs~fG~I~sVkitgks--------rGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      ..-+||-+|+..+.++.+.   +.|.+||.|..|.+.+..        -.-++|+|...++|..||...+|..+.|+.++
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            3567888999887665554   589999999999763321        12489999999999999999999999999999


Q ss_pred             ccccCCC
Q 001991          344 IHYSIPK  350 (985)
Q Consensus       344 V~~a~pk  350 (985)
                      ..+..++
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            8887654

>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=86.06  E-value=1.2  Score=46.63  Aligned_cols=68  Identities=7%  Similarity=0.062  Sum_probs=46.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcc-cCcE---EEEE--e-----ccccceEEEEEeCCHHHHHHHHHHccCcccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQ-FGDI---RTIY--T-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR  340 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~-fG~I---~sVk--i-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr  340 (985)
                      ....+|.|++||+++|++++.+.+.. +++.   ..+.  .     ....-.-|||.|.+.+++......++|..+.+.
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            34569999999999999999998887 7766   3332  1     111234699999999999999999999877653

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=85.76  E-value=0.84  Score=51.61  Aligned_cols=77  Identities=10%  Similarity=0.084  Sum_probs=62.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccC--CEEEEEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYG--EIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG--~I~~Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ..++||+||-+.+|++||.+....-|  .+.++++.     +.+||||+|-..+..+.++.++.|-.++|.|..-.|...
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            34799999999999999999888766  34445443     458999999999999999999999999999988777766


Q ss_pred             cCcc
Q 001991          433 RPGG  436 (985)
Q Consensus       433 ~~k~  436 (985)
                      ....
T Consensus       160 NK~~  163 (498)
T KOG4849|consen  160 NKTN  163 (498)
T ss_pred             chhh
Confidence            5443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=85.74  E-value=2.5  Score=37.10  Aligned_cols=55  Identities=22%  Similarity=0.250  Sum_probs=43.0

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhcc---CCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIY---GEIREIRDTQHKHNHKFIEFYDIRAAETALRTL  417 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~f---G~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L  417 (985)
                      ...|+|++++. ++.++|+.+|..|   .....|..+.+  .-|-|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdD--tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDD--TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecC--CcEEEEECCHHHHHHHHHcC
Confidence            34799999865 8889999999998   12345665544  45889999999999999865

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=82.51  E-value=4.6  Score=35.49  Aligned_cols=54  Identities=20%  Similarity=0.431  Sum_probs=41.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhccc----CcEEEEEeccccceEEEEEeCCHHHHHHHHHHc
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQF----GDIRTIYTACKHRGFVMISYYDIRAARNAMKAL  332 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~f----G~I~sVkitgksrGfAFV~F~d~esA~kAi~~L  332 (985)
                      ..+|+|+++.. ++.++|+.+|..|    ++..-=.+.   -.-|-|.|.+.+.|.+|+.+|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWId---DtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWID---DTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEec---CCcEEEEECCHHHHHHHHHcC
Confidence            46799999964 9999999999999    543322332   225778999999999999754

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=82.33  E-value=2.4  Score=47.42  Aligned_cols=64  Identities=16%  Similarity=0.164  Sum_probs=52.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccc
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  341 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~  341 (985)
                      ..=|-|-++|+ -.-.-|..+|++||+|...... ..-.+-+|.|.+.-+|++||. .+|+.|.|..
T Consensus       197 D~WVTVfGFpp-g~~s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  197 DTWVTVFGFPP-GQVSIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             cceEEEeccCc-cchhHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            45566778887 4556788899999999998874 556699999999999999995 7888887653

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=81.88  E-value=1  Score=56.11  Aligned_cols=76  Identities=17%  Similarity=0.244  Sum_probs=65.1

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCcee--CCceEEEEeccCcc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEASRPGG  436 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I--~Gr~IkV~~A~~k~  436 (985)
                      +.+.++.|.+-..+-.-|..+|.+||.|.+++..++ -..|.|+|...+.|..|+.+|+|+++  -|-+.+|.+|+.-.
T Consensus       298 qp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  298 QPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             cchhhhhcccccchHHHHHHHHHhhcchhhheeccc-ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            345677888888999999999999999999886543 56799999999999999999999976  58889999998643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	985
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-06
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-06
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		6e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		8e-06
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		2e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		2e-05
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		2e-05
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		3e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		6e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		6e-05
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		1e-04
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		1e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-04
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		1e-04
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		1e-04
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		2e-04
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		2e-04
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		2e-04
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		2e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-04
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		2e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-04
1drz_A	97	U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOM		4e-04
3cul_A	98	Aminoacyl-Trna Synthetase Ribozyme Length = 98		4e-04
1cx0_A	95	Hepatitis Delta Virus Ribozyme Length = 95		5e-04
1a9n_B	96	Crystal Structure Of The Spliceosomal U2b''-U2a' Pr		6e-04

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/151 (28%), Positives = 68/151 (45%), Gaps = 14/151 (9%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 332
           L V  +  ++ D EL ALF   G I T      Y      G+  + +     ++ A+K L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 333 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--- 389
               +R ++L + Y+ P    S KD N   L V NL  +++ ++L  IFG YG I +   
Sbjct: 66  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 390 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 418
           +RD  T       F+ +     A+ A+  LN
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/141 (26%), Positives = 63/141 (44%), Gaps = 15/141 (10%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           LFV N+  ++ + E++ LFE++G    ++   K +GF  I       A  A   L N PL
Sbjct: 25  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 338 RRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE----IRDT 393
           R ++L + ++           +  +L V NL   VS E L + F ++G++      + D 
Sbjct: 84  RGKQLRVRFA----------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDR 133
Query: 394 QHKHNHKFIEFYDIRAAETAL 414
                   +EF    AA  AL
Sbjct: 134 GRPSGKGIVEFSGKPAARKAL 154

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F QFG I  I  +   K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 43/151 (28%), Positives = 67/151 (44%), Gaps = 14/151 (9%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 332
           L V  +  +  D EL ALF   G I T      Y      G+  + +     ++ A+K L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 333 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--- 389
               +R ++L + Y+ P    S KD N   L V NL  +++ ++L  IFG YG I +   
Sbjct: 77  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 390 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 418
           +RD  T       F+ +     A+ A+  LN
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 69/160 (43%), Gaps = 15/160 (9%)
Query: 278 LFVRNINSNVEDSELK-ALFEQFG-------DIRTIYTACKHRGFVMISYYDIRAARNAM 329
           LFV N+N N    ELK  + + F        D+R   T    R F    Y D  +A +  
Sbjct: 10  LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYVDFESAEDLE 62
Query: 330 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE 389
           KAL+   L+    +I    PK   S+K+ +  TL+  NL   V+ +EL ++F    EIR 
Sbjct: 63  KALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 390 IRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 429
           +          +IEF     AE        +++ G+ I L
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 72/160 (45%), Gaps = 15/160 (9%)
Query: 278 LFVRNINSNVEDSELK-ALFEQFG-------DIRTIYTACKHRGFVMISYYDIRAARNAM 329
           LF+ N+N N   +ELK A+ E F        D+RT      +R F    Y D  +A +  
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 330 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE 389
           KAL+   L+    +I    PK   S+K     TL+  NL  +++ +EL ++F    EIR 
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 390 IRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 429
           +          +IEF     AE  L     +++ G+ + L
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F QFG I  I  +   K RG   + + ++ +A N
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A++++Q  P   + + I Y+
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 86

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F QFG I  I  +   K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAET 412
           +++G L V  L    + + L Q+F  YG+I E+     R+TQ      F+ F +I  A+ 
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 413 ALRTLNRSDVAGKQIKLE 430
           A+  +N   V G+QI+++
Sbjct: 70  AMMAMNGKSVDGRQIRVD 87

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 45/161 (27%), Positives = 72/161 (44%), Gaps = 22/161 (13%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRAARNA 328
           L V  +  N+   E ++LF   G+I +    CK           G+  ++Y D + A  A
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIES----CKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI- 387
           +  L    L+ + + + Y+ P  + S +DAN   L V  L  +++ +EL Q+F  YG I 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPS-SASIRDAN---LYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 388 --REIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 424
             R + D  T       FI F     AE A++ LN    +G
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 32/107 (29%), Positives = 49/107 (45%), Gaps = 17/107 (15%)
Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 413
           ++  L+V  L  +++ EE   +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 414 LRTLNRSDVAGKQIKLEASRPGGAR------------RFMVQSEQEQ 448
           + TLN   +  K IK+  +RP  A             + M Q E EQ
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQ 107

>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: Composition-based stats.
 Identities = 43/151 (28%), Positives = 66/151 (43%), Gaps = 14/151 (9%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKAL 332
           L V  +  N+   E K+LF   GDI +          +  G+  ++Y D   A  A+  L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 333 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR- 391
               L+ + + + Y+ P  + S +DAN   L V  L  ++S +E+ Q+F  YG I   R 
Sbjct: 67  NGLKLQTKTIKVSYARPS-SASIRDAN---LYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 392 ----DTQHKHNHKFIEFYDIRAAETALRTLN 418
                T       FI F     AE A++ LN
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153

>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 = 46.6 bits (109), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 34/155 (21%), Positives = 72/155 (46%), Gaps = 12/155 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR------GFVMISYYDIRAAR 326
           +P  +L+V +++ +V ++ L   F   G I +I   C+        G+  +++     A 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 386
            A+  +    ++ + + I +S  + +PS + +  G + + NLD S+  + L+  F  +G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 387 I---REIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           I   + + D      + F+ F    AAE A+  +N
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 66  NALRSMQGFPFYDKPMRIQYA 86

>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 = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 38/169 (22%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 332
           ++V +I   + +  ++  F  FG I++I         KH+GF  + Y    AA+ A++ +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 333 QNKPLRRRKL------DIHYSIP-KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 385
            +  L  R +      +I  + P  D  +E+      + V ++   +S +++  +F  +G
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 386 EIRE---IRD-TQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 429
           +I+     RD T  KH  + FIE+   ++++ A+ ++N  D+ G+ +++
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module Length = 96

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 66  NALRSMQGFPFYDKPMRIQYA 86

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 4   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 63
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 64  NALRSMQGFPFYDKPMRIQYA 84

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 66  NALRSMQGFPFYDKPMRIQYA 86

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A N
Sbjct: 3   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A++++Q  P   + + I Y+
Sbjct: 63  ALRSMQGFPFYDKPMRIQYA 82

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 326
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 3   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 62
Query: 327 NAMKALQNKPLRRRKLDIHYS 347
           NA++++Q  P   + + I Y+
Sbjct: 63  NALRSMQGFPFYDKPMRIQYA 83

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/155 (21%), Positives = 72/155 (46%), Gaps = 12/155 (7%)
Query: 273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR------GFVMISYYDIRAAR 326
           +P  +L+V +++ +V ++ L   F   G I +I   C+        G+  +++     A 
Sbjct: 8   YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 66
Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 386
            A+  +    ++ + + I +S  + +PS + +  G + + NLD S+  + L+  F  +G 
Sbjct: 67  RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124
Query: 387 I---REIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           I   + + D      + F+ F    AAE A+  +N
Sbjct: 125 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159

>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bound To Glc6p Length = 90

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A N
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A++++Q  P   + + I Y+
Sbjct: 62  ALRSMQGFPFYDKPMRIQYA 81

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 38/141 (26%), Positives = 59/141 (41%), Gaps = 15/141 (10%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           LFV N+ +++ + + K LFE++G+   ++   + RGF  I       A  A   L    L
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 338 RRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE----IRDT 393
           + R L I ++           +   L V NL   VS E L Q F  +G + +    + D 
Sbjct: 84  KSRPLRIRFA----------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR 133
Query: 394 QHKHNHKFIEFYDIRAAETAL 414
                  F+EF     A  AL
Sbjct: 134 GRATGKGFVEFAAKPPARKAL 154

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 38/169 (22%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 332
           ++V +I   + +  ++  F  FG I++I         KH+GF  + Y    AA+ A++ +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 333 QNKPLRRRKL------DIHYSIP-KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 385
            +  L  R +      +I  + P  D  +E+      + V ++   +S +++  +F  +G
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 386 EIREI---RD-TQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 429
           +I+     RD T  KH  + FIE+   ++++ A+ ++N  D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184

>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC Ribozyme Complex Length = 97

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A N
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 66
Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A+++ Q  P   +   I Y+
Sbjct: 67  ALRSXQGFPFYDKPXRIQYA 86

>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme Length = 98

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A N
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 67
Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A+++ Q  P   +   I Y+
Sbjct: 68  ALRSXQGFPFYDKPXRIQYA 87

>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme Length = 95

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A N
Sbjct: 5   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 64
Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A+++ Q  P   +   I Y+
Sbjct: 65  ALRSXQGFPFYDKPXRIQYA 84

>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein Complex Bound To A Fragment Of U2 Small Nuclear Rna Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    ALF QFG +  I      K RG   + + ++ ++ N
Sbjct: 5   PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTN 64
Query: 328 AMKALQNKPLRRRKLDIHYS 347
           A++ LQ  P   + + I Y+
Sbjct: 65  ALRQLQGFPFYGKPMRIQYA 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	985
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-30
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-27
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-27
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-25
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-25
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-10
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-24
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-23
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-22
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-22
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-04
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-21
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-20
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-20
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-07
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-20
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-20
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-19
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-14
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	8e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	9e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-05
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-10
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-11
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-08
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-11
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-10
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-10
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-08
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	6e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	8e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-09
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-09
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-09
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-06
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-09
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-09
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-06
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	6e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-06
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-08
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-08
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	8e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-06
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-04
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-04
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	4e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	9e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-08
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-08
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-07
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-07
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-07
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-05
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	7e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-07
2div_A	99	TRNA selenocysteine associated protein; structural	5e-07
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	8e-07
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	9e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	9e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	7e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-05
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	6e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	9e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	6e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-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 =  117 bits (294), Expect = 4e-30
 Identities = 30/196 (15%), Positives = 59/196 (30%), Gaps = 39/196 (19%)

Query: 274 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
            S  L V  ++ S +    +  +F  +G++  +       G  M+   D  A   A+  L
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 333 QNKPLRRRKLDIHYS------------IPKDNPSEKDANQG------------------- 361
            N  +  +K+++  S            +   + S KD ++                    
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 362 --TLVVFNLDSSVSTEELHQIFGIYG-----EIREIRDTQHKHNHKFIEFYDIRAAETAL 414
              L  FN    V+ E   +I    G      ++       + +   +E+     A   L
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 415 RTLNRSDVAGKQIKLE 430
             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 = 59.3 bits (143), Expect = 5e-10
 Identities = 23/107 (21%), Positives = 47/107 (43%), Gaps = 6/107 (5%)

Query: 358 ANQGTLVVFNLDSSVSTEE-LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT 416
           A+   L+V+ LD S    + +  +F +YG + +++  + K     +E  D  A + A+  
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 417 LNRSDVAGKQIKLEASR-----PGGARRFMVQSEQEQDDLNLCQIPF 458
           LN + + G+++ +  S+     PG +      S   +D        F
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRF 108

>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 = 50.9 bits (121), Expect = 4e-07
 Identities = 10/82 (12%), Positives = 27/82 (32%), Gaps = 5/82 (6%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFG-----DIRTIYTACKHRGFVMISYYDIRAAR 326
           +HPS  L   N    V +     + ++ G      ++      +     ++ +     A 
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 327 NAMKALQNKPLRRRKLDIHYSI 348
             +  L +  ++       Y++
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 =  110 bits (275), Expect = 3e-27
 Identities = 36/195 (18%), Positives = 68/195 (34%), Gaps = 34/195 (17%)

Query: 274 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
            +  L V N+N   V    L  LF  +GD++ +      +   ++   D   A+ AM  L
Sbjct: 33  GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 92

Query: 333 QNKPLRRRKLDIHYSIPKDNPSEKDANQG------------------------------- 361
               L  + + I  S  ++    ++  +                                
Sbjct: 93  NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 152

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 420
           TL + N+  SVS E+L  +F   G + +  +  Q       I+   +  A  AL  L+  
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 212

Query: 421 DVA-GKQIKLEASRP 434
           D+     +++  S+ 
Sbjct: 213 DLGENHHLRVSFSKS 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 = 57.3 bits (138), Expect = 3e-09
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 1/97 (1%)

Query: 353 PSEKDANQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 411
           P    A    L+V NL+   V+ + L  +FG+YG+++ ++   +K  +  ++  D   A+
Sbjct: 27  PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQ 86

Query: 412 TALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
            A+  LN   + GK I++  S+    +      E + 
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG 123

>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 =  108 bits (271), Expect = 5e-27
 Identities = 36/194 (18%), Positives = 68/194 (35%), Gaps = 34/194 (17%)

Query: 275 SRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           +  L V N+N   V    L  LF  +GD++ +      +   ++   D   A+ AM  L 
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 334 NKPLRRRKLDIHYSIPKDNPSEKDANQG-------------------------------T 362
              L  + + I  S  ++    ++  +                                T
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           L + N+  SVS E+L  +F   G + +  +  Q       I+   +  A  AL  L+  D
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182

Query: 422 VA-GKQIKLEASRP 434
           +     +++  S+ 
Sbjct: 183 LGENHHLRVSFSKS 196

>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 = 56.1 bits (135), Expect = 6e-09
 Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 359 NQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL 417
               L+V NL+   V+ + L  +FG+YG+++ ++   +K  +  ++  D   A+ A+  L
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 61

Query: 418 NRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
           N   + GK I++  S+    +      E + 
Sbjct: 62  NGHKLHGKPIRITLSKHQNVQLPREGQEDQG 92

>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 = 53.4 bits (128), Expect = 5e-08
 Identities = 25/105 (23%), Positives = 42/105 (40%), Gaps = 4/105 (3%)

Query: 245 QKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI-R 303
               D+     ++    GS   ++ +   PS TL + NI  +V + +LK LF   G + +
Sbjct: 92  GLTKDYGNSPLHRFKKPGSKNFQNIF--PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK 149

Query: 304 TIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR-RKLDIHYS 347
                 K R   +I    +  A  A+  L N  L     L + +S
Sbjct: 150 GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 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 =  106 bits (268), Expect = 1e-25
 Identities = 30/185 (16%), Positives = 61/185 (32%), Gaps = 11/185 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
               L V N+  ++   + + L   FG +   +        + +G+    Y    +A  A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVS-TEELHQIFGIYGEI 387
              L  KPL  R L +H++      +    +   L V  L    +  + L +        
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAG-QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 388 REIRDTQHKHNHK----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQ 443
              +    +         +E+     AE A +  +   + G  +++    PG   R M+ 
Sbjct: 213 TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLA 272

Query: 444 SEQEQ 448
           +    
Sbjct: 273 ALIAA 277

>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 =  102 bits (256), Expect = 4e-24
 Identities = 29/175 (16%), Positives = 66/175 (37%), Gaps = 17/175 (9%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
            R + +R +  +V + E+  L   +  ++  +   K++G   ++  +   A  A+ A   
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-KYKGTAFVTLLNGEQAEAAINAFHQ 79

Query: 335 KPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ 394
             LR R+L +            DA    L V NL  S++ ++  ++   +G +       
Sbjct: 80  SRLRERELSV-------QLQPTDAL---LCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

Query: 395 HKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQS 444
            +   +     F E+    +A  A   L    +  + + +  +  G     ++ S
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHS 184

>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 = 63.8 bits (156), Expect = 4e-11
 Identities = 15/104 (14%), Positives = 44/104 (42%), Gaps = 11/104 (10%)

Query: 332 LQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR 391
           L  + +R+R          ++   +  N+  +++  L   V+ +E+H +   Y  ++   
Sbjct: 3   LDPEEIRKRL---------EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCF 52

Query: 392 DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG 435
             ++K    F+   +   AE A+   ++S +  +++ ++     
Sbjct: 53  VDKYK-GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 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 = 53.8 bits (130), Expect = 7e-08
 Identities = 16/86 (18%), Positives = 25/86 (29%), Gaps = 5/86 (5%)

Query: 272 EHPSRTLFVRNINSNVEDSE-LKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAAR 326
              SR L V  +     D + L               AC    + +GF ++ Y     A 
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAE 240

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDN 352
            A +      L    L + +  P   
Sbjct: 241 EAQQQADGLSLGGSHLRVSFCAPGPP 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 =  102 bits (256), Expect = 3e-25
 Identities = 33/169 (19%), Positives = 65/169 (38%), Gaps = 7/169 (4%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARN 327
                 LF+ N+N N   +ELK    +      +         +R F  + +        
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 387
           A++ L    +   ++ +     +D+   + A   TL+  NL  +++ +EL ++F    EI
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGRDSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEI 126

Query: 388 REIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG 436
           R +          +IEF     AE  L     +++ 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 = 59.5 bits (145), Expect = 2e-10
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHNHK---FIEFYDI 407
               +      L + NL+ + S  EL           ++         ++   +++F   
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64

Query: 408 RAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
              E AL  L    V G +IKLE  +   +++
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKPKGRDSKK 95

>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 = 98.8 bits (247), Expect = 6e-24
 Identities = 33/173 (19%), Positives = 64/173 (36%), Gaps = 20/173 (11%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIY-------TACKHRGFVMISYYDIRAARN 327
           +  +FV  +     + +L+ LFEQ+G +  I           + +G   +++Y  +AA  
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 387
           A  AL N  +           P D+          L +  +    +  ++  +F  +G+I
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122

Query: 388 REI---RDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
            E    R        +   F+ F     A+TA++ ++       Q     S P
Sbjct: 123 EECRILRGPDGL--SRGCAFVTFTTRAMAQTAIKAMH-----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 = 58.4 bits (142), Expect = 6e-10
 Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 12/102 (11%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD-TQHKHNHK---FIEFYDIRAAE 411
           +   + V  +  + S ++L ++F  YG + E   +RD +Q+    K   F+ FY  +AA 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 412 TALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNL 453
            A   L+       ++      P   +    +     +D  L
Sbjct: 62  EAQNALH-----NMKVLPGMHHPIQMKPADSEKNNAVEDRKL 98

>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 = 99.7 bits (249), Expect = 4e-23
 Identities = 33/175 (18%), Positives = 67/175 (38%), Gaps = 16/175 (9%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT---IYTAC--KHRGFVMISYYDIRAA 325
                 TL++ N   +     ++ L +    +     + +      R F  I       A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 326 RNAMKALQNKPLRRRKLDIHYSIP--KDNPSEKDANQG-TLVVFNLDSSVSTEE-LHQIF 381
           R  ++ L    +    L    S P  K   ++    +G  +++ NL + +  E  L + F
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232

Query: 382 GIYGEIREIR---DTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
             +G I +I      +    +    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 = 95.4 bits (238), Expect = 1e-21
 Identities = 23/166 (13%), Positives = 54/166 (32%), Gaps = 20/166 (12%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARNAMKALQ 333
           T+ V+N+  +   +++   F+  G I  +  A    K+  F  I +     A  A+    
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT- 101

Query: 334 NKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT 393
           +K + + ++ +            +     L + N   S +   +  +      +      
Sbjct: 102 HKVVGQNEIIVS--------HLTECT---LWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150

Query: 394 QHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
                +      +I+      A   +  LN   + G  +  + S P
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 196

>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 = 58.1 bits (141), Expect = 4e-09
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 350 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYD 406
            +    ++    T++V NL  S +  ++++ F   G I  +        +     IEF  
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR 90

Query: 407 IRAAETALRTLNRSDVAGKQIKLE 430
              A  A+   ++  V   +I + 
Sbjct: 91  YDGALAAITKTHKV-VGQNEIIVS 113

>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 = 8e-23
 Identities = 34/185 (18%), Positives = 79/185 (42%), Gaps = 10/185 (5%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAAR 326
            +P  +L+V +++ +V ++ L   F   G I +I         +  G+  +++     A 
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 386
            A+  +    ++ + + I +S     PS + +  G + + NLD S+  + L+  F  +G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRD--PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129

Query: 387 IREIR---DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQ 443
           I   +   D      + F+ F    AAE A+  +N   +  +++ +   +    R   + 
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189

Query: 444 SEQEQ 448
           +  ++
Sbjct: 190 ARAKE 194

>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 = 64.6 bits (158), Expect = 8e-12
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 6/94 (6%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI---REIRD--TQHKHNHKFIEFYD 406
           NPS       +L V +L   V+   L++ F   G I   R  RD  T+    + ++ F  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 407 IRAAETALRTLNRSDVAGKQIKLE-ASRPGGARR 439
              AE AL T+N   + GK +++  + R    R+
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRK 100

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 95.1 bits (237), Expect = 4e-22
 Identities = 38/202 (18%), Positives = 85/202 (42%), Gaps = 33/202 (16%)

Query: 258 GVSAGSVVGEHPYGEHPS----------RTLFVRNINSNVEDSELKALFEQFGDIRTIYT 307
           G    S+ G    G   +            ++V +I   + +  ++  F  FG I++I  
Sbjct: 1   GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60

Query: 308 AC-----KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK-------DNPSE 355
           +      KH+GF  + Y    AA+ A++ + +  L  R + +             D  +E
Sbjct: 61  SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE 120

Query: 356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHK---FIEFYDI 407
           +      + V ++   +S +++  +F  +G+I+         T     HK   FIE+   
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG---KHKGYGFIEYEKA 177

Query: 408 RAAETALRTLNRSDVAGKQIKL 429
           ++++ A+ ++N  D+ G+ +++
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRV 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 = 62.7 bits (153), Expect = 4e-11
 Identities = 23/130 (17%), Positives = 46/130 (35%), Gaps = 14/130 (10%)

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 386
           + M ++       R                 A    + V ++   +  + + Q F  +G 
Sbjct: 2   SHMASMTGGQQMGRG-------SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGP 54

Query: 387 IRE---IRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRF 440
           I+      D+     HK   F+E+    AA+ AL  +N   + G+ IK+      G  + 
Sbjct: 55  IKSIDMSWDSVTM-KHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP 113

Query: 441 MVQSEQEQDD 450
           ++    E+  
Sbjct: 114 IIDQLAEEAR 123

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 59.6 bits (145), Expect = 5e-10
 Identities = 20/93 (21%), Positives = 47/93 (50%), Gaps = 5/93 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
               ++V +++ ++ D ++K++FE FG I++   A      KH+G+  I Y   +++++A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
           + ++    L  + L +  ++    P    A  G
Sbjct: 184 VSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG 216

>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 = 90.8 bits (226), Expect = 4e-22
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 6/85 (7%)

Query: 272 EHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIY--TACKHRGFVMISYYDIRAA 325
             P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A
Sbjct: 5   TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPK 350
            NA++++Q  P   + + I Y+   
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 = 59.5 bits (145), Expect = 4e-11
 Identities = 20/95 (21%), Positives = 47/95 (49%), Gaps = 14/95 (14%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEEL----HQIFGIYGEIREIRDTQHKHNHK-- 400
           ++P+  P+       T+ + NL+  +  +EL    H IF  +G+I +I  ++     +  
Sbjct: 1   AVPETRPNH------TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL-KMRGQ 53

Query: 401 -FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
            F+ F ++ +A  ALR++       K ++++ ++ 
Sbjct: 54  AFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 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 = 93.0 bits (232), Expect = 6e-22
 Identities = 43/165 (26%), Positives = 70/165 (42%), Gaps = 14/165 (8%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAM 329
           +  L V  +  ++ D EL ALF   G I T      Y      G+  + +     ++ A+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 330 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE 389
           K L    +R ++L + Y+ P    S KD N   L V NL  +++ ++L  IFG YG I +
Sbjct: 63  KVLNGITVRNKRLKVSYARPG-GESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQ 118

Query: 390 IRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKL 429
               + K   +     F+ +     A+ A+  LN     G    L
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPL 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 = 61.1 bits (149), Expect = 5e-11
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 5/87 (5%)

Query: 358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAET 412
           A+   L+V  L   ++  EL+ +F   G I     +RD  T + + + F++F     ++ 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 413 ALRTLNRSDVAGKQIKLEASRPGGARR 439
           A++ LN   V  K++K+  +RPGG   
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGESI 87

>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 = 42.9 bits (102), Expect = 1e-04
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
               L+V N+   + D +L  +F ++G I            + RG   + Y     A+ A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 329 MKALQNKPL 337
           + AL N   
Sbjct: 148 ISALNNVIP 156

>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 = 89.2 bits (222), Expect = 9e-21
 Identities = 41/167 (24%), Positives = 69/167 (41%), Gaps = 16/167 (9%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRGFVMISYYDIRAARNA 328
              L V  +  N+   E ++LF   G+I +     +        G+  ++Y D + A  A
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESC-KLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIR 388
           +  L    L+ + + + Y+ P    S +DAN   L V  L  +++ +EL Q+F  YG I 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSA-SIRDAN---LYVSGLPKTMTQKELEQLFSQYGRII 116

Query: 389 EIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
             R    +         FI F     AE A++ 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 = 60.7 bits (148), Expect = 9e-11
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 413
           ++  L+V  L  +++ EE   +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 414 LRTLNRSDVAGKQIKLEASRPGGAR 438
           + TLN   +  K IK+  +RP  A 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSAS 85

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 87.3 bits (216), Expect = 2e-20
 Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 6/101 (5%)

Query: 265 VGEHPYGEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIY--TACKHRGFVMIS 318
           +G  P    PS+ + + NIN  V   +L+    AL    GDI  I    +  + G   I 
Sbjct: 19  LGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIV 78

Query: 319 YYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
           +    +A+  ++A Q  P +   L I +S    +   +D +
Sbjct: 79  FATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDGS 119

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 63.4 bits (154), Expect = 3e-12
 Identities = 18/112 (16%), Positives = 39/112 (34%), Gaps = 9/112 (8%)

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEEL----HQIFGIY 384
           MK        R+ +D         P   + +Q  +++ N++  V  E+L    + +    
Sbjct: 1   MKETAAAKFERQHMD--SPDLGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQ 57

Query: 385 GEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           G+I +I    +       +I F    +A+  +         G  + +  S  
Sbjct: 58  GDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSET 109

>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 = 88.8 bits (221), Expect = 2e-20
 Identities = 26/170 (15%), Positives = 61/170 (35%), Gaps = 22/170 (12%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----------KHRGFVMISYYDIRA 324
           +R L+V NI   + +  +   F     +  +  A           + + F  + +  +  
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 384
              AM A      + + L I                  L +  L + ++ +++ ++   +
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLP----GAHKLFIGGLPNYLNDDQVKELLTSF 118

Query: 385 GEIRE---IRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIK 428
           G ++    ++D+      K   F E+ DI   + A+  LN   +  K++ 
Sbjct: 119 GPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 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 = 51.5 bits (124), Expect = 2e-07
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 6/85 (7%)

Query: 268 HPYGEHPS-RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYD 321
           H Y   P    LF+  + + + D ++K L   FG ++             +G+    Y D
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 322 IRAARNAMKALQNKPLRRRKLDIHY 346
           I     A+  L    L  +KL +  
Sbjct: 146 INVTDQAIAGLNGMQLGDKKLLVQR 170

>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 = 88.2 bits (219), Expect = 5e-20
 Identities = 28/195 (14%), Positives = 66/195 (33%), Gaps = 34/195 (17%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----------KHRGFVMISYYDIR 323
            +R L+V NI   + +  +   F     +  +  A           + + F  + +  + 
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 324 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG----------------TLVVFN 367
               AM A      + + L I              N                   L +  
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

Query: 368 LDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEFYDIRAAETALRTLNRSD 421
           L + ++ +++ ++   +G ++    ++D+      K   F E+ DI   + A+  LN   
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180

Query: 422 VAGKQIKLEASRPGG 436
           +  K++ ++ +  G 
Sbjct: 181 LGDKKLLVQRASVGA 195

>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 = 85.7 bits (212), Expect = 5e-20
 Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 3/109 (2%)

Query: 255 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF 314
           S+  V  GS +G+      PSR + +R +  +V + E+ +L   FG +  +    K +  
Sbjct: 11  SSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNL-LMLKGKNQ 69

Query: 315 VMISYYDIRAARNAMKALQNKP--LRRRKLDIHYSIPKDNPSEKDANQG 361
             I      AA   +    +    LR + + I +S  K+  ++   NQ 
Sbjct: 70  AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 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 = 48.0 bits (114), Expect = 8e-07
 Identities = 21/112 (18%), Positives = 39/112 (34%), Gaps = 9/112 (8%)

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 384
             +      +  L  R   +  S     PS        + +  L   V+  E+  +   +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR------VIHIRKLPIDVTEGEVISLGLPF 55

Query: 385 GEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNRSDVAGKQIKLEASRP 434
           G++  +   + K N  FIE     AA T +   T     + G+ I ++ S  
Sbjct: 56  GKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 84.1 bits (208), Expect = 1e-19
 Identities = 23/103 (22%), Positives = 41/103 (39%), Gaps = 3/103 (2%)

Query: 261 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYY 320
            GS    H     PSR + +R +  +V + E+ +L   FG +  +    K +    I   
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNL-LMLKGKNQAFIEMN 60

Query: 321 DIRAARNAMKALQNKP--LRRRKLDIHYSIPKDNPSEKDANQG 361
              AA   +    +    LR + + I +S  K+  ++   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 = 47.9 bits (114), Expect = 6e-07
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNR 419
            + +  L   V+  E+  +   +G++  +   + K N  FIE     AA T +   T   
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVT 76

Query: 420 SDVAGKQIKLEASRP 434
             + G+ I ++ S  
Sbjct: 77  PVLRGQPIYIQFSNH 91

>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 = 85.7 bits (213), Expect = 2e-19
 Identities = 30/163 (18%), Positives = 66/163 (40%), Gaps = 11/163 (6%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFG---DIRTIYTA-CKHRGFVMISYYDIRAARNAMKA 331
           R L+V N++  + +  LK  F+  G   +I+ +     K+  +  + Y+    A  A++ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 332 LQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR 391
           L  K +    + I+++           +   L V +L+ +V  E L   F  +       
Sbjct: 61  LNGKQIENNIVKINWAFQS--QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 392 -----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 429
                 T     + F+ F     A+ A+ ++   D+ G+ +++
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 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 = 59.8 bits (146), Expect = 2e-10
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEI---REIRD-TQHKHNHKFIEFYDIRAAETALRTL 417
            L V NLD +++ + L Q F + G I   + + D      N+ F+E++    A  AL+TL
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 418 NRSDVAGKQIKLEASRPGGARR 439
           N   +    +K+  +       
Sbjct: 62  NGKQIENNIVKINWAFQSQQSS 83

>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 = 43.7 bits (104), Expect = 5e-05
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
            +  LFV ++N NV+D  L+  F+ F    + +          RG+  +S+     A+NA
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145

Query: 329 MKALQNKPLRRRKLDIHYS 347
           M ++Q + L  R L I+++
Sbjct: 146 MDSMQGQDLNGRPLRINWA 164

>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 = 85.5 bits (212), Expect = 2e-18
 Identities = 39/146 (26%), Positives = 57/146 (39%), Gaps = 15/146 (10%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 336
            LFV N+ +++ + + K LFE++G+   ++   + RGF  I       A  A   L    
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTI 82

Query: 337 LRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR----D 392
           L+ R L I         +   A    L V NL   VS E L Q F  +G + +      D
Sbjct: 83  LKSRPLRI-------RFATHGAA---LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD 132

Query: 393 TQHKHNHKFIEFYDIRAAETALRTLN 418
                   F+EF     A  AL    
Sbjct: 133 RGRATGKGFVEFAAKPPARKALERCG 158

>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 = 62.4 bits (152), Expect = 1e-10
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 8/91 (8%)

Query: 349 PKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIREI---RDTQHKHNHKFIEF 404
               P EK   Q   L V NL + ++ E+  ++F  YGE  E+   RD        FI  
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----RGFGFIRL 65

Query: 405 YDIRAAETALRTLNRSDVAGKQIKLEASRPG 435
                AE A   L+ + +  + +++  +  G
Sbjct: 66  ESRTLAEIAKAELDGTILKSRPLRIRFATHG 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 = 52.4 bits (126), Expect = 2e-07
 Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 5/91 (5%)

Query: 273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNA 328
                L V+N++  V +  L+  F QFG +           +  G   + +     AR A
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153

Query: 329 MKALQNK-PLRRRKLDIHYSIPKDNPSEKDA 358
           ++   +   L           P +   ++D 
Sbjct: 154 LERCGDGAFLLTTTPRPVIVEPMEQFDDEDG 184

>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 = 77.7 bits (192), Expect = 2e-17
 Identities = 20/83 (24%), Positives = 38/83 (45%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA 331
              +RTL  +N++ N+ + ELK +FE   +IR +    K +G   I +     A   ++ 
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 332 LQNKPLRRRKLDIHYSIPKDNPS 354
            Q   +  R + ++Y+  K    
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 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 = 68.4 bits (168), Expect = 2e-14
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 2/91 (2%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 408
           P  +   + A   TL+  NL  +++ +EL ++F    EIR +          +IEF    
Sbjct: 7   PCTSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 409 AAETALRTLNRSDVAGKQIKLEASRPGGARR 439
            AE  L     +++ G+ + L  +   G  R
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 23/86 (26%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC--KHRGFVMISYYDIRAARNAMKA 331
            +R L++RN+   +   E+  +F ++G IR I      + RG   + Y DI  A+NA+  
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66

Query: 332 LQNKPLRRRKLDIHYSIPKDNPSEKD 357
           L    +  R L + Y        + D
Sbjct: 67  LSGFNVSNRYLVVLYYNANRAFQKMD 92

>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 = 67.4 bits (165), Expect = 1e-13
 Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 4/90 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETALRTLN 418
            L + NL   ++ EE++ IFG YG IR+IR        +   ++ + DI  A+ A+  L+
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE-TRGTAYVVYEDIFDAKNAVDHLS 68

Query: 419 RSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
             +V+ + + +       A + M   ++E+
Sbjct: 69  GFNVSNRYLVVLYYNANRAFQKMDTKKKEE 98

>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 = 74.1 bits (183), Expect = 2e-15
 Identities = 29/167 (17%), Positives = 62/167 (37%), Gaps = 25/167 (14%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISYYDIRAA 325
           S  +F+  +N +  +  L+  F ++G +    T           + RGF  +S+    + 
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTV----TDLKIMKDPATGRSRGFGFLSFEKPSSV 58

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 385
              +K      L  + +D   +IP+    ++    G + V  +   V  +E  + F  +G
Sbjct: 59  DEVVKTQHI--LDGKVIDPKRAIPR----DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWG 112

Query: 386 EIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI 427
            I +      +DT       F+ +    A +   +     D   ++I
Sbjct: 113 TIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKI 158

>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 = 50.6 bits (122), Expect = 2e-07
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARN 327
             +  +FV  I  +V   E +  F Q+G I            + RGF  ++Y    A   
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144

Query: 328 AMKALQNKPLRRRKLDIHYSIPK 350
             +  +    + RK++I  + P+
Sbjct: 145 VCQ-NKFIDFKDRKIEIKRAEPR 166

>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 = 74.6 bits (184), Expect = 3e-15
 Identities = 38/196 (19%), Positives = 71/196 (36%), Gaps = 29/196 (14%)

Query: 267 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMI 317
           E P      R LF+  ++    D  L++ FEQ+G +    T C         + RGF  +
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60

Query: 318 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVF--NLDSSVSTE 375
           +Y  +     AM A +   +  R ++   ++ +++     A+     +F   +       
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 376 ELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQI--- 427
            L   F  YG+I  I     + + K     F+ F D  + +  +       V G      
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178

Query: 428 ----KLEASRPGGARR 439
               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 = 55.8 bits (135), Expect = 7e-09
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 6/100 (6%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 320
            + P      + +FV  I  + E+  L+  FEQ+G I  I         K RGF  +++ 
Sbjct: 95  SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

Query: 321 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
           D  +    +   +   +     ++  ++ K   +   ++Q
Sbjct: 155 DHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSSQ 193

>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 = 16/90 (17%), Positives = 35/90 (38%), Gaps = 5/90 (5%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAA 325
           G+ P + +    +N NV ++ LK +  ++G++  +         KH G   + +   R A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPSE 355
           +  +K L    +    +     I      +
Sbjct: 62  KETVKNLHLTSVMGNIIHAQLDIKGQQRMK 91

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 65.1 bits (159), Expect = 6e-13
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
            +    L+ +V    L  +   YGE+ E+    H    K      + F   R A+  ++ 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           L+ + V G  I  +    G  R 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRM 90

>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 = 69.2 bits (170), Expect = 2e-14
 Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           P+  L+V  +  N   + L   F++FG IRTI    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMR 74

Query: 334 NKPLRRRKLDIHYSIPKDNPS 354
             PL      +     K  PS
Sbjct: 75  GFPLGGPDRRLRVDFAKSGPS 95

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 59.9 bits (146), Expect = 3e-11
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            L V  L  + S   L + F  +G IR I D     +  +I++  + AA+ A   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTI-DHVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 422 VAGKQIKL 429
           + G   +L
Sbjct: 78  LGGPDRRL 85

>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 = 68.8 bits (169), Expect = 3e-14
 Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIR 408
              E D    TL V NL   V+   + Q+F   G  +    I +      + F+EFY+ R
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 409 AAETALRTLNRSDVAGKQIKLEASRPGGARR 439
            A  AL  +N   + GK++K+  +    +++
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQK 97

>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 = 52.6 bits (127), Expect = 1e-08
 Identities = 16/91 (17%), Positives = 43/91 (47%), Gaps = 3/91 (3%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYTACKHRGFVMISYYDIRAARNA 328
           +   RTL+V N++ +V +  +  LF Q G     + I     +  +  + +Y+ R A  A
Sbjct: 12  DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 71

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
           + A+  + +  +++ ++++    +     ++
Sbjct: 72  LAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 68.6 bits (168), Expect = 3e-14
 Identities = 13/79 (16%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
            S  + +R +   V +++L    ++FG I  +      +   ++ + D+  A NA+    
Sbjct: 20  ASPVVHIRGLIDGVVEADLVEALQEFGPISYV-VVMPKKRQALVEFEDVLGACNAVNYAA 78

Query: 334 NKP--LRRRKLDIHYSIPK 350
           +    +      ++YS  +
Sbjct: 79  DNQIYIAGHPAFVNYSTSQ 97

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 49.8 bits (119), Expect = 1e-07
 Identities = 17/100 (17%), Positives = 32/100 (32%), Gaps = 9/100 (9%)

Query: 336 PLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH 395
                 ++ +    K   S        + +  L   V   +L +    +G I  +     
Sbjct: 3   HHHHHHMENYDDPHKTPASP------VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

Query: 396 KHNHKFIEFYDIRAAETALR--TLNRSDVAGKQIKLEASR 433
           K     +EF D+  A  A+     N+  +AG    +  S 
Sbjct: 57  K-RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 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 = 67.7 bits (166), Expect = 5e-14
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 413
           S   +    L + NL  +V+ ++L Q+FG             K  + F+++ D   A  A
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRA 60

Query: 414 LRTLN-RSDVAGKQIKLEASRPGGARR 439
           + TL+ + ++ GK ++++ S     R 
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRS 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 = 57.6 bits (140), Expect = 1e-10
 Identities = 19/87 (21%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNA 328
             G      L++ N++  V   +L+ LF                G+  + Y D   A  A
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRA 60

Query: 329 MKALQNKP-LRRRKLDIHYSIPKDNPS 354
           ++ L  K  L  + +++ YS+ K   S
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRS 87

>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 = 67.9 bits (166), Expect = 5e-14
 Identities = 17/92 (18%), Positives = 39/92 (42%), Gaps = 5/92 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
            S  + VR +  +V +++L    E+FG I  +      +   ++ + +I +A+  +    
Sbjct: 14  VSPVVHVRGLCESVVEADLVEALEKFGTICYV-MMMPFKRQALVEFENIDSAKECVTFAA 72

Query: 334 NKP--LRRRKLDIHYSIPKD--NPSEKDANQG 361
           + P  +  ++   +YS  K    P     + G
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 48.6 bits (116), Expect = 3e-07
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            + V  L  SV   +L +    +G I  +     K     +EF +I +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVTFAADVP 75

Query: 422 --VAGKQIKLEASR 433
             +AG+Q     S 
Sbjct: 76  VYIAGQQAFFNYST 89

>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 = 68.1 bits (167), Expect = 6e-14
 Identities = 23/108 (21%), Positives = 48/108 (44%), Gaps = 8/108 (7%)

Query: 253 GVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY------ 306
           G S + +    +   +  GE P++ L+++N++  V + +L +LF +F + +         
Sbjct: 4   GSSGEEIRKIPMFSSYNPGE-PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM 62

Query: 307 TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
           T  + RG   I++ +   A  A+  +    L  + L I +   K   S
Sbjct: 63  TG-RMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRS 109

>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 = 60.4 bits (147), Expect = 3e-11
 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
            L + NL   V+  +L  +F  + E +           +     FI F +   A  AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 417 LNRSDVAGKQIKLEASRPGGAR 438
           +N   + GK + +E  +    R
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQR 108

>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 = 68.3 bits (167), Expect = 1e-13
 Identities = 15/93 (16%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----------KHRGFVMISYYDIR 323
           P+  ++V+N+  +V++ +LK +F ++ D  +               + +G   I   + +
Sbjct: 44  PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 103

Query: 324 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 356
           AA  A+K      L  + + + ++       + 
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 = 54.4 bits (131), Expect = 8e-09
 Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 18/113 (15%)

Query: 332 LQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI---- 387
           +  + +    +         +    + N   + V NL   V  ++L  IFG Y +     
Sbjct: 25  ISREEMETLSV-------FRSYEPGEPNC-RIYVKNLAKHVQEKDLKYIFGRYVDFSSET 76

Query: 388 -REIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
            R + D +     +     FI   + +AA  AL+  N   + GK + ++ +R 
Sbjct: 77  QRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129

>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 = 67.1 bits (164), Expect = 1e-13
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 325
           G           +  +N+ +    +E++  F +FG +  +          ++ + +   A
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-GITAIVEFLEPLEA 59

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 356
           R A + 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 = 55.6 bits (134), Expect = 1e-09
 Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            ++  NL +     E+ + F  +G +  +   +       +EF +   A  A R L  S 
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAYSK 70

Query: 422 VAGKQIKLE 430
                + LE
Sbjct: 71  FHHVPLYLE 79

>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 = 68.4 bits (167), Expect = 1e-13
 Identities = 29/143 (20%), Positives = 48/143 (33%), Gaps = 20/143 (13%)

Query: 312 RGFVMISYYDIRAARNAMKALQNKP----LRRRKLDIHYSIPKDNPSEKDANQG------ 361
           +G       D   A    K   N                    +       +        
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPL 72

Query: 362 --TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETALRT 416
              + V NL ++ +  EL + FG YG +R +       N     F+EF D R A  A+R 
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV---ARNPPGFAFVEFEDPRDAADAVRE 129

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           L+   + G ++++E S     +R
Sbjct: 130 LDGRTLCGCRVRVELSNGE--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 = 63.7 bits (155), Expect = 5e-12
 Identities = 19/84 (22%), Positives = 40/84 (47%)

Query: 267 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAAR 326
            H         ++V N+ +N   +EL+  F  +G +R+++ A    GF  + + D R A 
Sbjct: 65  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAA 124

Query: 327 NAMKALQNKPLRRRKLDIHYSIPK 350
           +A++ L  + L   ++ +  S  +
Sbjct: 125 DAVRELDGRTLCGCRVRVELSNGE 148

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.6 bits (163), Expect = 1e-13
 Identities = 11/81 (13%), Positives = 26/81 (32%), Gaps = 1/81 (1%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 408
                        T  + N+    +  +L  +F  +G I + +    +    FI++    
Sbjct: 16  VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEKGCCFIKYDTHE 74

Query: 409 AAETALRTLNRSDVAGKQIKL 429
            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 = 58.5 bits (142), Expect = 9e-11
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
             T ++ NI     +++L  LF+ FG I         +G   I Y     A   + AL N
Sbjct: 27  VTTAYIGNIPHFATEADLIPLFQNFGFILDFKH-YPEKGCCFIKYDTHEQAAVCIVALAN 85

Query: 335 KPLRRRKL 342
            P + R L
Sbjct: 86  FPFQGRNL 93

>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 = 66.4 bits (162), Expect = 2e-13
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 3/88 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           PSR L +R +   V ++E+ AL   FG +  I    K +    +      AA   +    
Sbjct: 14  PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYS 72

Query: 334 NKP--LRRRKLDIHYSIPKDNPSEKDAN 359
                LR + + I YS  K+  +   ++
Sbjct: 73  AVTPHLRNQPIYIQYSNHKELKTSGPSS 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 = 47.1 bits (112), Expect = 9e-07
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNR 419
            L +  L   V+  E+  +   +G++  I   + K N  F+E     AA T +   +   
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATEEAAITMVNYYSAVT 75

Query: 420 SDVAGKQIKLEASR 433
             +  + I ++ S 
Sbjct: 76  PHLRNQPIYIQYSN 89

>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 = 66.6 bits (163), Expect = 2e-13
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 351 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 410
           D  ++      T+    + S ++ + + Q F  +G+I EIR    K  + F+ F    +A
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESA 74

Query: 411 ETALRTLNRSDVAGKQIKLEASRPGGARR 439
             A+ ++N + + G  +K    +      
Sbjct: 75  AHAIVSVNGTTIEGHVVKCYWGKESPDMT 103

>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 = 55.8 bits (135), Expect = 1e-09
 Identities = 12/85 (14%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           + T++   I S + D  ++  F  FG I  I      +G+  + +    +A +A+ ++  
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEI-RVFPEKGYSFVRFSTHESAAHAIVSVNG 83

Query: 335 KPLRRRKLDIHYSIPKDNPSEKDAN 359
             +    +  ++     + +   ++
Sbjct: 84  TTIEGHVVKCYWGKESPDMTSGPSS 108

>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 = 65.8 bits (161), Expect = 3e-13
 Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 1/86 (1%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
             + L+VRN+  +  +  ++  F        +    K R +  + + +   A  AMKAL 
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPG-AVERVKKIRDYAFVHFSNREDAVEAMKALN 72

Query: 334 NKPLRRRKLDIHYSIPKDNPSEKDAN 359
            K L    +++  + P D  S   ++
Sbjct: 73  GKVLDGSPIEVTLAKPVDKDSSGPSS 98

>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 = 63.4 bits (155), Expect = 1e-12
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 413
            +  ++   L V NL  S S E + + F        +   +   ++ F+ F +   A  A
Sbjct: 9   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG-AVERVKKIRDYAFVHFSNREDAVEA 67

Query: 414 LRTLNRSDVAGKQIKLEASRP 434
           ++ LN   + G  I++  ++P
Sbjct: 68  MKALNGKVLDGSPIEVTLAKP 88

>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 = 65.7 bits (161), Expect = 3e-13
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 412
             +    +  L V NL   ++ EE+ ++F  YG+  E+   + K    FI       AE 
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEI 66

Query: 413 ALRTLNRSDVAGKQIKLEASRPGGARR 439
           A   L+   + GKQ+++  +    +  
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 = 59.6 bits (145), Expect = 4e-11
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
               LFV N+  ++ + E++ LFE++G    ++   K +GF  I       A  A   L 
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELD 72

Query: 334 NKPLRRRKLDIHYSIPKDNPS 354
           N PLR ++L + ++    + +
Sbjct: 73  NMPLRGKQLRVRFACHSASLT 93

>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 = 65.0 bits (159), Expect = 6e-13
 Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETA 413
             N   + V NL   + T+++  +F  YG IR+I D +++       F+EF D R AE A
Sbjct: 19  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI-DLKNRRGGPPFAFVEFEDPRDAEDA 77

Query: 414 LRTLNRSDVAGKQIKLEASRPGGARR 439
           +   +  D  G ++++E  R G    
Sbjct: 78  VYGRDGYDYDGYRLRVEFPRSGRGTG 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 = 56.9 bits (138), Expect = 4e-10
 Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 4/93 (4%)

Query: 252 GGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH 311
           G   + G+S G          +    ++V N+  ++   +++ +F ++G IR I    + 
Sbjct: 1   GSSGSSGMSGGG--VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR 58

Query: 312 --RGFVMISYYDIRAARNAMKALQNKPLRRRKL 342
               F  + + D R A +A+           +L
Sbjct: 59  GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL 91

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 64.6 bits (158), Expect = 8e-13
 Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 3/98 (3%)

Query: 255 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF 314
           S+  V  GS +     GE  +  LFVR    +V++SEL  +F  FG ++ +       GF
Sbjct: 11  SSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---ILNGF 67

Query: 315 VMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
             + + +  +A  A++ +  K    + L++ YS     
Sbjct: 68  AFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 64.6 bits (158), Expect = 9e-13
 Identities = 19/91 (20%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 408
              +  E + +   L V      V   EL++IFG +G ++E++     +   F+EF +  
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---ILNGFAFVEFEEAE 76

Query: 409 AAETALRTLNRSDVAGKQIKLEASRPGGARR 439
           +A  A+  ++    A + +++  S+    R 
Sbjct: 77  SAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 63.9 bits (156), Expect = 1e-12
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 367 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ 426
           NL +     EL + F  YG +R +   ++     F+EF D R AE A+R L+   + G +
Sbjct: 7   NLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66

Query: 427 IKLEASRPGGARR 439
           +++E S     R 
Sbjct: 67  VRVELSTGMPRRS 79

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 57.7 bits (140), Expect = 2e-10
 Identities = 20/80 (25%), Positives = 38/80 (47%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 337
           ++V N+ +     EL+  F  +G +RT++ A    GF  + + D R A +A++ L  K +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 338 RRRKLDIHYSIPKDNPSEKD 357
              ++ +  S      S  D
Sbjct: 63  CGSRVRVELSTGMPRRSRFD 82

>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 = 63.1 bits (154), Expect = 3e-12
 Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 7/90 (7%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY------TACKHRGFVMISYYDIRAA 325
           +  +  + VRNI       E++ LF  FG+++T+           HRGF  + +   + A
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71

Query: 326 RNAMKALQN-KPLRRRKLDIHYSIPKDNPS 354
           + A  AL +   L  R+L + ++  +    
Sbjct: 72  KKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 = 53.5 bits (129), Expect = 7e-09
 Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHK--- 400
           S        K      ++V N+    +  E+ ++F  +GE++ +R          H+   
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61

Query: 401 FIEFYDIRAAETALRTL-NRSDVAGKQIKLEASRP 434
           F++F   + A+ A   L + + + G+++ LE +  
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 412
            S +D    TL V  L  +++  +L   F  +GEIR I     +    FI+F   +AAE 
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQRQQCAFIQFATRQAAEV 63

Query: 413 AL-RTLNRSDVAGKQIKL 429
           A  ++ N+  V G+++ +
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 = 53.8 bits (130), Expect = 3e-09
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 335
            TL+V  +   + +++L+  F QFG+IRTI T  + +    I +   +AA  A +   NK
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQFATRQAAEVAAEKSFNK 71

>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 = 63.1 bits (154), Expect = 3e-12
 Identities = 23/100 (23%), Positives = 49/100 (49%), Gaps = 9/100 (9%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIR 408
           + S   A    L V NL ++V+ E L + F  +G++     ++D      + FI F +  
Sbjct: 3   SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD------YAFIHFDERD 56

Query: 409 AAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
            A  A+  +N  D+ G+ I++  ++P   +R   +++++ 
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQA 96

>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 = 61.9 bits (151), Expect = 6e-12
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-HRGFVMISYYDIRAARNAMKAL 332
             + LFVRN+ + V +  L+  F QFG +       K  + +  I + +   A  AM+ +
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKL----ERVKKLKDYAFIHFDERDGAVKAMEEM 65

Query: 333 QNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
             K L    ++I ++ P D   ++   Q
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQ 93

>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 = 67.2 bits (163), Expect = 3e-12
 Identities = 24/93 (25%), Positives = 47/93 (50%), Gaps = 6/93 (6%)

Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIR--TIYTACKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F QFG I    +  + K RG   + + ++ +A N
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
           A++++Q  P   + + I Y+    +   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 = 54.1 bits (129), Expect = 7e-08
 Identities = 14/75 (18%), Positives = 26/75 (34%)

Query: 267 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAAR 326
           +      P+  LF+ N+     +  L  LF QF   + +           + + +   A 
Sbjct: 199 QPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAG 258

Query: 327 NAMKALQNKPLRRRK 341
            A  ALQ   + +  
Sbjct: 259 AARDALQGFKITQNN 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 = 51.0 bits (121), Expect = 6e-07
 Identities = 33/217 (15%), Positives = 68/217 (31%), Gaps = 15/217 (6%)

Query: 362 TLVVFNLDSSVSTEEL----HQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAET 412
           T+ + NL+  +  +EL    + IF  +G+I +I       + K     F+ F ++ +A  
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 67

Query: 413 ALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVI 472
           ALR++       K ++++ ++        ++    + D    +       +     +   
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127

Query: 473 TSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLD 532
                  G++Q           A    H     P  +P    +   G   G   P     
Sbjct: 128 GGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPP 187

Query: 533 EMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIAD 569
           +     Q P   P      +         N P    +
Sbjct: 188 QQLMPGQMPPAQPL---SENPPNHILFLTNLPEETNE 221

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.0 bits (108), Expect = 3e-05
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            L + NL    +   L  +F  +   +E+R    +H+  F+EF +   A  A   L    
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 422 V-AGKQIKLE 430
           +     +K+ 
Sbjct: 269 ITQNNAMKIS 278

>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 = 62.2 bits (152), Expect = 5e-12
 Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
            S  LFVRN++    + +L+ LF  +G +  ++        K +GF  +++     A  A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
              +  +  + R L +  S  K   S+   + G
Sbjct: 67  YAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 53.0 bits (128), Expect = 8e-09
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIR 408
           S   +  G L V NL  + S E+L ++F  YG + E+       T+      F+ F    
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 409 AAETALRTLNRSDVAGKQIKLEASRP 434
            A  A   ++     G+ + +  S  
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTI 87

>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 = 63.7 bits (155), Expect = 6e-12
 Identities = 25/117 (21%), Positives = 51/117 (43%), Gaps = 6/117 (5%)

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 387
           A+++     L + + D H+    +   +      TL V NL    + E+++++F   G+I
Sbjct: 8   ALRSDSYVELSQYR-DQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 388 REIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
           ++I     K         F+E+Y    AE A+R +N + +  + I+ +        R
Sbjct: 67  KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR 123

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 57.9 bits (140), Expect = 5e-10
 Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
            S TL+V N++    + ++  LF + GDI+ I            GF  + YY    A NA
Sbjct: 38  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           M+ +    L  R +   +      
Sbjct: 98  MRYINGTRLDDRIIRTDWDAGFKE 121

>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 = 61.5 bits (150), Expect = 8e-12
 Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 1/94 (1%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDTQHKHNHKFIEFY 405
           S      S       TLV+ NL  S + E L ++F     I+           + FIEF 
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFA 61

Query: 406 DIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
               A+ AL + N+ ++ G+ I+LE   P G+  
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95

>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 = 61.5 bits (150), Expect = 1e-11
 Identities = 16/83 (19%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARNAMKA 331
            S+TL + N++ +  +  L+ +FE+   I+ +      K +G+  I +     A+ A+ +
Sbjct: 14  ESKTLVLSNLSYSATEETLQEVFEKATFIK-VPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 332 LQNKPLRRRKLDIHYSIPKDNPS 354
              + +  R + +    P+ +P+
Sbjct: 73  CNKREIEGRAIRLELQGPRGSPN 95

>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 = 60.9 bits (148), Expect = 2e-11
 Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 4/90 (4%)

Query: 351 DNPSEKDANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRA 409
            N ++  +    + + NL+++ V   ++  IF  YG +           + F+++ + R 
Sbjct: 18  TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS---VHKGYAFVQYSNERH 74

Query: 410 AETALRTLNRSDVAGKQIKLEASRPGGARR 439
           A  A+   N   +AG+ + +  +      R
Sbjct: 75  ARAAVLGENGRVLAGQTLDINMAGEPKPDR 104

>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 = 54.7 bits (132), Expect = 3e-09
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 274 PSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
            +  +F+ N+N+  V+ S+++ +F ++G +        H+G+  + Y + R AR A+   
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGE 82

Query: 333 QNKPLRRRKLDIHYSIPKDNP 353
             + L  + LDI+ +      
Sbjct: 83  NGRVLAGQTLDINMAGEPKPD 103

>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 = 22/95 (23%), Positives = 38/95 (40%), Gaps = 2/95 (2%)

Query: 260 SAGSVVGEHP--YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMI 317
           S+GS     P   G   +  ++V N+  +   S+LK    + G +    T    R    +
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 318 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
            Y D  AA+ A+  LQ   L    L +  +  + +
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.0 bits (135), Expect = 7e-10
 Identities = 16/87 (18%), Positives = 29/87 (33%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 408
           P   P E       + V NL       +L +     G +      Q      F+ + D  
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSA 67

Query: 409 AAETALRTLNRSDVAGKQIKLEASRPG 435
           AA+ A+  L    +    +++  +R  
Sbjct: 68  AAQQAVSCLQGLRLGTDTLRVALARQQ 94

>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 = 59.9 bits (146), Expect = 2e-11
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 413
           S    N   + V N+ ++ +++EL  +F   G + E        ++ F+       A+ A
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAA 59

Query: 414 LRTLNRSDVAGKQIKLEASRPGGARR 439
           +  LN  +V GK+I +E S  G  + 
Sbjct: 60  IAQLNGKEVKGKRINVELSTKGQKKS 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 = 57.2 bits (139), Expect = 2e-10
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
            +  +FV N+++     EL++LFE+ G +         + +  +       A+ A+  L 
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAAIAQLN 64

Query: 334 NKPLRRRKLDIHYSIPKDNPS 354
            K ++ +++++  S      S
Sbjct: 65  GKEVKGKRINVELSTKGQKKS 85

>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 = 59.9 bits (146), Expect = 2e-11
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHK---FIEFYDIRAAETALR 415
            + +  L  +V+ + + +IF  YG+I+ I    +  H H  K   ++EF +   AE AL+
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 416 TLNRSDVAGKQIKLEASRP 434
            ++   + G++I   A   
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 = 51.0 bits (123), Expect = 3e-08
 Identities = 10/85 (11%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YTACKHRGFVMISYYDIRAARN 327
               + +  +  NV    +  +F  +G I+ I            +G+  + + +   A  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDN 352
           A+K +    +  +++     +    
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWP 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 365 VFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA 423
           + NL   +VS E+L +IF  YG I +I     K+   FI+F + ++   A+   ++    
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 424 GKQIKLEASRPGGARRF 440
           GK++ LE S      +F
Sbjct: 72  GKKLILEVSSSNARPQF 88

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 59.9 bits (146), Expect = 3e-11
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 274 PSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
           P   LF+ N+   NV   +L  +F  +G I  I        F  I + + ++ R+A++  
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECE 65

Query: 333 QNKPLRRRKLDIHYSIPKDNPSEKDANQGT 362
             +    +KL +  S     P     + GT
Sbjct: 66  SQEMNFGKKLILEVSSSNARPQFDHGDHGT 95

>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 = 60.6 bits (147), Expect = 2e-11
 Identities = 16/96 (16%), Positives = 35/96 (36%), Gaps = 9/96 (9%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGD-------IRTIYTACKHRGFVMISYYDIRAAR 326
            +  LF+  I    +  E+     +  +         +     K+RGF  + Y   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 327 NAMKALQNKPLRR--RKLDIHYSIPKDNPSEKDANQ 360
            A + L    ++    ++ + ++ P+ +  E     
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 = 51.3 bits (123), Expect = 4e-08
 Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRDTQHKHNHK---FIEFYDIRAAE 411
               L +  +      EE+ +      E    +        K  ++   F+E+   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 412 TALRTLNRSDVA--GKQIKLEASRP 434
            A R L    +   G QI ++ + P
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEP 91

>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 = 59.9 bits (146), Expect = 3e-11
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 367 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ 426
           NL    + +E+  +F  YG++ E        N+ F+   D  AAE A+R L+   + G  
Sbjct: 15  NLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71

Query: 427 IKLEASRPGGARR 439
           I +EAS+      
Sbjct: 72  INVEASKNKSKAS 84

>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 = 54.5 bits (132), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           G      LF+ N+     + E+++LFEQ+G +         + +  +   D  AA +A++
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIR 60

Query: 331 ALQNKPLRRRKLDIHYSIPKDNPS 354
            L +  L    +++  S  K   S
Sbjct: 61  NLHHYKLHGVNINVEASKNKSKAS 84

>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 = 59.9 bits (146), Expect = 3e-11
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
           PSR +++ +I  +  + ++  L    G +  +         + +G+  I + D+ ++ +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPS 354
           ++ L    L  R L   YS   D   
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISG 86

>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 = 51.5 bits (124), Expect = 3e-08
 Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 11/91 (12%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FIEFYDIRAAETALRT 416
           + ++    + E++  +    G +  +       T      K   FIEF D+ ++ +A+R 
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGR---SKGYAFIEFRDLESSASAVRN 63

Query: 417 LNRSDVAGKQIKLEASRPGGARRFMVQSEQE 447
           LN   +  + +K   S         ++    
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>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 = 60.4 bits (147), Expect = 3e-11
 Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 6/96 (6%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIE 403
           P DN S ++ +  T+    L + +   +L   F   G++R++     R+++      ++E
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
           F +I++   A+  L    + G  I ++AS+    R 
Sbjct: 74  FCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRL 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 = 49.6 bits (119), Expect = 2e-07
 Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAAR 326
           E  +RT+F   + + +   +L+  F   G +R +         + +G   + + +I++  
Sbjct: 22  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 81

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDN 352
            A+  L  + L    + +  S  + N
Sbjct: 82  LAI-GLTGQRLLGVPIIVQASQAEKN 106

>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 = 61.7 bits (149), Expect = 4e-11
 Identities = 23/123 (18%), Positives = 56/123 (45%), Gaps = 4/123 (3%)

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLV-VFNLDSSVST 374
           M  ++   +A+ A++A+ +       L    +      +    +    + V NL   V+ 
Sbjct: 1   MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTL 60

Query: 375 EELHQIFGIYGEI-REIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEA 431
           + LHQIF  +G + + I  T++      +++ D  +A+ A  +L+  ++  A   ++++ 
Sbjct: 61  DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

Query: 432 SRP 434
           S+ 
Sbjct: 121 SKL 123

>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 = 52.4 bits (125), Expect = 6e-08
 Identities = 26/125 (20%), Positives = 47/125 (37%), Gaps = 11/125 (8%)

Query: 260 SAGSVVGEHPYGEHPSRTLF--VRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VM 316
           ++ + V         S  L   V N+   V    L  +F +FG +  I T  K+  F  +
Sbjct: 29  ASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQAL 88

Query: 317 ISYYDIRAARNAMKALQNKPL--RRRKLDIHYSIPKD------NPSEKDANQGTLVVFNL 368
           + Y D  +A++A  +L  + +      L I +S          N   +D  +  L   + 
Sbjct: 89  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 148

Query: 369 DSSVS 373
             S+ 
Sbjct: 149 QPSLD 153

>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 = 17/92 (18%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
               LFV +I+   ++ E++  F  +G+I+ I+          +G+ ++ Y   + A  A
Sbjct: 71  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
            +AL    +  + + + +   K     K + +
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKGPKRVKKSEK 162

>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 = 53.7 bits (129), Expect = 2e-08
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L V ++      +E+ + F  YGEI+ I     R T     +  +E+   + A  A   
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           LN +++ G+ I+++     G +R
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKR 156

>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 = 61.0 bits (148), Expect = 6e-11
 Identities = 27/142 (19%), Positives = 54/142 (38%), Gaps = 14/142 (9%)

Query: 312 RGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG---------T 362
           +G       D   A    K   N      +     +      +E   +           +
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS 72

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 417
           L V NL    S + L ++F  YG + ++     R T+      F+ F+D R AE A+  +
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132

Query: 418 NRSDVAGKQIKLEASRPGGARR 439
           + + + G++++++ +R G    
Sbjct: 133 DGAVLDGRELRVQMARYGRPPD 154

>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 = 55.6 bits (134), Expect = 4e-09
 Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 5/104 (4%)

Query: 255 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----- 309
               V+ GS    H        +L V N+        L+ +FE++G +  +Y        
Sbjct: 50  KTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 109

Query: 310 KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP 353
           + RGF  + ++D R A +AM A+    L  R+L +  +     P
Sbjct: 110 ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 153

>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 = 58.8 bits (143), Expect = 7e-11
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 413
                   TL V+  D  ++   L   F  +G I ++     + N  F+ +  + +A+ A
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQA 65

Query: 414 LRTLNRSDVAGKQIKLEASRP 434
           +  LN + V   Q+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 = 50.7 bits (122), Expect = 5e-08
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 335
            TL+V   +  +  + L+  F  FG+I  +      R    ++Y  + +A  A+  L   
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGT 72

Query: 336 PLRRRKLDIHYSIPKDNPSEK 356
            +   +L ++ +  +      
Sbjct: 73  QVESVQLKVNIARKQPMLDSG 93

>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 = 1e-10
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 424
           V N+  + + +EL   F  YG + E        ++ F+       A  A+R L+ ++  G
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIECD---IVKDYAFVHMERAEDAVEAIRGLDNTEFQG 71

Query: 425 KQIKLEASRPGGARR 439
           K++ ++ S       
Sbjct: 72  KRMHVQLSTSRLRTA 86

>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 = 56.5 bits (137), Expect = 4e-10
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
            S  L V NI+    + EL+A FE++G +         + +  +       A  A++ L 
Sbjct: 9   ASTKLHVGNISPTCTNQELRAKFEEYGPVIECD---IVKDYAFVHMERAEDAVEAIRGLD 65

Query: 334 NKPLRRRKLDIHYSIPKDNPS 354
           N   + +++ +  S  +   +
Sbjct: 66  NTEFQGKRMHVQLSTSRLRTA 86

>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 = 58.1 bits (141), Expect = 1e-10
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 365 VFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA 423
           + NL   +VS E+L +IF  YG I +I     K+   FI+F + ++   A+   ++    
Sbjct: 27  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIEXESQEMNF 83

Query: 424 GKQIKLEASRPG 435
           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 = 56.2 bits (136), Expect = 5e-10
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 266 GEHPYGEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRA 324
           G  P G H    LF+ N+   NV   +L  +F  +G I  I        F  I + + ++
Sbjct: 13  GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQS 69

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPK 350
            R+A++    +    +KL +  S   
Sbjct: 70  VRDAIEXESQEMNFGKKLILEVSSSN 95

>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 = 57.7 bits (140), Expect = 2e-10
 Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 8/97 (8%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH--------RGFVMISYYDI 322
           G   S  LF++N+N +  +  LK +F + G I++   + K          GF  + Y   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 323 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
             A+ A+K LQ   +   KL++  S     P+   ++
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97

>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 = 56.9 bits (138), Expect = 4e-10
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FIEFYDIRA 409
           +    L + NL+ S + E L  +F   G I+       ++           F+E+     
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 410 AETALRTLNRSDVAGKQIKLEASRPGGARR 439
           A+ AL+ L    V G ++++  S       
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPA 92

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 58.5 bits (141), Expect = 2e-10
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 349 PKDNPSEKDANQGTLV-VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDI 407
           P +       N+  L+ + N    ++ + L+ +    G+++ I   +       +EF  +
Sbjct: 13  PGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESV 72

Query: 408 RAAETALRTLNRSDVAGKQIKLE 430
             A+ A   LN +D+      L+
Sbjct: 73  LCAQKAKAALNGADIYAGCCTLK 95

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 50.5 bits (120), Expect = 1e-07
 Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 272 EHPSRTLF--VRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAM 329
              ++ L   ++N    +    L  +    G ++ I    ++    M+ +  +  A+ A 
Sbjct: 20  SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAK 79

Query: 330 KALQNKPL--RRRKLDIHYSIPKD 351
            AL    +      L I Y+ P  
Sbjct: 80  AALNGADIYAGCCTLKIEYARPTR 103

>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 = 57.6 bits (140), Expect = 2e-10
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
           TL V NL    S + L ++F  YG + ++       T+      F+ F+D R A+ A   
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           ++ +++ G++++++ +R G    
Sbjct: 75  MDGAELDGRELRVQVARYGRRDL 97

>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 = 57.6 bits (140), Expect = 2e-10
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 320
           G          TL V N+        L+ +FE++G +  +Y          RGF  + ++
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63

Query: 321 DIRAARNAMKALQNKPLRRRKLDIHYSIPK 350
           D R A++A  A+    L  R+L +  +   
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>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 = 56.3 bits (136), Expect = 4e-10
 Identities = 12/77 (15%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           G   S  + V+N+  +    E+  L + +  ++  Y   +++    ++  +   A+NA++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-RNKRTAFVTLLNGEQAQNAIQ 58

Query: 331 ALQNKPLRRRKLDIHYS 347
                  R + L +   
Sbjct: 59  MFHQYSFRGKDLIVQLQ 75

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 56.3 bits (136), Expect = 4e-10
 Identities = 12/75 (16%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
               ++V NL    + +E+H +   Y  ++     ++K    F+   +   A+ A++  +
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK-RTAFVTLLNGEQAQNAIQMFH 61

Query: 419 RSDVAGKQIKLEASR 433
           +    GK + ++   
Sbjct: 62  QYSFRGKDLIVQLQP 76

>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 = 4e-10
 Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
               LFV  ++    + ++   F ++G+I+ I+          +G+ ++ Y   + A+ A
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
           M+ L  + L  + + + +   +  P  K     
Sbjct: 81  MEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGR 113

>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 = 52.0 bits (125), Expect = 4e-08
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L V  +    + E++H  F  YGEI+ I     R T +   +  +E+   + A+ A+  
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           LN  D+ G+ I ++     G  +
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPK 106

>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 = 56.5 bits (137), Expect = 5e-10
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVMISYYDIRAARNAMK 330
           PS+TLFV+ ++ +  +  LK  F+     R +    T    +GF  + +     A+ A +
Sbjct: 14  PSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETG-SSKGFGFVDFNSEEDAKAAKE 72

Query: 331 ALQNKPLRRRKLDIHYSIPKDNPS 354
           A+++  +   K+ + ++ PK    
Sbjct: 73  AMEDGEIDGNKVTLDWAKPKGEGG 96

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEF 404
           S     P+ +     TL V  L    + E L + F      R +  R+T       F++F
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDF 61

Query: 405 YDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
                A+ A   +   ++ G ++ L+ ++P G   
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGG 96

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 56.5 bits (137), Expect = 5e-10
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 11/92 (11%)

Query: 351 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FI 402
              S     +  L V  L   V  + LH  F  +G+I +I      +T+    H+   F+
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE---KHRGFAFV 59

Query: 403 EFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           EF     A  A+  +N S++ G+ I++  ++P
Sbjct: 60  EFELAEDAAAAIDNMNESELFGRTIRVNLAKP 91

>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 = 56.1 bits (136), Expect = 6e-10
 Identities = 24/87 (27%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNA 328
             R L+V  +   V+D  L A F  FGDI  I     Y   KHRGF  + +     A  A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSE 355
           +  +    L  R + ++ + P      
Sbjct: 71  IDNMNESELFGRTIRVNLAKPMRIKES 97

>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 = 56.5 bits (137), Expect = 6e-10
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 5/98 (5%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIR 323
           P  +   R++FV NI     + +LK +F + G + +          K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 324 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
            A +AM+ L  +    R L +  +  + N  E  +   
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 = 46.9 bits (112), Expect = 1e-06
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
           ++ V N+    + E+L  IF   G +   R    +   K     F E+ D   A +A+R 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           LN  + +G+ ++++ +     + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKE 92

>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 = 56.2 bits (136), Expect = 8e-10
 Identities = 19/105 (18%), Positives = 42/105 (40%), Gaps = 11/105 (10%)

Query: 263 SVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMI 317
           S     P      +T+F+RN++ + E+  L  + +QFGD++ +           +G    
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

Query: 318 SYYDIRAARNAMKALQNKPLRR------RKLDIHYSIPKDNPSEK 356
            +    AA+  + A   +          R+L +  ++ +D  +  
Sbjct: 63  QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 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 = 48.9 bits (117), Expect = 3e-07
 Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 17/99 (17%)

Query: 350 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---F 401
                       T+ + NL      E L ++   +G+++ +      DT+H    K   F
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH---SKGCAF 61

Query: 402 IEFYDIRAAETALRTLNRS------DVAGKQIKLEASRP 434
            +F    AA+  L   +         + G+Q+K++ +  
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>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 = 56.7 bits (137), Expect = 9e-10
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
           P+  L V  ++    + +L+ +F ++G I  +         + RGF  + + ++  A+ A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 329 MKALQNKPLRRRKLDIHYSIPK 350
            +      L  R++ + +SI K
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 54.7 bits (132), Expect = 5e-09
 Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 5/91 (5%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 403
                         L VF L    +  +L ++F  YG I ++     + + +     F+ 
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           F ++  A+ A    N  ++ G++I+++ S  
Sbjct: 95  FENVDDAKEAKERANGMELDGRRIRVDFSIT 125

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 56.7 bits (137), Expect = 1e-09
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 255 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----- 309
             Q        G  P       +L V N+        L+ +FE++G +  +Y        
Sbjct: 27  GQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 86

Query: 310 KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 350
           + RGF  + ++D R A +AM A+    L  R+L +  +   
Sbjct: 87  ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 54.0 bits (130), Expect = 1e-08
 Identities = 24/128 (18%), Positives = 51/128 (39%), Gaps = 6/128 (4%)

Query: 318 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEE 376
           S++    +   +    +         +            D    T L V NL    S + 
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDT 63

Query: 377 LHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA 431
           L ++F  YG + ++     R T+      F+ F+D R AE A+  ++ + + G++++++ 
Sbjct: 64  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

Query: 432 SRPGGARR 439
           +R G    
Sbjct: 124 ARYGRPPD 131

>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 = 54.9 bits (133), Expect = 1e-09
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 6/89 (6%)

Query: 258 GVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRG 313
           G S  S  G  P  E   RT+FV N+ + V +  L  LF Q G +  +        K + 
Sbjct: 1   GSSGSS--GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS 58

Query: 314 FVMISYYDIRAARNAMKALQNKPLRRRKL 342
           F  + +    +   A+  L    L  R +
Sbjct: 59  FGFVCFKHPESVSYAIALLNGIRLYGRPI 87

>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 = 51.9 bits (125), Expect = 2e-08
 Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDI 407
           P++++A++ T+ V NL++ V  E L+++F   G + ++     R+ + K +  F+ F   
Sbjct: 10  PAQEEADR-TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK-SFGFVCFKHP 67

Query: 408 RAAETALRTLNRSDVAGKQIK 428
            +   A+  LN   + G+ I 
Sbjct: 68  ESVSYAIALLNGIRLYGRPIN 88

>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 = 55.3 bits (134), Expect = 1e-09
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
            + T+ V N++ +  +++L+ LF  FG I  IY A      + +GF  IS++    A  A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           +  +         L++ ++ P  N
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTN 97

>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 = 54.5 bits (132), Expect = 2e-09
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDI 407
           P+ +  +  T+ V NL       +L ++F  +G I  I     + T       FI F+  
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 408 RAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
             A  A+  ++        + +E ++P     
Sbjct: 68  EDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>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 = 55.3 bits (134), Expect = 1e-09
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 406
            P  +     T+ V  LD  VS   L ++F   G +        R T     + F+EF  
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRP 434
              A+ A++ ++   + 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 = 53.0 bits (128), Expect = 9e-09
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 5/88 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
              T++V  ++  V +  L  LF Q G +   +        +H+G+  + +     A  A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEK 356
           +K +    L  + + ++ +   +     
Sbjct: 74  IKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>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 = 55.4 bits (134), Expect = 1e-09
 Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 5/90 (5%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIR 323
           P        LFV +I+   ++ E++  F  +G+I+ I+          +G+ ++ Y   +
Sbjct: 20  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79

Query: 324 AARNAMKALQNKPLRRRKLDIHYSIPKDNP 353
            A  A +AL    +  + + + +   K   
Sbjct: 80  QALAAKEALNGAEIMGQTIQVDWCFVKGPK 109

>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 = 55.0 bits (133), Expect = 2e-09
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L V ++      +E+ + F  YGEI+ I     R T     +  +E+   + A  A   
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           LN +++ G+ I+++     G +R
Sbjct: 88  LNGAEIMGQTIQVDWCFVKGPKR 110

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.3 bits (134), Expect = 2e-09
 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
               LFV  ++    + ++   F ++G+I+ I+          +G+ ++ Y   + A+ A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNP 353
           M+ L  + L  + + + +   +  P
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVRGPP 106

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.9 bits (125), Expect = 3e-08
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L V  +    + E++H  F  YGEI+ I     R T +   +  +E+   + A+ A+  
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 417 LNRSDVAGKQIKLEASRP 434
           LN  D+ G+ I ++    
Sbjct: 85  LNGQDLMGQPISVDWCFV 102

>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 = 55.5 bits (134), Expect = 2e-09
 Identities = 22/116 (18%), Positives = 48/116 (41%), Gaps = 7/116 (6%)

Query: 324 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGI 383
           A    M+   +K +           P     +K+ ++ ++ V N+D   + ++L   F  
Sbjct: 1   AIAPCMQTTHSK-MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 59

Query: 384 YGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
            G I  I     + + H   + +IEF +  + + A+  ++ +   G+ IK+   R 
Sbjct: 60  CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT 114

>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 = 46.3 bits (110), Expect = 4e-06
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAAR 326
           E   R+++V N++      +L+A F   G I  I   C       +G+  I + +  +  
Sbjct: 33  EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92

Query: 327 NAMKALQNKPLRRRKL 342
            A+ A+     R R +
Sbjct: 93  AAV-AMDETVFRGRTI 107

>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 = 55.3 bits (134), Expect = 2e-09
 Identities = 18/113 (15%), Positives = 43/113 (38%), Gaps = 15/113 (13%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-------HRGFVMISYYDIRAARN 327
           S  +F++N++ ++++  L   F  FG+I     +CK        +G+  + +    AA  
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNI----LSCKVVCDENGSKGYGFVHFETQEAAER 60

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDN----PSEKDANQGTLVVFNLDSSVSTEE 376
           A++ +    L  RK+ +     +         +      + + N     +   
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA 113

>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 = 53.8 bits (130), Expect = 6e-09
 Identities = 18/91 (19%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 361 GTLVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHNHKFIEFYDIRAAETALRTL 417
           G + + NLD S+  + L+  F  +G I   + + D      + F+ F    AAE A+  +
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 418 NRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
           N   +  +++ +   +    R   + +  ++
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKE 96

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 55.9 bits (135), Expect = 2e-09
 Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 12/106 (11%)

Query: 332 LQNKPLRRRKLDIHYSIPKDNPSEKDANQG-TLVVFNLDSSVSTEELHQIFGIYGEIREI 390
           +    +   +  +         S   A     L V  L   V  + LH  F  +G+I +I
Sbjct: 34  VAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 93

Query: 391 -----RDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIK 428
                 +T+    H+   F+EF     A  A+  +N S++ G+ I+
Sbjct: 94  QIPLDYETEK---HRGFAFVEFELAEDAAAAIDNMNESELFGRTIR 136

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 54.4 bits (131), Expect = 6e-09
 Identities = 23/88 (26%), Positives = 31/88 (35%), Gaps = 5/88 (5%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGF 314
                 G         R L+V  +   V+D  L A F  FGDI  I         KHRGF
Sbjct: 48  GGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGF 107

Query: 315 VMISYYDIRAARNAMKALQNKPLRRRKL 342
             + +     A  A+  +    L  R +
Sbjct: 108 AFVEFELAEDAAAAIDNMNESELFGRTI 135

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 54.7 bits (132), Expect = 3e-09
 Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 13/100 (13%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRT----------IYT---ACKHRGFVMISYY 320
            + T+FV+ +  NV    +   F+Q G I+T          +YT     K +G   +S+ 
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 321 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
           D  +A+ A+     K      + + ++  + + +    N 
Sbjct: 66  DPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNG 105

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 49.7 bits (119), Expect = 2e-07
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 14/94 (14%)

Query: 355 EKDANQ-GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--------KHNHK----- 400
           E+D +   T+ V  L  +V+ E +   F   G I+  + T          +   K     
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 401 FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
            + F D  +A+ A+   +  + +G  IK+  +  
Sbjct: 61  TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATR 94

>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 = 54.1 bits (131), Expect = 3e-09
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 5/94 (5%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKF 401
           S               L VF L    +  +L ++F  YG I ++     + ++      F
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG 435
           + F ++  A+ A    N  ++ G++I++     G
Sbjct: 62  VYFENVDDAKEAKERANGMELDGRRIRVSGPSSG 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 = 53.4 bits (129), Expect = 6e-09
 Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
           P+  L V  ++    + +L+ +F ++G I  +         + RGF  + + ++  A+ A
Sbjct: 14  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73

Query: 329 MKALQNKPLRRRKLDIHYS 347
            +      L  R++ +   
Sbjct: 74  KERANGMELDGRRIRVSGP 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 53.9 bits (130), Expect = 4e-09
 Identities = 16/94 (17%), Positives = 34/94 (36%), Gaps = 13/94 (13%)

Query: 265 VGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG-----DIRTIY--TACKHRGFVMI 317
           +G H    H   T+ +RNI  +     +      +      +IR I      ++RGF  +
Sbjct: 1   MGHHH--HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFV 58

Query: 318 SYYDIRAARNAMKALQNKPLRR----RKLDIHYS 347
                  A   ++ LQ+         + + + ++
Sbjct: 59  QLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 13/85 (15%), Positives = 30/85 (35%), Gaps = 11/85 (12%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETAL 414
           T+++ N+      + +      Y    +  IR  + K   +     F++      A   L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 415 RTLNRSD----VAGKQIKLEASRPG 435
           + L        + GK I ++ ++  
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKSA 95

>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 = 53.3 bits (129), Expect = 5e-09
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 11/75 (14%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FIEFYDIRAAETA 413
            L V  L   V  + LH  F  +G+I +I      +T+    H+   F+EF     A  A
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE---KHRGFAFVEFELAEDAAAA 65

Query: 414 LRTLNRSDVAGKQIK 428
           +  +N S++ G+ I+
Sbjct: 66  IDNMNESELFGRTIR 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 = 53.3 bits (129), Expect = 5e-09
 Identities = 22/74 (29%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
             R L+V  +   V+D  L A F  FGDI  I         KHRGF  + +     A  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 329 MKALQNKPLRRRKL 342
           +  +    L  R +
Sbjct: 66  IDNMNESELFGRTI 79

>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 = 52.5 bits (127), Expect = 7e-09
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDI---RTIY---TACKHRGFVMISYYDIRAARNA 328
           +  LFV ++N NV+D  L+  F+ F        ++   T    RG+  +S+     A+NA
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG-SSRGYGFVSFTSQDDAQNA 59

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           M ++Q + L  R L I+++   ++
Sbjct: 60  MDSMQGQDLNGRPLRINWAAKLEH 83

>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 = 46.3 bits (111), Expect = 1e-06
 Identities = 12/73 (16%), Positives = 28/73 (38%), Gaps = 5/73 (6%)

Query: 367 NLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           +L+ +V  E L   F  +             T     + F+ F     A+ A+ ++   D
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 67

Query: 422 VAGKQIKLEASRP 434
           + G+ +++  +  
Sbjct: 68  LNGRPLRINWAAK 80

>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 = 52.9 bits (128), Expect = 8e-09
 Identities = 21/94 (22%), Positives = 43/94 (45%), Gaps = 5/94 (5%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAA 325
           G   S  L+V +++ N+ +  L+ +FE FG I  I         + +G+  I++ D   A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
           R A++ L    L  R + + +   + +     ++
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94

>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 = 48.7 bits (117), Expect = 2e-07
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L V +L  +++ + L  IF  +G+I  I      DT     + FI F D   A  AL  
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 417 LNRSDVAGKQIKLEASRP 434
           LN  ++AG+ +++     
Sbjct: 67  LNGFELAGRPMRVGHVTE 84

>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 = 53.0 bits (128), Expect = 8e-09
 Identities = 20/103 (19%), Positives = 48/103 (46%), Gaps = 7/103 (6%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRA 324
           P G+    T+FV  I+  ++++E+++ F ++G ++ +          +G+  +S+Y+   
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFN 367
            +  ++         +KL +  +I K N S         ++FN
Sbjct: 63  VQKIVE--SQINFHGKKLKLGPAIRKQNLSTYHVQPRP-LIFN 102

>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 = 39.1 bits (92), Expect = 6e-04
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD-TQHKHNHKFIEFYDIRAA 410
           E      T+ V  +D  +   E+   F  YG ++E   I D T     + F+ FY+    
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63

Query: 411 ETALRTLNRSDVAGKQIK 428
           +  +   ++ +  GK++K
Sbjct: 64  QKIVE--SQINFHGKKLK 79

>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 = 53.1 bits (128), Expect = 9e-09
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 10/97 (10%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARN 327
               R LFV  +N    + ++  LF+ FG I             +G   + +     A+ 
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71

Query: 328 AMKALQNK---PLRRRKLDIHYSIPKDNPSEKDANQG 361
           A+ AL      P     L + ++   D   E   + G
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFA---DTDKESGPSSG 105

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 45.4 bits (108), Expect = 4e-06
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 14/90 (15%)

Query: 352 NPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEF 404
           + SE    +   L V  L+   S E++ ++F  +G I E   +R      + K   F++F
Sbjct: 6   SGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG--PDGSSKGCAFVKF 63

Query: 405 YDIRAAETALRTLNRSDVAGKQIKLEASRP 434
                A+ A+  L+     G Q    AS  
Sbjct: 64  SSHTEAQAAIHALH-----GSQTMPGASSS 88

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 16/86 (18%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAET 412
              +  L +  L  S + EEL +I   +G ++++R             ++E+ +   A  
Sbjct: 14  SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQ 73

Query: 413 ALRTLNRSDVAGKQIKLEASRPGGAR 438
           A+  ++   +    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 = 11/83 (13%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAM 329
               LF+  +  +    EL+ + +  G ++ +        K +G   + Y +   A  A+
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75

Query: 330 KALQNKPLRRRKLDIHYSIPKDN 352
             +    ++   + +  S    +
Sbjct: 76  MKMDGMTIKENIIKVAISNSGPS 98

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR--GFVMISYYDIRAARNAMKAL 332
            R L +RNI  +++   L +L  Q+G + +            V ++Y     AR A+  L
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKL 74

Query: 333 QNKPLRRRKLDIHYSIPK 350
               L    L + Y   +
Sbjct: 75  NGFQLENFTLKVAYIPDE 92

>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 = 2e-08
 Identities = 12/71 (16%), Positives = 22/71 (30%), Gaps = 2/71 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK--FIEFYDIRAAETALRTLNR 419
            L + N+   +  E L  +   YG +                + +     A  AL  LN 
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76

Query: 420 SDVAGKQIKLE 430
             +    +K+ 
Sbjct: 77  FQLENFTLKVA 87

>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 = 52.7 bits (127), Expect = 1e-08
 Identities = 19/93 (20%), Positives = 47/93 (50%), Gaps = 8/93 (8%)

Query: 354 SEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHNHK---FIEFYD 406
           S+K+  +G  L +++L      ++L Q+F  +G +   +   D Q   + K   F+ + +
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS-KCFGFVSYDN 76

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
             +A+ A++++N   +  K++K++  R     +
Sbjct: 77  PVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 109

>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 = 49.6 bits (119), Expect = 2e-07
 Identities = 20/118 (16%), Positives = 49/118 (41%), Gaps = 14/118 (11%)

Query: 252 GGVSNQGVSAGSVVGEHPYGEHPSRT-LFVRNINSNVEDSELKALFEQFGDIRTIYTACK 310
           G   + G++  S+       E P    LF+ ++     D +L  +F  FG++     + K
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNV----VSAK 56

Query: 311 ---------HRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
                     + F  +SY +  +A+ A++++    +  ++L +     K++     ++
Sbjct: 57  VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 52.3 bits (126), Expect = 2e-08
 Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIE 403
           S      SE  +    L V N+       +L Q+FG +G+I ++    ++   K   F+ 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
           F +   A+ A   L+ + V G++I++  +       
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEVNNATARVMTN 97

>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 = 51.5 bits (124), Expect = 3e-08
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARNAMK 330
             + L V NI     D +L+ +F QFG I     I+     +GF  +++ +   A  A +
Sbjct: 14  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73

Query: 331 ALQNKPLRRRKLDIHYSIPKDNPSEK 356
            L    +  RK++++ +  +   +  
Sbjct: 74  KLHGTVVEGRKIEVNNATARVMTNSG 99

>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 = 52.2 bits (126), Expect = 2e-08
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 5/93 (5%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 406
             S   +++G L V  L    + + L Q+F  YG+I E+     R+TQ      F+ F +
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
           I  A+ A+  +N   V G+QI+++ +      R
Sbjct: 64  IDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96

>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 = 50.3 bits (121), Expect = 8e-08
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
               LFV  ++ +  +  L+ +F ++G I  +         + RGF  +++ +I  A++A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           M A+  K +  R++ +  +    +
Sbjct: 71  MMAMNGKSVDGRQIRVDQAGKSSD 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 = 52.6 bits (126), Expect = 2e-08
 Identities = 11/69 (15%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 272 EHPSRTLFVRN--INSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAM 329
            + +++L V N  + + V  ++L  + E+ G +  +     ++ +    Y     ++ A 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAY 80

Query: 330 KALQNKPLR 338
             L  K + 
Sbjct: 81  VTLNGKEVV 89

>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 = 50.3 bits (120), Expect = 1e-07
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 362 TLVVFN--LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 418
           +LVV N  L + VS  +L  +    G +  +    +K  + F  +     ++ A  TLN
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-PYSFARYRTTEESKRAYVTLN 84

>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 = 52.2 bits (125), Expect = 2e-08
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 272 EHPSRTLFVRNI-NSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           +   R + + N+ +S   DS +  L E +G I+      + +    I       A   + 
Sbjct: 22  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVD 80

Query: 331 ALQNKP--LRRRKLDIHYS 347
               K    + R + +  S
Sbjct: 81  HCLKKALWFQGRCVKVDLS 99

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 52.0 bits (125), Expect = 3e-08
 Identities = 23/108 (21%), Positives = 44/108 (40%), Gaps = 10/108 (9%)

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGE 386
           +  AL   PL    L    +       E    +G  L +++L    +  +L   F  +G 
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEG--PEGCNLFIYHLPQEFTDTDLASTFLPFGN 66

Query: 387 I---REIRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIK 428
           +   +   D Q   + K   F+ F +  +A+ A++ +N   V  K++K
Sbjct: 67  VISAKVFIDKQTSLS-KCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK 113

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 45.1 bits (107), Expect = 8e-06
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 13/74 (17%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRAARNA 328
           LF+ ++     D++L + F  FG++     + K          + F  +S+ +  +A+ A
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNV----ISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98

Query: 329 MKALQNKPLRRRKL 342
           +KA+    +  ++L
Sbjct: 99  IKAMNGFQVGTKRL 112

>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 = 51.9 bits (125), Expect = 3e-08
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 4/92 (4%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAM 329
               LF+  +N    +  LKA+F + G I  +        K RGF  I++ +   A+NA 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 330 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
           K +  K L  + + +  +      S       
Sbjct: 66  KDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPP 97

>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 = 50.4 bits (121), Expect = 1e-07
 Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 13/97 (13%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEFYDIRAAET 412
           + G L +  L+   + + L  +FG +G I E   I+D   K   +   FI F +   A+ 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKS--RGFAFITFENPADAKN 63

Query: 413 ALRTLNRSDVAGKQIKLE-----ASRPGGARRFMVQS 444
           A + +N   + GK IK+E     + + GG RR    S
Sbjct: 64  AAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASS 100

>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 = 51.1 bits (123), Expect = 3e-08
 Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 8/89 (8%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YTACKHRG 313
           S+GS             T++V N+  ++ +++L  +F ++G +  +       T  K +G
Sbjct: 2   SSGSSGMSGGLAP-SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR-KSKG 59

Query: 314 FVMISYYDIRAARNAMKALQNKPLRRRKL 342
              I + D  +A+N  +A+ NK L  R +
Sbjct: 60  VAFILFLDKDSAQNCTRAINNKQLFGRVI 88

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 49.9 bits (120), Expect = 1e-07
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 403
                     ++ T+ V NL  S++  +L++IF  YG++ ++   + K   K     FI 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 404 FYDIRAAETALRTLNRSDVAGKQIK 428
           F D  +A+   R +N   + G+ IK
Sbjct: 65  FLDKDSAQNCTRAINNKQLFGRVIK 89

>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 = 52.4 bits (126), Expect = 3e-08
 Identities = 28/128 (21%), Positives = 57/128 (44%), Gaps = 13/128 (10%)

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTE 375
           ++S YD       ++ LQ +  +         IP    + +      L+V  + ++V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 376 ELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
           +L Q+F  YG I  +     R+T+    + F++F    +A+ A+  LN  ++  K++K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 431 ASRPGGAR 438
            +  G  R
Sbjct: 118 LAASGHQR 125

>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 = 47.8 bits (114), Expect = 1e-06
 Identities = 20/115 (17%), Positives = 40/115 (34%), Gaps = 13/115 (11%)

Query: 256 NQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK----- 310
            Q         +        R L V  I + V++ +L+ LFE++G I     + K     
Sbjct: 23  QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI----ESVKIVCDR 78

Query: 311 ----HRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
                RG+  + +    +A+ A+  L    +  ++L +  +             G
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVG 133

>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 = 51.9 bits (125), Expect = 3e-08
 Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 14/105 (13%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------K 310
           S+GS        +     +FV  +  +  D+ L+  FE FGDI                K
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDI----EEAVVITDRQTGK 57

Query: 311 HRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE 355
            RG+  ++  D  AA  A K   N  +  RK +++ +     P  
Sbjct: 58  SRGYGFVTMADRAAAERACKDP-NPIIDGRKANVNLAYLGAKPRS 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 = 39.6 bits (93), Expect = 6e-04
 Identities = 22/96 (22%), Positives = 37/96 (38%), Gaps = 6/96 (6%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIE 403
              + S+KD     + V  L    +   L + F  +G+I E      R T     + F+ 
Sbjct: 6   SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
             D  AAE A +  N   + G++  +  +  G   R
Sbjct: 66  MADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPR 100

>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 = 51.6 bits (124), Expect = 4e-08
 Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 8/93 (8%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 320
           G     +H +  LF+  I  N+++ +LK LFE+FG I  +          H+G   ++Y 
Sbjct: 4   GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63

Query: 321 DIRAARNAMKALQNK---PLRRRKLDIHYSIPK 350
           +  +A  A  AL  +   P   R + +  +  +
Sbjct: 64  ERESALKAQSALHEQKTLPGMNRPIQVKPADSE 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 = 40.8 bits (96), Expect = 2e-04
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 12/88 (13%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEFYD 406
              KD +   L +  +  ++  ++L  +F  +G+I E   ++D +    HK   F+ + +
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKD-RFTGMHKGCAFLTYCE 64

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRP 434
             +A  A   L+      ++     +RP
Sbjct: 65  RESALKAQSALH-----EQKTLPGMNRP 87

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 50.8 bits (121), Expect = 4e-08
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 7/86 (8%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           S  L ++N+ + ++   L+ L  Q G + + +      G  +  Y     A  A  AL N
Sbjct: 7   SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-GIALCKYTTREEANKAQMALNN 65

Query: 335 KPLRRRKLDIHYSIPKDNPSEKDANQ 360
             L         +I  ++PSE +   
Sbjct: 66  CVLANT------TIFAESPSENEVQS 85

>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 = 51.2 bits (123), Expect = 4e-08
 Identities = 20/97 (20%), Positives = 44/97 (45%), Gaps = 5/97 (5%)

Query: 261 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFV 315
           A ++      G      L+V +++ N+ +  L+ +FE FG I +I         + +G+ 
Sbjct: 12  AAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYG 71

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
            I++ D   A+ A++ L    L  R + + +   + +
Sbjct: 72  FITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 48.1 bits (115), Expect = 6e-07
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 5/91 (5%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIE 403
             +N  +  A    L V +L  +++ + L  IF  +G I  I      +T     + FI 
Sbjct: 15  MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           F D   A+ AL  LN  ++AG+ +K+     
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPMKVGHVTE 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 = 52.0 bits (124), Expect = 4e-08
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-HNHKFIEFYDIRAAETALRTLNRSD 421
           ++V NL   V+ + LHQIF  +G + +I            +++ D  +A+ A  +L+  +
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90

Query: 422 V--AGKQIKLEASRP 434
           +  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 = 50.8 bits (121), Expect = 1e-07
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 260 SAGSVVGEHPYGEHPSRTLF--VRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VM 316
           ++ + V         S  L   V N+   V    L  +F +FG +  I T  K+  F  +
Sbjct: 11  ASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQAL 70

Query: 317 ISYYDIRAARNAMKALQNKPL--RRRKLDIHYSIPKD 351
           + Y D  +A++A  +L  + +      L I +S    
Sbjct: 71  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107

>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 = 50.8 bits (122), Expect = 5e-08
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 15/93 (16%)

Query: 265 VGEHPYGEHP--SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----------- 311
           +G H +      + T+FV+ +  NV    +   F+Q G I+T     +            
Sbjct: 1   MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60

Query: 312 --RGFVMISYYDIRAARNAMKALQNKPLRRRKL 342
             +G   +S+ D  +A+ A+     K      +
Sbjct: 61  KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 93

>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 = 49.2 bits (118), Expect = 2e-07
 Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 13/94 (13%)

Query: 350 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--------KHNHK- 400
             +     ++  T+ V  L  +V+ E +   F   G I+  + T          +   K 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 401 ----FIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
                + F D  +A+ A+   +  + +G  IK+ 
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.4 bits (121), Expect = 5e-08
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 1/74 (1%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           G    R++FV      V+ ++L   F  FG + ++        F ++   D+ A    + 
Sbjct: 4   GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL- 62

Query: 331 ALQNKPLRRRKLDI 344
           +     L   +L +
Sbjct: 63  SQSQHSLGGHRLRV 76

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 44.2 bits (105), Expect = 9e-06
 Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           ++ V      V + +L + F  +G +  +   + K     +E  D+ A E  L   ++  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHS 68

Query: 422 VAGKQIKLEASRP 434
           + G ++++     
Sbjct: 69  LGGHRLRVRPREQ 81

>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 = 56.0 bits (134), Expect = 6e-08
 Identities = 63/460 (13%), Positives = 131/460 (28%), Gaps = 149/460 (32%)

Query: 31  FWKPNTMSDQQDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIV 90
           FW   T+  +Q+  V     KFV      N+         +L     T  R       + 
Sbjct: 68  FW---TLLSKQEEMVQ----KFVEEVLRINY--------KFLMSPIKTEQRQPSMMTRMY 112

Query: 91  GEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSE------------ 138
            E+      +  +N      K   N++       L   R  +  ++              
Sbjct: 113 IEQ-----RDRLYNDNQVFAKY--NVSRLQPYLKL---RQALLELRPAKNVLIDGVLGSG 162

Query: 139 -SSLFSSSLSDI-FTRKMKLSGNEI--LSRQPLNAVASHHQPEEPFESLKEIEAQTIGNL 194
            + +            KM     +I  L+      + + + PE   E L+++  Q   N 
Sbjct: 163 KTWVALDVCLSYKVQCKM---DFKIFWLN------LKNCNSPETVLEMLQKLLYQIDPNW 213

Query: 195 --LPDEDDLFSGVTDDMGH---NFQANT--------VDDLED------FD-----LFSSG 230
               D           +         +         + ++++      F+     L ++ 
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT- 272

Query: 231 GGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHP--SRTLFVRNINSNVE 288
                    R   V   +DF+   +   +S    +  H     P   ++L ++ ++   +
Sbjct: 273 ---------RFKQV---TDFLSAATTTHIS----LDHHSMTLTPDEVKSLLLKYLDCRPQ 316

Query: 289 DSELKALFEQFGDIRTIYTACKHRGFV--MISYYDIRAARNAMKALQN-KPLRRRKLD-- 343
           D     L  +                   +I+     + R+ +    N K +   KL   
Sbjct: 317 D-----LPRE---------VLTTNPRRLSIIA----ESIRDGLATWDNWKHVNCDKLTTI 358

Query: 344 IHYSIPKDNPSEKDANQGTLVVFNLDSSVST-------------------EELHQ----- 379
           I  S+    P+E       L VF   + + T                    +LH+     
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418

Query: 380 ---------IFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 410
                    I  IY E++   + ++  +   ++ Y+I   
Sbjct: 419 KQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 458

>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 = 45.6 bits (107), Expect = 1e-04
 Identities = 93/683 (13%), Positives = 191/683 (27%), Gaps = 215/683 (31%)

Query: 173 HHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDL-------EDFD 225
           HH     FE   E +     ++L   +D F  V +     F    V D+       E+ D
Sbjct: 2   HHHHHMDFE-TGEHQ-YQYKDILSVFEDAF--VDN-----FDCKDVQDMPKSILSKEEID 52

Query: 226 -LFSSGGGMELEGDDRLFAV----QKN--SDFVGGVSNQG----VSAGSVVGEHPYGEHP 274
            +  S     + G  RLF      Q+     FV  V        +S        P     
Sbjct: 53  HIIMSKD--AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMM-- 108

Query: 275 SRTLFVRNINSNVEDSELKALF-----EQFGDIRTIYTACKHRGFVMISYYDIRAARNAM 329
              +++   +    D+++ A +     + +  +R      +    V+I         + +
Sbjct: 109 -TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI---------DGV 158

Query: 330 K----------ALQNKPLRRRKLD-IHY-SIPKDNPSEKDANQGTLVVFNLDSSVSTEEL 377
                         +  ++ +    I + ++   N  E        +++ +D +  T   
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN-WTSRS 217

Query: 378 HQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA 437
                I   I  I+        +       +  E  L  L   +V   +    A      
Sbjct: 218 DHSSNIKLRIHSIQA-------ELRRLLKSKPYENCLLVL--LNVQNAKA-WNA------ 261

Query: 438 RRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRS------ 491
             F         +L+ C+I              ++T+          L +AT +      
Sbjct: 262 --F---------NLS-CKI--------------LLTTR--FKQVTDFLSAATTTHISLDH 293

Query: 492 PAIALTESHQTSSV--------PNGLPSLARVGS------IG----------KQFGHYEP 527
            ++ LT   +  S+        P  LP      +      I             + H   
Sbjct: 294 HSMTLTPD-EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352

Query: 528 N-------LSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSV-----G 575
           +        SL+ ++         P    +  D L+   P +     A I + +      
Sbjct: 353 DKLTTIIESSLNVLE---------PAEYRKMFDRLSV-FPPS-----AHIPTILLSLIWF 397

Query: 576 TKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHG-----NPYVWNNSNSHQQ- 629
             IK   D   +        L+E        P+  + S+          + N    H+  
Sbjct: 398 DVIKS--DVMVVVNKLHKYSLVE------KQPKESTISIPSIYLELKVKLENEYALHRSI 449

Query: 630 --HPSSPMVWPN---SPSFLNGLHANRVA-HMPG---------FPRVPPLMLN------- 667
             H + P  + +    P +L+    + +  H+           F     + L+       
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM---VFLDFRFLEQK 506

Query: 668 --ATSPAHHHIGSAPAVNPSLWDRQH--AYAGESPETSNFHLGSLGSGGFLGRSPSH--- 720
               S A +  GS   +  +L   +    Y  ++       + ++    FL +   +   
Sbjct: 507 IRHDSTAWNASGS---ILNTLQQLKFYKPYICDNDPKYERLVNAILD--FLPKIEENLIC 561

Query: 721 --HVDIASQNILSHVGGNCMDMT 741
             + D+  +  L        +  
Sbjct: 562 SKYTDLL-RIALMAEDEAIFEEA 583

>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 = 50.8 bits (122), Expect = 6e-08
 Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 6/108 (5%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKF 401
           S       +  +N   + V +L   ++TE++   F  +G I +        T     + F
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKL-EASRPGGARRFMVQSEQEQ 448
           + F++   AE A++ +    + G+QI+   A+R   A +   +S  +Q
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQ 109

>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 = 50.8 bits (122), Expect = 7e-08
 Identities = 20/108 (18%), Positives = 43/108 (39%), Gaps = 7/108 (6%)

Query: 261 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YTACKHRGF 314
             S              +FV +++  +   ++KA F  FG I          T  K +G+
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATG-KSKGY 59

Query: 315 VMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT 362
             +S+++   A NA++ +  + L  R++  +++  K    +      T
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT 107

>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 = 50.2 bits (121), Expect = 6e-08
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAE 411
           +A+  ++ V N+D   + EEL   F   G +  +     + + H     +IEF D  +  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 412 TALRTLNRSDVAGKQIKLEASRP 434
           T+L  L+ S   G+QIK+   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 = 45.6 bits (109), Expect = 2e-06
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAAR 326
           E  +R+++V N++      EL+A F   G +  +   C       +GF  I + D  + R
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 327 NAMKALQNKPLRRRKLDIHYSIPK 350
            ++ AL     R R++ +      
Sbjct: 63  TSL-ALDESLFRGRQIKVIPKRTN 85

>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 = 50.3 bits (121), Expect = 7e-08
 Identities = 19/99 (19%), Positives = 41/99 (41%), Gaps = 14/99 (14%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----------RGFVMISYY 320
           G   S  +F+ N++  +++  L   F  FG I                   +G+  I++ 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFA 56

Query: 321 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
              A+  A++A+  + L  R + + Y+  KD+     ++
Sbjct: 57  SFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 46.0 bits (110), Expect = 2e-06
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI------RDTQHKHNHKFIEFYDIRAAET 412
               + + NLD  +  + L+  F  +G I +        DT +   + FI F    A++ 
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 413 ALRTLNRSDVAGKQIKLEASRPGGARR 439
           A+  +N   +  + I +  +    ++ 
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDSKG 90

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 50.8 bits (122), Expect = 8e-08
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 4/94 (4%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT---IYTAC-KHRGFVMISYYDIRAAR 326
           G      L V N++  V D++++ LF +FG ++     Y    +  G   + +     A 
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 90

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
            AMK  +  PL  R +DI     + +      + 
Sbjct: 91  KAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 = 42.0 bits (99), Expect = 1e-04
 Identities = 14/82 (17%), Positives = 32/82 (39%), Gaps = 4/82 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD-TQHKHNHKFIEFYDIRAAETALRTL 417
            L+V NLD  VS  ++ ++F  +G +++     D +        + F     A  A++  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96

Query: 418 NRSDVAGKQIKLEASRPGGARR 439
               + G+ + ++         
Sbjct: 97  KGVPLDGRPMDIQLVASQIDLE 118

>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 = 49.9 bits (120), Expect = 1e-07
 Identities = 19/94 (20%), Positives = 29/94 (30%), Gaps = 11/94 (11%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI--REIRDTQHKHNHK-----FIEFY 405
              +      L + NL+ + S  EL              + D             +++F 
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD---VRTGTNRKFGYVDFE 66

Query: 406 DIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
                E AL  L    V G +IKLE  +     R
Sbjct: 67  SAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTR 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 = 44.2 bits (105), Expect = 1e-05
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGD-----IRTIYTACKHRGFVMISYYDIRAARNA 328
               LF+ N+N N   +ELK    +        +  + T   +R F  + +        A
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTG-TNRKFGYVDFESAEDLEKA 74

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           +  L    +   ++ +     +D 
Sbjct: 75  L-ELTGLKVFGNEIKLEKPKGRDG 97

>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 = 49.5 bits (119), Expect = 1e-07
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFG---DIRTIY---TACKHRGFVMISYYDIRAARN 327
               +FV +++  +  + + A F  FG   D R +    T  K +G+  +S+++   A N
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATG-KSKGYGFVSFFNKWDAEN 63

Query: 328 AMKALQNKPLRRRKLDIHYSIPK 350
           A++ +  + L  R++  +++  K
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 47.5 bits (114), Expect = 4e-07
 Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAE 411
             +   + V +L   ++T  +   F  +G I + R      T     + F+ F++   AE
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 412 TALRTLNRSDVAGKQIKLEASRP 434
            A++ +    + G+QI+   +  
Sbjct: 63  NAIQQMGGQWLGGRQIRTNWATR 85

>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 = 50.1 bits (120), Expect = 1e-07
 Identities = 19/100 (19%), Positives = 39/100 (39%), Gaps = 14/100 (14%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-------------RGFVMISYYD 321
           +  ++V+ +N +V   +L   F+Q G ++      +              +G   +SY D
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

Query: 322 IRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
              A+ A++    K  +  KL +  +  K  P     + G
Sbjct: 75  PPTAKAAVEWFDGKDFQGSKLKVSLARKK-PPMNSGPSSG 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 = 49.3 bits (118), Expect = 3e-07
 Identities = 18/101 (17%), Positives = 39/101 (38%), Gaps = 13/101 (12%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK------ 400
           S       ++D++   + V  L+ SV+ ++L   F   G ++  + T     H       
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 401 -------FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
                   + + D   A+ A+   +  D  G ++K+  +R 
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

>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 = 49.1 bits (118), Expect = 1e-07
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 9/79 (11%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YT-ACKHRGFVMISYYDIR 323
           G   S  L++R +     D +L  L + +G I +        T  CK  GFV   +    
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFV--DFDSPS 58

Query: 324 AARNAMKALQNKPLRRRKL 342
           AA+ A+ AL+   ++ +  
Sbjct: 59  AAQKAVTALKASGVQAQMA 77

>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 = 47.9 bits (115), Expect = 3e-07
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNR 419
           +  L    + ++L ++   YG+I   +    K  +K     F++F    AA+ A+  L  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 420 SDVAGKQIKLEASRPG 435
           S V  +  K      G
Sbjct: 70  SGVQAQMAKQSGPSSG 85

>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 = 49.9 bits (120), Expect = 1e-07
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 3/78 (3%)

Query: 365 VFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           V NLD  +  E L + F  +G I     + +        F+ F     A  A+  +N   
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI 79

Query: 422 VAGKQIKLEASRPGGARR 439
           VA K + +  ++    R+
Sbjct: 80  VATKPLYVALAQRKEERQ 97

>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 = 49.1 bits (118), Expect = 2e-07
 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
           L+V+N++  ++D  L+  F  FG I   + +    + +GF  + +     A  A+  +  
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 335 KPLRRRKLDIHYSIPKDNPSEKDAN 359
           + +  + L +  +  K+      ++
Sbjct: 78  RIVATKPLYVALAQRKEERQSGPSS 102

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARN 327
           G   +  +FVRN+  +     LK  F + G +          K +G  ++ +     A  
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 63

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPS 354
           A + +    L  R++D+        PS
Sbjct: 64  ACRMMNGMKLSGREIDVRIDRNASGPS 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 48.3 bits (116), Expect = 3e-07
 Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 3/89 (3%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAA 410
           S   +    + V NL    + + L   F   G +       +         ++F     A
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61

Query: 411 ETALRTLNRSDVAGKQIKLEASRPGGARR 439
           E A R +N   ++G++I +   R      
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNASGPS 90

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 49.6 bits (119), Expect = 2e-07
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRA 409
            +E  +    L V N+       +L Q+FG +G+I +   I + +      F+ F +   
Sbjct: 22  NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 81

Query: 410 AETALRTLNRSDVAGKQIKLEASRP 434
           A+ A   L+ + V G++I++  +  
Sbjct: 82  ADRAREKLHGTVVEGRKIEVNNATA 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 = 49.6 bits (119), Expect = 2e-07
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARN 327
            +   + L V NI     D +L+ +F QFG I     I+     +GF  +++ +   A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84

Query: 328 AMKALQNKPLRRRKLDIHYSIPK 350
           A + L    +  RK++++ +  +
Sbjct: 85  AREKLHGTVVEGRKIEVNNATAR 107

>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 = 52.0 bits (124), Expect = 2e-07
 Identities = 26/172 (15%), Positives = 53/172 (30%), Gaps = 18/172 (10%)

Query: 197 DEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSN 256
           D  + F+   +  GH+     +D  +D    S+  G   E  D         D +     
Sbjct: 1   DVGEEFNQEAEYGGHDQ----IDLYDDVISPSANNGDAPEDRD-------YMDTLPPTVG 49

Query: 257 QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYTAC----- 309
             V  G+              L++ N+     D +L       G  DI  I         
Sbjct: 50  DDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG 109

Query: 310 KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
           + +GF ++      +++  M  L  + L  +   +     +     +  ++ 
Sbjct: 110 QSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

>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 = 44.7 bits (105), Expect = 6e-05
 Identities = 15/94 (15%), Positives = 38/94 (40%), Gaps = 7/94 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETAL 414
            L + NL    + E+L +     G  +I EI+  +++ N +      +      +++  +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 415 RTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
             L + ++ G+   +         +F +QS +  
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTT 163

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 261 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFV 315
             S       G+     + V+N+   V   E+   F  +  I        +      G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYS 347
           M+++     A  A+  L ++P+  RK+ +   
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 43.4 bits (103), Expect = 2e-05
 Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 5/92 (5%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 403
                S        + V N+  +VS +E+   F  Y  I      ++           + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRPG 435
           F     A  A+  LN   +  +++KL     G
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>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 = 49.2 bits (118), Expect = 2e-07
 Identities = 15/104 (14%), Positives = 38/104 (36%), Gaps = 6/104 (5%)

Query: 261 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIY---TACKHRGFV 315
             S        + P  T F+ N+  +V +  +K  F       +R         + +GF 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
              + D+ +  +A+  L  + L  +++ +  +    +     ++
Sbjct: 61  YAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 44.6 bits (106), Expect = 7e-06
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK---FIEFYDIRAAETALRT 416
           T  + NL   V+ E + + F       +R  R+  +    K   + EF D+ +  +AL +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           LN   +  K+I+++ +     + 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 6/92 (6%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIY---TACKHRGFVMISYY 320
                 + P  T F+ N+  +V +  +K  F       +R         + +GF    + 
Sbjct: 10  HRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFE 69

Query: 321 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
           D+ +  +A+  L  + L  R++ +  +    +
Sbjct: 70  DLDSLLSALS-LNEESLGNRRIRVDVADQAQD 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 = 42.2 bits (100), Expect = 6e-05
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK---FIEFYDIRAAETALRT 416
           T  + NL   V+ E + + F       +R  R+  +    K   + EF D+ +  +AL +
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 417 LNRSDVAGKQIKLEASRP 434
           LN   +  ++I+++ +  
Sbjct: 80  LNEESLGNRRIRVDVADQ 97

>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 = 47.6 bits (114), Expect = 5e-07
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           G   S  +FV     ++ + EL+  F Q+GD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 331 ALQNKPLRRRKLDIHYSIPKDNPS 354
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>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 = 47.7 bits (114), Expect = 5e-07
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 11/96 (11%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRD--TQHKHNHKFIEFYD 406
            S       +L + +L+  +    + + F   GE    ++ IR+  T     + F+EF D
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 407 IRAAETALRTLNRSDVAG----KQIKL-EASRPGGA 437
           +  AE  L  +N   + G    K+ KL  A+  G +
Sbjct: 62  LATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97

>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 = 43.5 bits (103), Expect = 2e-05
 Identities = 12/71 (16%), Positives = 30/71 (42%), Gaps = 8/71 (11%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGD-------IRTIYTACKHRGFVMISYYDIRAAR 326
            + +L++ ++   ++++ +   F   G+       IR   T     G+  + + D+  A 
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTG-IPAGYCFVEFADLATAE 66

Query: 327 NAMKALQNKPL 337
             +  +  KPL
Sbjct: 67  KCLHKINGKPL 77

>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 = 47.7 bits (114), Expect = 6e-07
 Identities = 16/94 (17%), Positives = 32/94 (34%), Gaps = 5/94 (5%)

Query: 262 GSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVM 316
            S       G+     + V+N+   V   E+   F  +  I        +      G  M
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 317 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 350
           +++     A  A+  L ++P+  RK+ +      
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>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 = 43.4 bits (103), Expect = 2e-05
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 5/91 (5%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 403
                S        + V N+  +VS +E+   F  Y  I      ++           + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           F     A  A+  LN   +  +++KL     
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>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 = 47.7 bits (114), Expect = 7e-07
 Identities = 15/95 (15%), Positives = 30/95 (31%), Gaps = 12/95 (12%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDIRAA 325
              T+FV N++  V   +LK +F   G +                 RG   +++     A
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVV----VRADILEDKDGKSRGIGTVTFEQSIEA 69

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
             A+     + L  R + +          +    +
Sbjct: 70  VQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPE 104

>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 = 43.5 bits (103), Expect = 2e-05
 Identities = 17/111 (15%), Positives = 39/111 (35%), Gaps = 9/111 (8%)

Query: 349 PKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---F 401
              + + +    G+ + V NLD  V  ++L ++F + G +     + D   K   +    
Sbjct: 3   SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS--RGIGT 60

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLN 452
           + F     A  A+   N   +  + + ++       +      E+ Q    
Sbjct: 61  VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGP 111

>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 = 47.6 bits (114), Expect = 8e-07
 Identities = 16/116 (13%), Positives = 34/116 (29%), Gaps = 19/116 (16%)

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 384
             +    L+   ++ +              +   N   L + NL  S+  +EL  +   +
Sbjct: 1   GSSGSSGLKASGVQAQM--------AKQQEQDPTN---LYISNLPLSMDEQELENMLKPF 49

Query: 385 GEI---REIRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           G++   R +RD       +   F         E  +   N   +         + P
Sbjct: 50  GQVISTRILRD--SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 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 = 46.5 bits (111), Expect = 2e-06
 Identities = 11/90 (12%), Positives = 29/90 (32%), Gaps = 15/90 (16%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDIRAARNAM 329
           L++ N+  ++++ EL+ + + FG +     + +         RG               +
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQV----ISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 330 KALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
                K ++        + P      K + 
Sbjct: 84  GHFNGKFIKTPPGVSAPTEPLL---CKFSG 110

>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 = 47.5 bits (113), Expect = 9e-07
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNA 328
           P        + V  +  +    +LK    + GD+   Y      G  ++ +        A
Sbjct: 10  PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKEDMTYA 67

Query: 329 MKALQNKPLRRRKLDIHY 346
           ++ L N   R  + +  Y
Sbjct: 68  VRKLDNTKFRSHEGETAY 85

>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 = 41.3 bits (97), Expect = 1e-04
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            +VV  L  S S ++L       G++       ++     +EF        A+R L+ + 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKEDMTYAVRKLDNTK 75

Query: 422 VAGKQIKLEASRP 434
               + +    R 
Sbjct: 76  FRSHEGETAYIRV 88

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.4 bits (113), Expect = 9e-07
 Identities = 10/77 (12%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARN 327
           +  +R+++++   ++    ++K   E  G +  I          +G + + +  I +A+ 
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 328 AMKALQNKPLRRRKLDI 344
            ++    +  +   L I
Sbjct: 68  FVE-TPGQKYKETDLLI 83

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.9 bits (109), Expect = 3e-06
 Identities = 11/98 (11%), Positives = 34/98 (34%), Gaps = 8/98 (8%)

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHNHK---FIEFYDIRAA 410
           + D    ++ +    +  + +++ +     G++  I+         K   F+ F  I +A
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65

Query: 411 ETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
           +  +            + +       A++     E++Q
Sbjct: 66  KKFV-ETPGQKYKETDLLILFKDDYFAKK---NEERKQ 99

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 49.1 bits (117), Expect = 1e-06
 Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT---IYTAC-KHRGFVMISYYDIRA 324
             G      L V N++  V D++++ LF +FG ++     Y    +  G   + +     
Sbjct: 82  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 141

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
           A  AMK  +  PL  R +DI     + +      + 
Sbjct: 142 ALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 41.8 bits (98), Expect = 3e-04
 Identities = 18/113 (15%), Positives = 41/113 (36%), Gaps = 9/113 (7%)

Query: 333 QNKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIREIR 391
           + KPL  +    H          +    G  L+V NLD  VS  ++ ++F  +G +++  
Sbjct: 62  RPKPLPDKWQ--HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA- 118

Query: 392 DTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
              +  + +      + F     A  A++      + G+ + ++         
Sbjct: 119 AVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLE 171

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.4 bits (115), Expect = 1e-06
 Identities = 11/96 (11%), Positives = 37/96 (38%), Gaps = 7/96 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETAL 414
            + V +     + ++L Q+    G  ++ E++  +++ N +      +      +    L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 415 RTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDD 450
             L    + G+++ +  +      +F  Q+ + +  
Sbjct: 117 ELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECV 152

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 47.6 bits (113), Expect = 2e-06
 Identities = 12/114 (10%), Positives = 39/114 (34%), Gaps = 8/114 (7%)

Query: 255 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG-----DIRTIY--T 307
                   +++  +    +    ++V + +    D +L  +    G     +++      
Sbjct: 35  PKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94

Query: 308 ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK-DNPSEKDANQ 360
             + +G+  +      +    ++ L  K L   K+D+  +  +  +  E  A +
Sbjct: 95  NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARK 148

>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 = 37/98 (37%), Gaps = 12/98 (12%)

Query: 266 GEHPYGEHPSRTLFVRNINSNV---------EDSELKALFEQFGDIRTI-YTACKHRGFV 315
           G        ++TL+V  I+  +          +S ++ +F + GDI  I Y   K+ GFV
Sbjct: 125 GGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFV 184

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP 353
              +     A  A +A+ N+ L            +   
Sbjct: 185 --KFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.4 bits (117), Expect = 2e-06
 Identities = 23/123 (18%), Positives = 42/123 (34%), Gaps = 11/123 (8%)

Query: 325 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVST---------E 375
            + A++        R K   +        S +  N+ TL V  +D ++++          
Sbjct: 100 GKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNK-TLYVGGIDGALNSKHLKPAQIES 158

Query: 376 ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG 435
            +  +F   G+I  IR      N  F++F     AE A   ++   +     K    R  
Sbjct: 159 RIRFVFSRLGDIDRIR-YVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217

Query: 436 GAR 438
           G  
Sbjct: 218 GTG 220

>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 = 51.0 bits (121), Expect = 1e-06
 Identities = 22/132 (16%), Positives = 52/132 (39%), Gaps = 7/132 (5%)

Query: 323 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFG 382
              +   K  + +     +L +    P ++P+ +     TL V  ++   +  +L + F 
Sbjct: 67  MERKRREKIERRQQEVETELKMW--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124

Query: 383 IYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA 437
           +YG I+ I     K + K     FIE+   R   +A +  +   + G+++ ++  R    
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184

Query: 438 RRFMVQSEQEQD 449
           + +  +      
Sbjct: 185 KGWRPRRLGGGL 196

>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 = 46.8 bits (110), Expect = 3e-05
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
             +TLFV  +N +  +S+L+  FE +G I+ I+        K RG+  I Y   R   +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSEK 356
            K    K +  R++ +     +     +
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWR 188

>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 = 46.8 bits (111), Expect = 2e-06
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 12/83 (14%)

Query: 360 QGTLV-VFNLDSSVSTEEL---HQIFGIYGEIREI---RDTQHKHNHK-----FIEFYDI 407
           Q  LV V  L   ++  E+    + FG +G+I ++     T +  +       ++ +   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 408 RAAETALRTLNRSDVAGKQIKLE 430
             A  A++ +N   V 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 = 41.0 bits (96), Expect = 2e-04
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 11/85 (12%)

Query: 277 TLFVRNINSNVEDSEL---KALFEQFGDIRTIY--------TACKHRGFVMISYYDIRAA 325
            +FV  ++  + D E+      F +FG I  +          +        ++Y     A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPK 350
             A++ + N  +  R L       K
Sbjct: 77  LRAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 46.4 bits (110), Expect = 2e-06
 Identities = 13/80 (16%), Positives = 23/80 (28%), Gaps = 4/80 (5%)

Query: 274 PSRTLFVRNI-NSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
             R + + +         +L  L E FG I              I       A+ A+   
Sbjct: 14  TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYY 72

Query: 333 QNKP--LRRRKLDIHYSIPK 350
              P  +  + + +H S   
Sbjct: 73  TTTPALVFGKPVRVHLSQKY 92

>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 = 44.9 bits (107), Expect = 5e-06
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMK 330
           R ++V N+  +    ++K LF QFG +  +         K +GF  +   +  +   A+ 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60

Query: 331 ALQNKPLRRRKLDIHYSIPKDNPSEKDAN 359
            L N     R + +  + PK +      +
Sbjct: 61  KLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>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 = 42.5 bits (101), Expect = 3e-05
 Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            + V NL  S ++E++ ++F  +G++  +     R+T+      F+E  +  +   A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           L+ +D  G+ I++  + P  +  
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLE 84

>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 = 45.2 bits (107), Expect = 5e-06
 Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 5/82 (6%)

Query: 268 HPYGEHPSRT---LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRA 324
              G    R+   + V  +  +    +LK    + GD+   Y      G  ++ +     
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKED 62

Query: 325 ARNAMKALQNKPLRRRKLDIHY 346
              A++ L N   R  + +  Y
Sbjct: 63  MTYAVRKLDNTKFRSHEGETAY 84

>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 = 43.2 bits (102), Expect = 3e-05
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            +VV  L  S S ++L       G++       ++     +EF        A+R L+ + 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD--VYRDGTGVVEFVRKEDMTYAVRKLDNTK 74

Query: 422 VAGKQIKLEASRP 434
               + +    R 
Sbjct: 75  FRSHEGETAYIRV 87

>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 = 45.0 bits (107), Expect = 6e-06
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDI 322
           G      L V N++  V D++++ LF +FG +                  G   + +   
Sbjct: 25  GVETGGKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVHYDRSGRSLGTADVHFERK 80

Query: 323 RAARNAMKALQNKPLRRRKLDIHY 346
             A  AMK     PL  R ++I  
Sbjct: 81  ADALKAMKQYNGVPLDGRPMNIQL 104

>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 = 42.3 bits (100), Expect = 5e-05
 Identities = 18/102 (17%), Positives = 39/102 (38%), Gaps = 5/102 (4%)

Query: 334 NKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIRE--- 389
           ++P +      H               G  L+V NLD  VS  ++ ++F  +G +++   
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 390 IRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
             D +        + F     A  A++  N   + G+ + ++
Sbjct: 62  HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 103

>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 = 44.5 bits (106), Expect = 7e-06
 Identities = 19/87 (21%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 325
           G H +  H S+ +FV     ++   EL+  F Q+G++  ++     R F  +++ D + A
Sbjct: 3   GSHHHHHHGSK-VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDN 352
           ++     ++  ++   + I  + PK N
Sbjct: 62  QSLCG--EDLIIKGISVHISNAEPKHN 86

>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 = 43.7 bits (104), Expect = 1e-05
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 9/82 (10%)

Query: 278 LFVRNINSNVEDSELKALFEQFG-----DIRTIY---TACKHRGFVMISYYDIRAARNAM 329
           L++ N+     D +L       G     +I+         + +GF ++      +++  M
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG-QSKGFALVGVGSEASSKKLM 62

Query: 330 KALQNKPLRRRKLDIHYSIPKD 351
             L  + L  +   +  S   +
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLE 84

>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 = 43.3 bits (103), Expect = 2e-05
 Identities = 12/81 (14%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 367 NLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNR 419
           NL    + E+L +     G  +I EI+  +++ N +      +      +++  +  L +
Sbjct: 8   NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK 67

Query: 420 SDVAGKQIKLEASRPGGARRF 440
            ++ G+   +  S        
Sbjct: 68  RELHGQNPVVTPSNKLEHHHH 88

>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 = 12/59 (20%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 331
           +FV  ++ +  + +++  F  FG++ +I         K RGF  I++ +    +  M+ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 9/75 (12%)

Query: 272 EHPSRTLFVRNINSNVEDSE------LKALFEQFGDIRTIYTAC---KHRGFVMISYYDI 322
           +     + V N+     D        +  +F +FG I   +      K +G++ + Y   
Sbjct: 12  DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASP 71

Query: 323 RAARNAMKALQNKPL 337
             A +A+K      L
Sbjct: 72  AHAVDAVKNADGYKL 86

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 350 KDNPSEKDANQGTLVVFNL------DSSVSTEELHQIFGIYGEIREI---RDTQHKHNHK 400
           KD P E D     +VV N+              +H+IF  +G+I       +      + 
Sbjct: 5   KDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYI 64

Query: 401 FIEFYDIRAAETALRTLNRSDVAGK 425
           F+E+     A  A++  +   +  +
Sbjct: 65  FLEYASPAHAVDAVKNADGYKLDKQ 89

>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 = 43.8 bits (104), Expect = 2e-05
 Identities = 16/110 (14%), Positives = 37/110 (33%), Gaps = 14/110 (12%)

Query: 251 VGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC- 309
           +G   +    +  +V    +       +F+  ++       L+  F QFG++      C 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEV----KECL 56

Query: 310 --------KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD 351
                   + RGF  +++ D       +       L  + +D   + P+ 
Sbjct: 57  VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRR 105

>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 = 43.0 bits (102), Expect = 2e-05
 Identities = 21/94 (22%), Positives = 44/94 (46%), Gaps = 6/94 (6%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 320
           G        S  +FV  I  N  ++EL+  F++FG +  +         + RGF  I++ 
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 321 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
           D ++   A+  +    +  +K+++  + P+D+ S
Sbjct: 61  DEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSKS 93

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 42.0 bits (99), Expect = 4e-05
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 9/70 (12%)

Query: 277 TLFVRNINSNVED------SELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARN 327
            + V N+     D      + +  +F +FG I   +      K +G++ + Y     A +
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

Query: 328 AMKALQNKPL 337
           A+K      L
Sbjct: 63  AVKNADGYKL 72

>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 = 42.4 bits (100), Expect = 5e-05
 Identities = 12/107 (11%), Positives = 35/107 (32%), Gaps = 6/107 (5%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRDTQHKHN-HKF 401
           S       + ++ +    + N+  S++  ++ Q           +  + D   +      
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 448
           ++F +   A  + R L+R  + G++  +        R        + 
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQG 107

>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 = 42.4 bits (100), Expect = 5e-05
 Identities = 12/86 (13%), Positives = 29/86 (33%), Gaps = 6/86 (6%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFG----DIRTIYTAC-KHRGFVMISYYDIRAA 325
                    + NI  ++   ++    E        +  +     +  G  ++ + +   A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKD 351
           R + + L  K L  R+  +H    +D
Sbjct: 71  RKSER-LHRKKLNGREAFVHVVTLED 95

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 42.3 bits (99), Expect = 6e-05
 Identities = 12/68 (17%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-------TACKHRGFVMISYYDIR 323
           G   SR +FV  +  ++++ E+ A F +FG +   +       +    +G+  + + +  
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 324 AARNAMKA 331
           + +  + A
Sbjct: 64  SVQALIDA 71

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 41.6 bits (98), Expect = 8e-05
 Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 5/72 (6%)

Query: 361 GTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALR 415
           G  V+ +    V  + L  +F   G++  +       T       F+E   +  A+  ++
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 416 TLNRSDVAGKQI 427
           + +   +  K  
Sbjct: 73  SFHGKRLDLKHR 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 41.3 bits (97), Expect = 1e-04
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 279 FVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKALQ 333
            + +    V    L +LF + G +  +         K +GF+ +    +  A+  +K+  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 334 NKPL 337
            K L
Sbjct: 76  GKRL 79

>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 = 41.7 bits (98), Expect = 9e-05
 Identities = 19/93 (20%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIR 408
           S   AN G + +  L    S EE+ Q F     +            +     F++F    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 409 AAETALRTLNRSDVAGKQIKLEASRPGGARRFM 441
            AE AL+  ++  +  + I++  S     R   
Sbjct: 69  IAEKALK-KHKERIGHRYIEIFKSSRAEVRTSG 100

>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 = 39.0 bits (91), Expect = 9e-04
 Identities = 10/83 (12%), Positives = 24/83 (28%), Gaps = 6/83 (7%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFG----DIRTIY-TACKHRGFVMISYYDIRAARNA 328
               + +R +       E+   F         +        +  G   + +     A  A
Sbjct: 14  NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA 73

Query: 329 MKALQNKPLRRRKLDIHYSIPKD 351
           +K    + +  R ++I  S   +
Sbjct: 74  LK-KHKERIGHRYIEIFKSSRAE 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 = 2e-04
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 13/63 (20%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISYYDIRAARNA 328
           +FV  ++ N    ++K  FEQFG +                +HRGF  +++         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKV----DDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 329 MKA 331
            + 
Sbjct: 58  CEI 60

>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 = 40.7 bits (96), Expect = 2e-04
 Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 14/95 (14%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVM 316
           G +  G      LFV  ++ +     L++ F Q+G++      C         + RGF  
Sbjct: 7   GMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEV----VDCVIMKDKTTNQSRGFGF 62

Query: 317 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD 351
           + + D       + + +   L  R +D     P+ 
Sbjct: 63  VKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRG 96

>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 = 41.1 bits (97), Expect = 2e-04
 Identities = 16/98 (16%), Positives = 38/98 (38%), Gaps = 14/98 (14%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVM 316
                 +   R LF+  ++    +  L+  +EQ+G +    T C         + RGF  
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKL----TDCVVMRDPASKRSRGFGF 73

Query: 317 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
           +++  +     AM A +   +  R ++   ++ ++   
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESG 110

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFG--DIRTIY---TACKHRGFVMISYYDIRAARNA 328
           P  T +V N+  N    ++ A+F+      +R +    T  K +GF  + + ++ + + A
Sbjct: 14  PPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTD-KFKGFCYVEFDEVDSLKEA 72

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPSE 355
           +       L  R L +  +  +     
Sbjct: 73  L-TYDGALLGDRSLRVDIAEGRKQDKS 98

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 6/95 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALF-EQFGDIRT----IYTACKHRGFVMISYYDIRAARNA 328
           P  +LFV ++  +V+D  L   F + +   R     +      +G+  + + D    + A
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRA 67

Query: 329 MKALQNKP-LRRRKLDIHYSIPKDNPSEKDANQGT 362
           +   Q    L  + + +  +IPK +  +   +  +
Sbjct: 68  LTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPS 102

>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 = 21/99 (21%), Positives = 38/99 (38%), Gaps = 6/99 (6%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRDTQHKHN-HKF 401
            + + + S   AN G + +  L    + EE+ Q F         I    D + K     F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRF 440
           ++F     AE AL   ++  +  + I++  S     R +
Sbjct: 89  VQFASQELAEKALG-KHKERIGHRYIEVFKSSQEEVRSY 126

>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 = 39.7 bits (93), Expect = 2e-04
 Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 11/80 (13%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA----------CKHRGFVMISYYDIRA 324
           +R L+V NI   + +  +   F     +  +  A           + + F  + +  +  
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65

Query: 325 ARNAMKALQNKPLRRRKLDI 344
              AM A      + + L I
Sbjct: 66  TTQAM-AFDGIIFQGQSLKI 84

>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 = 38.9 bits (91), Expect = 6e-04
 Identities = 12/78 (15%), Positives = 25/78 (32%), Gaps = 13/78 (16%)

Query: 367 NLDSSVSTEELHQIFGIYGEIREI----------RDTQHKHNHKFIEFYDIRAAETALRT 416
           N+   ++ E +   F     +  +                 N  F+EF  +     A+  
Sbjct: 13  NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA- 71

Query: 417 LNRSDVAGKQIKLEASRP 434
            +     G+ +K+   RP
Sbjct: 72  FDGIIFQGQSLKI--RRP 87

>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 = 41.0 bits (96), Expect = 3e-04
 Identities = 14/121 (11%), Positives = 36/121 (29%), Gaps = 4/121 (3%)

Query: 244 VQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--D 301
           V + S        Q +  GS   E          + +R +     ++++   F       
Sbjct: 15  VPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR 74

Query: 302 IRTIYTA-CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
           +        +  G   + +     A  AM       ++ R +++  +      +   ++Q
Sbjct: 75  VHIEIGPDGRVTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAYSSQ 133

Query: 361 G 361
            
Sbjct: 134 V 134

>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 = 39.6 bits (92), Expect = 3e-04
 Identities = 18/91 (19%), Positives = 41/91 (45%), Gaps = 6/91 (6%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQI----FGIYGEIREIRDTQHK--HNHKFIEFYDI 407
           S    N   + V N+D  +S +EL Q+    F  +G+++ +  + H        ++  ++
Sbjct: 3   SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENL 62

Query: 408 RAAETALRTLNRSDVAGKQIKLEASRPGGAR 438
           + A  A+ +L+R  +  K+I +  +      
Sbjct: 63  QDAIGAVNSLHRYKIGSKKILVSLATGASGP 93

>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 = 39.9 bits (94), Expect = 4e-04
 Identities = 13/91 (14%), Positives = 26/91 (28%), Gaps = 7/91 (7%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIR 323
                 +  L V  +     + +LK  F  FG++  +           +GF  + + +  
Sbjct: 9   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68

Query: 324 AARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
                M       +  R  D      K +  
Sbjct: 69  TQVKVMSQRHM--IDGRWCDCKLPNSKQSQD 97

>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 = 39.6 bits (93), Expect = 4e-04
 Identities = 12/85 (14%), Positives = 29/85 (34%), Gaps = 4/85 (4%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYTA-CKHRGFVMISYYDI 322
           G          T+ +R    NV +  +           IR +  A     G++ + + + 
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNE 60

Query: 323 RAARNAMKALQNKPLRRRKLDIHYS 347
              + A+K    + +  R +++   
Sbjct: 61  EEVKQALK-CNREYMGGRYIEVFRE 84

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 39.0 bits (92), Expect = 4e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISYYDIRAARNA 328
           +F+  ++       L+  F QFG++      C         + RGF  +++ D       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV----KECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 329 MKA 331
           +  
Sbjct: 59  LAQ 61

>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 = 14/72 (19%), Positives = 27/72 (37%), Gaps = 13/72 (18%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISY 319
              E  +  +FV  ++ +    +LK  F +FG++      C         + RGF  I +
Sbjct: 5   SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV----VDCTIKMDPNTGRSRGFGFILF 60

Query: 320 YDIRAARNAMKA 331
            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 = 39.4 bits (92), Expect = 6e-04
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 8/87 (9%)

Query: 266 GEHPYGEHPSRT------LFVRNINSNVEDSELKALFEQFGD--IRTIYTACKHRGFVMI 317
           G  P G H S+       + ++N+       +LK L  +       +        G   +
Sbjct: 13  GLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGAL 72

Query: 318 SYYDIRAARNAMKALQNKPLRRRKLDI 344
            +        A++ L N   R   + +
Sbjct: 73  EFPSEEILVEALERLNNIEFRGSVITV 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	985
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	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	99.95
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.95
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	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
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.94
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.94
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.94
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.94
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.92
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.79
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.79
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.79
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.79
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.77
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.77
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.76
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.76
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.76
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.75
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.74
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.74
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.72
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.71
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.71
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.67
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.66
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.62
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.6
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.6
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.6
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.59
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.58
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.56
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.55
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.55
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.55
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.54
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.54
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.54
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.54
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.53
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.53
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.53
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.53
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.52
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.52
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.52
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.52
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.52
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.52
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.52
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.52
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.52
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.52
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.52
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.52
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.52
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.52
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.51
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.51
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.51
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.51
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.51
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.51
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	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
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.51
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.51
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.51
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.51
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.51
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.5
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.5
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.5
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.5
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.5
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.5
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.5
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.5
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.5
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.5
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.5
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.5
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.5
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.5
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.5
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.5
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.5
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.5
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.5
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.5
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.49
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.49
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.49
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.49
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.49
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.49
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.49
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.49
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.49
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.49
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.49
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.49
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.49
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.49
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.49
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.49
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.49
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.48
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.48
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.48
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.48
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.48
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.48
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.48
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.48
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.48
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.48
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.48
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.48
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.48
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.48
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.47
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.47
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.47
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.47
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.47
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.47
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.47
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.47
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.47
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.47
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.47
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.47
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.47
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.47
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.47
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.47
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.47
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.46
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.46
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.46
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.46
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.46
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.46
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.46
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.46
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.46
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.46
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.46
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.46
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.46
2div_A	99	TRNA selenocysteine associated protein; structural	99.46
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.46
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.46
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.46
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.46
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.46
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.46
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.45
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.45
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.45
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.45
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.45
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.45
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.45
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.45
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.45
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.45
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.45
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.45
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.45
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.45
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.45
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.45
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.45
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.44
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.44
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.44
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.44
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.44
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.44
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.44
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.44
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.44
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.44
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.44
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.44
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.44
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.44
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.43
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.43
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.43
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.43
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.43
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.43
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.43
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.43
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.43
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.43
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.43
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.43
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.43
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.43
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.43
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.43
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.43
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.43
1x5p_A	97	Negative elongation factor E; structure genomics,	99.43
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.42
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.42
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.42
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.42
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.42
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.42
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.42
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.42
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.42
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.42
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.42
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.42
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.42
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.42
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.42
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.41
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.41
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.41
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.41
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.41
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.41
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.41
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.41
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.41
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.41
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.41
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.41
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.41
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.4
1x5p_A	97	Negative elongation factor E; structure genomics,	99.4
2div_A	99	TRNA selenocysteine associated protein; structural	99.4
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.4
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.4
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.4
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.4
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.4
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.4
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.4
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.4
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.4
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.4
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.4
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.4
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.39
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.39
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.39
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.39
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.39
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.39
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.38
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.38
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.38
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.38
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.38
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.38
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.37
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.37
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.37
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.37
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.37
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.37
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.37
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.37
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.37
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.37
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.37
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.36
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.36
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.36
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.36
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.36
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.35
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.35
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.35
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.35
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.35
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.34
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.34
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.34
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.34
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.33
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.33
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.33
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.32
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.32
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.32
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.0
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.32
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.32
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.32
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.32
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.31
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.31
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.98
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.31
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.31
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.3
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.3
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.3
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.3
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.3
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.3
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.3
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.29
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.29
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.29
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.29
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.28
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.28
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.28
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.28
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.28
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.28
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.28
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.28
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.25
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.25
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.24
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.23
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.22
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.22
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.22
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.21
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.2
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.2
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.19
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.19
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.17
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.17
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.14
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.13
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.08
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.05
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.05
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.03
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.03
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.01
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	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	98.98
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.95
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.95
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.91
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.83
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.82
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.78
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.76
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.65
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	98.62
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.46
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.38
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.34
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.34
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.08
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.03
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.01
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.3
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.16
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.81
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.76
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.46
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.17
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.15
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.34
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	94.18
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.98
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.09
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.39
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.12
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	91.5
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	91.43
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	90.69
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	87.66

>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=100.00  E-value=1.4e-32  Score=296.08  Aligned_cols=235  Identities=15%  Similarity=0.178  Sum_probs=198.7

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      ..|||+||+. ++.+.|.+.              |+..        | |+...    -+.++|||||. |.+.++|+  .
T Consensus        23 ~~l~V~nLp~~~te~~l~~~--------------F~~~--------G-i~~~~----~~~~~g~afV~-f~~~~~A~--~   72 (284)
T 3smz_A           23 RKILIRGLPGDVTNQEVHDL--------------LSDY--------E-LKYCF----VDKYKGTAFVT-LLNGEQAE--A   72 (284)
T ss_dssp             CEEEEECCCTTCCHHHHHHH--------------TTTS--------C-EEEEE----EETTTTEEEEE-ESSHHHHH--H
T ss_pred             CEEEEeCCCCCCCHHHHHHH--------------HHHc--------C-CEEEE----EecCCCEEEEE-eCCHHHHH--H
Confidence            5799999998 888888887              7443        3 22211    15589999999 56888888  8


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI  305 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV  305 (985)
                      |+..++|..+. +..+.+..                          ....++|||+|||.++++++|+++|++||.|..+
T Consensus        73 A~~~l~~~~~~-g~~i~v~~--------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~  125 (284)
T 3smz_A           73 AINAFHQSRLR-ERELSVQL--------------------------QPTDALLCVANLPPSLTQQQFEELVRPFGSLERC  125 (284)
T ss_dssp             HHHHHTTCEET-TEECEEEE--------------------------CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEE
T ss_pred             HHHHcCCCeeC-CeEEEEEe--------------------------cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEE
Confidence            99999999997 43322211                          1245799999999999999999999999999998


Q ss_pred             Ee-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCcccccccceeeecCCCCC-CHHHHHH
Q 001991          306 YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSV-STEELHQ  379 (985)
Q Consensus       306 ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~sv-TeedLre  379 (985)
                      ++     ++.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.++.... ......+|||+|||..+ ++++|++
T Consensus       126 ~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~-~~~~~~~l~v~nlp~~~~~~~~l~~  204 (284)
T 3smz_A          126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTP-ALLHSRCLCVDRLPPGFNDVDALCR  204 (284)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCT-TTTSCSEEEEECCCTTCCCHHHHHH
T ss_pred             EEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCc-ccCCccEEEEecCCcccCCHHHHHH
Confidence            75     56789999999999999999999999999999999999998765442 33456799999999996 9999999


Q ss_pred             HhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchhh
Q 001991          380 IFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       380 lFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      +|++||.|.+|++..+    ++|+|||+|.+.++|.+|++.|||..|+|++|+|.|+.++..++
T Consensus       205 ~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  268 (284)
T 3smz_A          205 ALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGR  268 (284)
T ss_dssp             HTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCHH
T ss_pred             HhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCccc
Confidence            9999999999988754    47899999999999999999999999999999999999988766

>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=3e-31  Score=286.89  Aligned_cols=237  Identities=15%  Similarity=0.195  Sum_probs=189.2

Q ss_pred             CCCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhh
Q 001991          144 SSLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLE  222 (985)
Q Consensus       144 Ssl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edae  222 (985)
                      .....|||+||+. ++.+.|.+.              |+...++....+   ..+.    .+ ++|||||. |.+.++|+
T Consensus        39 ~~~~~l~V~nLp~~~t~~~l~~~--------------F~~~G~i~~v~i---~~~~----~~-~~g~afV~-f~~~~~A~   95 (292)
T 2ghp_A           39 RELTTVLVKNLPKSYNQNKVYKY--------------FKHCGPIIHVDV---ADSL----KK-NFRFARIE-FARYDGAL   95 (292)
T ss_dssp             ---CEEEEEEECTTCCHHHHHHH--------------HGGGSCEEEEEE---EECT----TS-SSEEEEEE-ESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHH--------------HHhcCCeEEEEE---EECC----CC-CcEEEEEE-ECCHHHHH
Confidence            3456899999998 888888888              744433322211   1122    22 68999999 55888878


Q ss_pred             hhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccC-c
Q 001991          223 DFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG-D  301 (985)
Q Consensus       223 e~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG-~  301 (985)
                        .|+. ++|..+. +..+.+..                           ...++|||+|||.++++++|+++|++|| .
T Consensus        96 --~A~~-~~~~~~~-g~~i~v~~---------------------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~  144 (292)
T 2ghp_A           96 --AAIT-KTHKVVG-QNEIIVSH---------------------------LTECTLWMTNFPPSYTQRNIRDLLQDINVV  144 (292)
T ss_dssp             --HHHT-TTTCEET-TEECEEEE---------------------------CCSCEEEEECCCTTCCHHHHHHHHHHTTCC
T ss_pred             --HHHH-hCCcEeC-CcEEEEEE---------------------------CCCCEEEEECCCCCCCHHHHHHHHHHhCCC
Confidence              7884 7999997 33322111                           2478999999999999999999999999 9


Q ss_pred             EEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCc---ccccccceeeecCCCC-CC
Q 001991          302 IRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE---KDANQGTLVVFNLDSS-VS  373 (985)
Q Consensus       302 I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~---~~~~~~tLfV~NLp~s-vT  373 (985)
                      |..|++    .+.++|||||+|.+.++|.+|++.|+|..+.|++|.|.++.++.....   ......+|||+|||.. ++
T Consensus       145 i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t  224 (292)
T 2ghp_A          145 ALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLD  224 (292)
T ss_dssp             CCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTTCC
T ss_pred             eEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCC
Confidence            999986    356899999999999999999999999999999999999987765432   2345679999999999 99


Q ss_pred             HHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          374 TEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       374 eedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      +++|+++|++||.|..|++..+      ++|||||+|.+.++|.+|+ .|||..|+|++|+|.|++++
T Consensus       225 ~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          225 ENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            9999999999999999998754      4689999999999999999 99999999999999999986

>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=7.8e-30  Score=265.33  Aligned_cols=166  Identities=19%  Similarity=0.343  Sum_probs=148.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++..+.|+.|++.+
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            357799999999999999999999999999999976     578899999999999999999999999999999999998


Q ss_pred             cCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       347 a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                      +......  ......+|||+|||..+|+++|+++|++||.|.+|+++.+   ++|||||+|.+.++|++|++.|||..|+
T Consensus        92 ~~~~~~~--~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~  169 (213)
T 4f02_A           92 SQRDPSL--RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN  169 (213)
T ss_dssp             CCCCTHH--HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             ccccccc--cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            8654322  2234568999999999999999999999999999998754   5789999999999999999999999999


Q ss_pred             CceEEEEeccCcchhh
Q 001991          424 GKQIKLEASRPGGARR  439 (985)
Q Consensus       424 Gr~IkV~~A~~k~~Rr  439 (985)
                      |++|+|.+++++.++.
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            9999999999876554

>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=99.96  E-value=1.7e-28  Score=264.18  Aligned_cols=195  Identities=16%  Similarity=0.285  Sum_probs=172.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      .++++|||+|||.++|+++|+++|+.|| |..+++ ++++|||||+|.+.++|++|++.|++..+.|++|.|.++.    
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            3678999999999999999999999999 999998 8899999999999999999999999999999999999853    


Q ss_pred             CCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       353 ~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                            ...+|||+|||..+++++|+++|++||.|..|++..+     ++|||||+|.+.++|.+|++.|||..+.|++|
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                  3468999999999999999999999999999988643     46899999999999999999999999999999


Q ss_pred             EEEeccCcchhhhhhhhhhhccCCCcc-cCCCCCC-Ccccc----ccccceEEE---ecCCCCccee
Q 001991          428 KLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDL-SSGQM----VSSGVITST---CMDNGSIQVL  485 (985)
Q Consensus       428 kV~~A~~k~~Rrl~qq~eq~q~e~nLy-kNlp~sv-t~e~L----~~fG~I~S~---~~enG~srgf  485 (985)
                      .|.++.++..+.      ......+|| +|||.++ ++++|    +.||.|.++   ...+|.++||
T Consensus       168 ~v~~a~~~~~~~------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~  228 (284)
T 3smz_A          168 YVHWTDAGQLTP------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGF  228 (284)
T ss_dssp             EEEECCGGGCCT------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEE
T ss_pred             EEEECCCCCCCc------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccE
Confidence            999998754221      123446788 9999996 88888    899999888   4467777775

>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=2.1e-28  Score=240.17  Aligned_cols=157  Identities=19%  Similarity=0.333  Sum_probs=143.4

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      |+|||+|||.++|+++|+++|++||+|.+|++    .++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++.+..
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            68999999999999999999999999999986    46688999999999999999999999999999999999987665


Q ss_pred             CCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCce
Q 001991          352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  426 (985)
Q Consensus       352 ~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~  426 (985)
                      ..  ......+|||+|||..+++++|+++|++||.|..+++..+     ++|||||+|.+.++|.+|++.|||..++|++
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            43  3445679999999999999999999999999999988643     4689999999999999999999999999999


Q ss_pred             EEEEeccC
Q 001991          427 IKLEASRP  434 (985)
Q Consensus       427 IkV~~A~~  434 (985)
                      |+|.||++
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=99.95  E-value=6.4e-28  Score=238.03  Aligned_cols=155  Identities=24%  Similarity=0.433  Sum_probs=142.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      +.++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
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            5789999999999999999999999999999975     46688999999999999999999999999999999999998


Q ss_pred             CCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCC-----CcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       349 pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~s-----kGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                      ++..    .....+|||+|||..+++++|+++|++||.|..+++..+.     +|||||+|.+.++|.+|++.|||..+.
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            7643    2456799999999999999999999999999999986543     689999999999999999999999998


Q ss_pred             C--ceEEEEec
Q 001991          424 G--KQIKLEAS  432 (985)
Q Consensus       424 G--r~IkV~~A  432 (985)
                      |  ++|+|.||
T Consensus       158 g~~~~l~V~~A  168 (168)
T 1b7f_A          158 GGSQPLSVRLA  168 (168)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCCeEEEEEeC
Confidence            7  99999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.95  E-value=7.9e-28  Score=236.31  Aligned_cols=155  Identities=25%  Similarity=0.431  Sum_probs=141.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ++++|||+|||+++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
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            3689999999999999999999999999999976     56788999999999999999999999999999999999997


Q ss_pred             CCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       349 pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                      +...    .....+|||+|||..+++++|+++|++||.|..+++..+     ++|||||+|.+.++|.+|++.|||..+.
T Consensus        81 ~~~~----~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~  156 (167)
T 1fxl_A           81 PSSA----SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS  156 (167)
T ss_dssp             CCCG----GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCT
T ss_pred             CCcc----cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccC
Confidence            6543    345678999999999999999999999999999998654     3789999999999999999999999999


Q ss_pred             Cce--EEEEec
Q 001991          424 GKQ--IKLEAS  432 (985)
Q Consensus       424 Gr~--IkV~~A  432 (985)
                      |+.  |+|.||
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  888886

>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=99.95  E-value=5.9e-28  Score=261.03  Aligned_cols=203  Identities=14%  Similarity=0.167  Sum_probs=166.0

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEec---cccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkit---gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.+.++|||+|||.++|+++|+++|+.||+|..|++.   ..++|||||+|.+.++|++|+ .+++..+.|+.|.|.
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVS  113 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHH-HhCCcEeCCcEEEEE
Confidence            3456778999999999999999999999999999999872   225899999999999999999 499999999999998


Q ss_pred             ccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccC-CEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCc
Q 001991          346 YSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRS  420 (985)
Q Consensus       346 ~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG-~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~  420 (985)
                      ++           ..++|||+|||..+++++|+++|++|| .|..|++..+    ++|||||+|.+.++|.+|++.|||.
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           367999999999999999999999999 9999998753    5899999999999999999999999


Q ss_pred             eeCCceEEEEeccCcchhhhhhhhhhhccCCCcc-cCCCCC-CCcccc----ccccceEEEec---CC--CCccee
Q 001991          421 DVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDD-LSSGQM----VSSGVITSTCM---DN--GSIQVL  485 (985)
Q Consensus       421 ~I~Gr~IkV~~A~~k~~Rrl~qq~eq~q~e~nLy-kNlp~s-vt~e~L----~~fG~I~S~~~---en--G~srgf  485 (985)
                      .+.|++|.|.++.++......  .........|| +|||.+ +++++|    ..||.|..+..   .+  |.++||
T Consensus       183 ~~~g~~l~v~~a~~~~~~~~~--~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~  256 (292)
T 2ghp_A          183 KIEGYTLVTKVSNPLEKSKRT--DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCC  256 (292)
T ss_dssp             EETTEECEEEECCCC-----------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEE
T ss_pred             EeCCcEEEEEECCCCcccccc--cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceE
Confidence            999999999999876533211  12233446788 999999 999999    89999999933   23  667765

>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=1e-27  Score=242.82  Aligned_cols=168  Identities=18%  Similarity=0.332  Sum_probs=141.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++. ++..+.|+.|.|
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            45567899999999999999999999999999999876     467899999999999999999974 999999999999


Q ss_pred             cccCCCCCCC--cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHh
Q 001991          345 HYSIPKDNPS--EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTL  417 (985)
Q Consensus       345 ~~a~pk~~~~--~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~L  417 (985)
                      .++.++....  ......++|||+|||.++++++|+++|++||.|..|++..+     ++|||||+|.+.++|.+|++. 
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            9987665432  22345579999999999999999999999999999998754     478999999999999999985 


Q ss_pred             CCceeCCceEEEEeccCcchhh
Q 001991          418 NRSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       418 NG~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      +|..|+|+.|.|.++.++.+.+
T Consensus       166 ~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          166 KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             SCCEETTEECEEEECC------
T ss_pred             CCcEECCEEEEEEecCChhHhc
Confidence            8999999999999999887654

>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=245.80  Aligned_cols=165  Identities=18%  Similarity=0.365  Sum_probs=146.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .+.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            35689999999999999999999999999999987     5678999999999999999999999999999999999887


Q ss_pred             CCCCCCC-------cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHH
Q 001991          348 IPKDNPS-------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALR  415 (985)
Q Consensus       348 ~pk~~~~-------~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~  415 (985)
                      .......       ......++|||+|||.++++++|+++|++||.|..|++..+     ++|||||+|.+.++|.+|++
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  185 (216)
T 2qfj_A          106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS  185 (216)
T ss_dssp             SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHH
Confidence            6554221       11234579999999999999999999999999999998754     37899999999999999999


Q ss_pred             HhCCceeCCceEEEEeccCcch
Q 001991          416 TLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       416 ~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      .|||..|+|++|+|.++.++..
T Consensus       186 ~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          186 SMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             HHTTCBCSSSBCEEEECSSCSS
T ss_pred             HccCCEeCCcEEEEEEecCCCC
Confidence            9999999999999999988653

>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=2.5e-27  Score=254.88  Aligned_cols=164  Identities=24%  Similarity=0.454  Sum_probs=147.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH----HhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLr----elFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      +..++++|||+|||.++++++|+    ++|++||.|..|++  +++++|||||+|.+.++|++|++.|+|..|.|+.|+|
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            45678999999999999999977    89999999999986  6789999999999999999999999999999999999


Q ss_pred             cccCCCCCCC----------------------------------------------------------------------
Q 001991          345 HYSIPKDNPS----------------------------------------------------------------------  354 (985)
Q Consensus       345 ~~a~pk~~~~----------------------------------------------------------------------  354 (985)
                      .|+..+....                                                                      
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            9986654200                                                                      


Q ss_pred             -------------------------------------cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCC
Q 001991          355 -------------------------------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKH  397 (985)
Q Consensus       355 -------------------------------------~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~sk  397 (985)
                                                           ......++|||+|||..+++++|+++|++||.|.+|++..+.+
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                                                 0112346899999999999999999999999999999998888


Q ss_pred             cEEEEEEcCHHHHHHHHHHhCCceeC-CceEEEEeccC
Q 001991          398 NHKFIEFYDIRAAETALRTLNRSDVA-GKQIKLEASRP  434 (985)
Q Consensus       398 GfaFVeF~d~edA~kAI~~LNG~~I~-Gr~IkV~~A~~  434 (985)
                      |||||+|.+.++|.+|++.|||..|. |++|+|.|++.
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

>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=3.6e-27  Score=247.87  Aligned_cols=164  Identities=22%  Similarity=0.316  Sum_probs=147.8

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          272 EHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       272 e~~srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ..++++|||+|||+ ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|++..|.|++|.|.++.++
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            45789999999999 99999999999999999999986566899999999999999999999999999999999998755


Q ss_pred             CCCCcc-------------------------------cccccceeeecCCCCCCHHHHHHHhhccC-CEEEEEEcCCCCc
Q 001991          351 DNPSEK-------------------------------DANQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDTQHKHN  398 (985)
Q Consensus       351 ~~~~~~-------------------------------~~~~~tLfV~NLp~svTeedLrelFs~fG-~I~~Vri~~~skG  398 (985)
                      .....+                               ..+.++|||+|||..+++++|+++|++|| .|..|++.++.+|
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            211000                               12357899999999999999999999999 9999999887899


Q ss_pred             EEEEEEcCHHHHHHHHHHhCCceeC-CceEEEEeccCc
Q 001991          399 HKFIEFYDIRAAETALRTLNRSDVA-GKQIKLEASRPG  435 (985)
Q Consensus       399 faFVeF~d~edA~kAI~~LNG~~I~-Gr~IkV~~A~~k  435 (985)
                      ||||+|.+.++|.+|++.|||..+. |++|+|.|++++
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 999999999874

>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=9.3e-28  Score=239.55  Aligned_cols=162  Identities=20%  Similarity=0.278  Sum_probs=144.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE----EeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV----kitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..+    ..+++++|||||+|.+.++|++|+ +|++..+.|++|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            45678999999999999999999999999976542    125789999999999999999999 5999999999999999


Q ss_pred             cCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCce
Q 001991          347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  426 (985)
Q Consensus       347 a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~  426 (985)
                      +.++...  .....++|||+|||..+++++|+++|++||.|..+...+.++|||||+|.+.++|.+|++.|||..|+|++
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            9876543  33467799999999999999999999999999888434557899999999999999999999999999999


Q ss_pred             EEEEeccCc
Q 001991          427 IKLEASRPG  435 (985)
Q Consensus       427 IkV~~A~~k  435 (985)
                      |+|.|++++
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            999999876

>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=3.8e-27  Score=233.73  Aligned_cols=153  Identities=16%  Similarity=0.346  Sum_probs=140.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhccc----C-------cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQF----G-------DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  342 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~f----G-------~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L  342 (985)
                      +.++|||+|||+++|+++|+++|++|    |       .|..+++ ++++|||||+|.+.++|++|+ .+++..+.|++|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~-~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i   80 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-ETTTTEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe-cCCCCEEEEEeCCHHHHHHHH-HhCCcEecCcee
Confidence            57899999999999999999999999    6       7888877 678999999999999999999 899999999999


Q ss_pred             cccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHh
Q 001991          343 DIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTL  417 (985)
Q Consensus       343 ~V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~L  417 (985)
                      .|.++.+....    ....+|||+|||..+++++|+++|++||.|..|++..+     ++|||||+|.+.++|.+|++.|
T Consensus        81 ~v~~~~~~~~~----~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  156 (172)
T 2g4b_A           81 KIRRPHDYQPL----PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             EEECCSSCCCC----TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             eecCCcccCCC----CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence            99987654332    34679999999999999999999999999999998655     3789999999999999999999


Q ss_pred             CCceeCCceEEEEec
Q 001991          418 NRSDVAGKQIKLEAS  432 (985)
Q Consensus       418 NG~~I~Gr~IkV~~A  432 (985)
                      ||..++|++|+|.||
T Consensus       157 ~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          157 NGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTCEETTEECEEEEC
T ss_pred             CCCEECCeEEEEEeC
Confidence            999999999999997

>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=2.7e-27  Score=241.49  Aligned_cols=162  Identities=22%  Similarity=0.313  Sum_probs=146.3

Q ss_pred             CCcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          274 PSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       274 ~srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      .+++|||+|||+ ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|+|..+.|++|.|.++.++..
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            358999999999 9999999999999999999998656689999999999999999999999999999999999875421


Q ss_pred             CCc-------------------------------ccccccceeeecCCCCCCHHHHHHHhhccC-CEEEEEEcCCCCcEE
Q 001991          353 PSE-------------------------------KDANQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDTQHKHNHK  400 (985)
Q Consensus       353 ~~~-------------------------------~~~~~~tLfV~NLp~svTeedLrelFs~fG-~I~~Vri~~~skGfa  400 (985)
                      ...                               ...+..+|||+|||..+++++|+++|++|| .|.+|++.++.+|+|
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            110                               012367899999999999999999999999 999999988889999


Q ss_pred             EEEEcCHHHHHHHHHHhCCceeC-CceEEEEeccCc
Q 001991          401 FIEFYDIRAAETALRTLNRSDVA-GKQIKLEASRPG  435 (985)
Q Consensus       401 FVeF~d~edA~kAI~~LNG~~I~-Gr~IkV~~A~~k  435 (985)
                      ||+|.+.++|.+|++.|||..++ |++|+|.|++++
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 999999999874

>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=99.94  E-value=1.9e-27  Score=234.86  Aligned_cols=156  Identities=18%  Similarity=0.393  Sum_probs=140.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ++++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
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            5789999999999999999999999999999986     577899999999999999999974  678999999999886


Q ss_pred             CCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       349 pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                      ++.    .....++|||+|||..+++++|+++|++||.|.+|++..+     ++|||||+|.+.++|.+|++ ++|..++
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    2234679999999999999999999999999999998754     57899999999999999998 9999999


Q ss_pred             CceEEEEeccCcc
Q 001991          424 GKQIKLEASRPGG  436 (985)
Q Consensus       424 Gr~IkV~~A~~k~  436 (985)
                      |++|+|.++.++.
T Consensus       155 g~~i~V~~a~pk~  167 (167)
T 2cjk_A          155 DRKIEIKRAEPRH  167 (167)
T ss_dssp             SSCEEEEECCCCC
T ss_pred             CeEEEEeecCCCC
Confidence            9999999999863

>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=5.2e-27  Score=237.95  Aligned_cols=161  Identities=16%  Similarity=0.325  Sum_probs=143.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhccc----C-------cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQF----G-------DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  342 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~f----G-------~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L  342 (985)
                      ..++|||+|||.++|+++|+++|++|    |       .|..+++ ++++|||||+|.+.++|++|+ .|+|..|.|++|
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            46899999999999999999999999    5       6777777 778999999999999999999 899999999999


Q ss_pred             cccccCCCCCCC----------------cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCC-----CcEEE
Q 001991          343 DIHYSIPKDNPS----------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKF  401 (985)
Q Consensus       343 ~V~~a~pk~~~~----------------~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~s-----kGfaF  401 (985)
                      .|.++.+.....                ......++|||+|||..+++++|+++|++||.|..|++..+.     +||||
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            999987653221                112355799999999999999999999999999999987653     78999


Q ss_pred             EEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       402 VeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      |+|.+.++|.+|++.|||..|+|++|+|.+++++.
T Consensus       161 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99999999999999999999999999999999865

>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=99.94  E-value=8.9e-27  Score=230.94  Aligned_cols=157  Identities=18%  Similarity=0.384  Sum_probs=138.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----cc--ccceEEEEEeCCHHHHHHHHHHccCcccc---ccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----AC--KHRGFVMISYYDIRAARNAMKALQNKPLR---RRKLD  343 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tg--ksrGfAFV~F~d~esA~kAi~~Lng~~I~---Gr~L~  343 (985)
                      +.++|||+|||+++|+++|+++|++||+|..|++     ++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            4689999999999999999999999999999976     22  78999999999999999999999998776   56777


Q ss_pred             ccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCC
Q 001991          344 IHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNR  419 (985)
Q Consensus       344 V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG  419 (985)
                      +.++.+...   .....++|||+|||..+|+++|+++|++||.|.+|++..+    ++|||||+|.+.++|.+|++.|||
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            777655433   2345679999999999999999999999999999998755    468999999999999999999999


Q ss_pred             ceeC---CceEEEEecc
Q 001991          420 SDVA---GKQIKLEASR  433 (985)
Q Consensus       420 ~~I~---Gr~IkV~~A~  433 (985)
                      ..+.   |++|+|.||.
T Consensus       159 ~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          159 AQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCCCTTCSSCCEEEECC
T ss_pred             CcccCCCCCCeEEEecC
Confidence            8776   4999999973

>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=99.94  E-value=8.6e-27  Score=242.73  Aligned_cols=159  Identities=18%  Similarity=0.208  Sum_probs=138.7

Q ss_pred             CCcEEEEecCC-CCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          274 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       274 ~srtLfVgNLP-~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      ++++|||+||| ..+++++|+++|++||.|.+|++....+|||||+|.+.++|++|++.|||..+.|++|+|.++..+..
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 79999999999999999999998666789999999999999999999999999999999999864321


Q ss_pred             CCc---------------------------------ccccccceeeecCCCCCCHHHHHHHhhccCCE--EEEEEcCC--
Q 001991          353 PSE---------------------------------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEI--REIRDTQH--  395 (985)
Q Consensus       353 ~~~---------------------------------~~~~~~tLfV~NLp~svTeedLrelFs~fG~I--~~Vri~~~--  395 (985)
                      .+.                                 ...+..+|||+|||.++|+++|+++|++||.|  .+|++..+  
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                                 00234579999999999999999999999999  88998765  


Q ss_pred             -CCcEEEEEEcCHHHHHHHHHHhCCceeCCc----eEEEEec
Q 001991          396 -KHNHKFIEFYDIRAAETALRTLNRSDVAGK----QIKLEAS  432 (985)
Q Consensus       396 -skGfaFVeF~d~edA~kAI~~LNG~~I~Gr----~IkV~~A  432 (985)
                       ++|+|||+|.+.++|.+||..|||..|.|+    ++.|.++
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             358999999999999999999999999886    5666664

>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=99.92  E-value=6.2e-25  Score=235.45  Aligned_cols=156  Identities=24%  Similarity=0.359  Sum_probs=141.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|||+|||+++|+++|+++|++||.|..|++ .+++|||||+|.+.++|++|++.|+|..|.|+.|.|.++.+ 
T Consensus        18 ~~~~~~~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           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH-   95 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC-
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc-
Confidence            3456789999999999999999999999999999998 67799999999999999999999999999999999999863 


Q ss_pred             CCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCC-ceeC--
Q 001991          351 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNR-SDVA--  423 (985)
Q Consensus       351 ~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG-~~I~--  423 (985)
                               ..+|||+|||..+|+++|+++|++||.|..|++..+    ++|||||+|.+.++|.+|+..||+ ..+.  
T Consensus        96 ---------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~  166 (261)
T 3sde_A           96 ---------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTT  166 (261)
T ss_dssp             ---------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSS
T ss_pred             ---------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecC
Confidence                     468999999999999999999999999999988654    578999999999999999999954 4554  


Q ss_pred             -CceEEEEeccCcch
Q 001991          424 -GKQIKLEASRPGGA  437 (985)
Q Consensus       424 -Gr~IkV~~A~~k~~  437 (985)
                       +++|.|.++.+...
T Consensus       167 ~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          167 TPRPVIVEPMEQFDD  181 (261)
T ss_dssp             SCCBCEEEECCCEES
T ss_pred             CCceEEEeeccccCc
Confidence             99999999987653

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.79  E-value=2.9e-19  Score=176.01  Aligned_cols=127  Identities=20%  Similarity=0.273  Sum_probs=114.0

Q ss_pred             cccceEEEEEeCCHHHHHHHHHHc-cCcccccccccccccCCCC------------CCCcccccccceeeecCCCCCCHH
Q 001991          309 CKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKLDIHYSIPKD------------NPSEKDANQGTLVVFNLDSSVSTE  375 (985)
Q Consensus       309 gksrGfAFV~F~d~esA~kAi~~L-ng~~I~Gr~L~V~~a~pk~------------~~~~~~~~~~tLfV~NLp~svTee  375 (985)
                      .+.+|+++|+|.+.++|++|++.+ ||..+.| .+.+.++..+.            .........++|||+|||..++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            456899999999999999999999 9999999 99999886531            112234456799999999999999


Q ss_pred             HHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          376 ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       376 dLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      +|+++|++||.|.+|+++.+++|||||+|.+.++|.+|++.|||..|.|++|+|.+++++.
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            9999999999999999998889999999999999999999999999999999999998753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.79  E-value=5.5e-20  Score=191.13  Aligned_cols=165  Identities=13%  Similarity=0.225  Sum_probs=125.2

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhh
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLED  223 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee  223 (985)
                      ....|||+||+. ++++.|.+.              |+...++....+   .   .|..++.++|||||. |.+.++++ 
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~--------------F~~~G~I~~v~i---~---~d~~tg~~~G~afV~-F~~~~~A~-   71 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEK--------------FSPAGPILSIRV---C---RDMITRRSLGYAYVN-FQQPADAE-   71 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHH--------------HGGGSCEEEEEE---E---ECTTTCCEEEEEEEE-ESSHHHHH-
T ss_pred             CCcEEEEeCCCCCCCHHHHHHH--------------HHhhCCEEEEEE---e---cccCCCCccccccce-eCCHHHHH-
Confidence            345799999998 888888888              844433322111   1   223478899999999 56888888 


Q ss_pred             hHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEE
Q 001991          224 FDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIR  303 (985)
Q Consensus       224 ~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~  303 (985)
                       +|+..++|..+.+ +.+.+.....                  .........++|||+|||.++|+++|+++|++||.|.
T Consensus        72 -~Ai~~~~~~~~~g-~~i~~~~~~~------------------~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~  131 (213)
T 4f02_A           72 -RALDTMNFDVIKG-KPVRIMWSQR------------------DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNIL  131 (213)
T ss_dssp             -HHHHHHTTCEETT-EECEEEECCC------------------CTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEE
T ss_pred             -HHHHHhhhhhcCC-cccccccccc------------------cccccccccccceECCcccccHHHHHHHHHhhcCCeE
Confidence             8999999998873 3221111000                  0001122457899999999999999999999999999


Q ss_pred             EEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          304 TIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       304 sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      .|++   .+.++|||||+|.+.++|++|++.|||..|.|++|.|.++.++.
T Consensus       132 ~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          132 SCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             EEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             EEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            9976   45579999999999999999999999999999999999998754

>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=99.79  E-value=7.9e-20  Score=182.11  Aligned_cols=162  Identities=19%  Similarity=0.266  Sum_probs=125.7

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhh
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLED  223 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee  223 (985)
                      .-..|||+||+. ++.+.|.+.              |..+.++    .+.++.   +..++.++|||||. |.+.++|+ 
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~--------------f~~~g~~----~~~~~~---~~~~~~~~g~afV~-f~~~~~a~-   68 (175)
T 1fje_B           12 TPFNLFIGNLNPNKSVAELKVA--------------ISELFAK----NDLAVV---DVRTGTNRKFGYVD-FESAEDLE-   68 (175)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHH--------------HHHHHHH----HTCCCC---EEEEETTTTEEEEE-ESSHHHHH-
T ss_pred             CCcEEEEeCCCCCCCHHHHHHH--------------HHHhCCc----ceEEEE---ECCCCccccEEEEE-ECCHHHHH-
Confidence            345799999998 788778776              6333322    121121   22478899999999 56788878 


Q ss_pred             hHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEE
Q 001991          224 FDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIR  303 (985)
Q Consensus       224 ~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~  303 (985)
                       +|+ .++|..+. +..+.+.....                  .......+.++|||+|||.++++++|+++|++||.|.
T Consensus        69 -~A~-~l~g~~~~-g~~l~v~~~~~------------------~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~  127 (175)
T 1fje_B           69 -KAL-ELTGLKVF-GNEIKLEKPKG------------------RDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR  127 (175)
T ss_dssp             -HHH-HGGGEEET-TEEEEEECCCC------------------SSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEE
T ss_pred             -HHH-hcCCCEeC-CeEEEEecCCC------------------ccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEE
Confidence             788 49999998 44433322111                  0112345679999999999999999999999999999


Q ss_pred             EEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          304 TIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       304 sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      .+..++.++|||||+|.+.++|.+|++.|+|..|.|++|.|.|+.++
T Consensus       128 ~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          128 LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             EecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99557889999999999999999999999999999999999999876

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.79  E-value=1.7e-19  Score=182.63  Aligned_cols=182  Identities=14%  Similarity=0.175  Sum_probs=127.3

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCc-CC--ChhhhhccCCCCeeeeecCCChhhhh
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNL-LP--DEDDLFSGVTDDMGHNFQANTVDDLE  222 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnI-Lp--dedDL~sG~SkGfGFV~ff~t~Edae  222 (985)
                      ..|||+||+. ++.+.|.+.              |+...++    .|-+ .+  .-.++..+.++|||||+ |.+.++|+
T Consensus         5 ~~l~V~nLp~~~te~~l~~~--------------F~~~g~i----~g~~~~~~~~v~~~~~~~~~g~afV~-F~~~~~A~   65 (198)
T 2yh0_A            5 RRLYVGNIPFGITEEAMMDF--------------FNAQMRL----GGLTQAPGNPVLAVQINQDKNFAFLE-FRSVDETT   65 (198)
T ss_dssp             CEEEEESCCTTCCHHHHHHH--------------HHHHHHH----HTCCSSSSCSEEEEEEETTTTEEEEE-ESCSHHHH
T ss_pred             eEEEEcCCCCCCCHHHHHHH--------------HHHHHhh----cccccCCCCceEEeEecCCCCEEEEE-eCCHHHHH
Confidence            4799999998 888888877              7333211    0200 01  11233356789999999 55777777


Q ss_pred             hhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCc-CCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCc
Q 001991          223 DFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSV-VGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD  301 (985)
Q Consensus       223 e~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~-~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~  301 (985)
                        +|+ .++|..|. +..+.+............ ........ .........+.++|||+|||.++++++|+++|++||.
T Consensus        66 --~Al-~l~g~~~~-g~~i~v~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~  140 (198)
T 2yh0_A           66 --QAM-AFDGIIFQ-GQSLKIRRPHDYQPLPGM-SENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGP  140 (198)
T ss_dssp             --HHG-GGTTEEET-TEEEEEECCCCCCCCCCS-SSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSC
T ss_pred             --HHH-HhcCCEEc-CceEEEeCCCCCCCCCCC-cCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCC
Confidence              788 78999997 444444332221000000 00000000 0011223467799999999999999999999999999


Q ss_pred             EEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          302 IRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       302 I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      |..|++     ++.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.++.++..
T Consensus       141 v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          141 LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999876     566799999999999999999999999999999999999987654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.78  E-value=1.9e-19  Score=176.28  Aligned_cols=158  Identities=20%  Similarity=0.283  Sum_probs=122.6

Q ss_pred             ccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhHH
Q 001991          148 DIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDL  226 (985)
Q Consensus       148 ~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~a  226 (985)
                      .|||+||+. ++.+.|.+.              |+...++..-.+   +.+.    .+.++|||||. |.+.++|+  .|
T Consensus         2 ~l~V~nlp~~~t~~~l~~~--------------f~~~G~i~~v~i---~~~~----~~~~~g~afV~-f~~~~~a~--~A   57 (166)
T 3md3_A            2 VLYVGNLDKAITEDILKQY--------------FQVGGPIANIKI---MIDK----NNKNVNYAFVE-YHQSHDAN--IA   57 (166)
T ss_dssp             EEEEEEEETTCCHHHHHHH--------------HGGGSCEEEEEE---ECCC----C-CCEEEEEEE-ESSHHHHH--HH
T ss_pred             EEEECCCCCcCCHHHHHHH--------------HHhcCCeEEEEE---EECC----CCCCCCEEEEE-eCCHHHHH--HH
Confidence            489999988 888888877              744443322111   1132    46689999999 55788878  89


Q ss_pred             HhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE
Q 001991          227 FSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY  306 (985)
Q Consensus       227 i~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk  306 (985)
                      +..++|..+. +..+.+.....                  .......+.++|||+|||.++++++|+++|++||.|..++
T Consensus        58 ~~~l~~~~~~-g~~i~v~~~~~------------------~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~  118 (166)
T 3md3_A           58 LQTLNGKQIE-NNIVKINWAFQ------------------SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH  118 (166)
T ss_dssp             HHHHTTCEET-TEECEEEECCC------------------CCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEE
T ss_pred             HHHcCCCccC-CCeeEEEEcCC------------------CCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEE
Confidence            9999999997 44332222111                  1112445678999999999999999999999999999987


Q ss_pred             e-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          307 T-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       307 i-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      +     ++.++|||||+|.+.++|.+|++.|+|..+.|++|.|.|+.
T Consensus       119 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             EEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            6     46789999999999999999999999999999999999985

>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=99.77  E-value=1.7e-19  Score=182.39  Aligned_cols=170  Identities=17%  Similarity=0.328  Sum_probs=119.8

Q ss_pred             CCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhh
Q 001991          145 SLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLED  223 (985)
Q Consensus       145 sl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee  223 (985)
                      ....|||+||+. ++.+.|.+.              |+.+.++....+   +.+   ..+|.++|||||. |.+.++|+ 
T Consensus        12 ~~~~l~V~nLp~~~te~~l~~~--------------F~~~G~i~~v~i---~~~---~~~g~~~g~afV~-f~~~~~A~-   69 (196)
T 1l3k_A           12 QLRKLFIGGLSFETTDESLRSH--------------FEQWGTLTDCVV---MRD---PNTKRSRGFGFVT-YATVEEVD-   69 (196)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHH--------------HGGGSCEEEEEE---EEC---TTTCCEEEEEEEE-ESSHHHHH-
T ss_pred             CCCEEEEeCCCCCCCHHHHHHH--------------HHhCCCEEEEEE---EEc---CCCCCccceEEEE-eCCHHHHH-
Confidence            345799999998 888888887              844433322111   112   2367899999999 55778878 


Q ss_pred             hHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEE
Q 001991          224 FDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIR  303 (985)
Q Consensus       224 ~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~  303 (985)
                       +|+.. +|..+. +..+.+......              .....+....+.++|||+|||.++|+++|+++|++||.|.
T Consensus        70 -~A~~~-~~~~~~-g~~l~v~~~~~~--------------~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~  132 (196)
T 1l3k_A           70 -AAMNA-RPHKVD-GRVVEPKRAVSR--------------EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE  132 (196)
T ss_dssp             -HHHHT-CSCEET-TEECEEEECCC-------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEE
T ss_pred             -HHHhc-CCCEEC-CEEeeeecccCc--------------ccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeE
Confidence             78876 778887 443333222110              0011122345669999999999999999999999999999


Q ss_pred             EEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCC
Q 001991          304 TIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS  354 (985)
Q Consensus       304 sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~  354 (985)
                      .|++     +++++|||||+|.+.++|.+|++. ++..|.|+.|.|.++.++....
T Consensus       133 ~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             EEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC------
T ss_pred             EEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHhc
Confidence            9876     467899999999999999999975 8999999999999999886653

>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=99.77  E-value=4.2e-19  Score=174.87  Aligned_cols=158  Identities=17%  Similarity=0.258  Sum_probs=122.2

Q ss_pred             CcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhh
Q 001991          146 LSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDF  224 (985)
Q Consensus       146 l~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~  224 (985)
                      -..||++||+. ++.+.|.+.              |+...++....+   .   .+..++.++|||||. |.+.++|+  
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~--------------f~~~G~i~~v~i---~---~~~~~~~~~g~afV~-f~~~~~A~--   59 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYAL--------------FRAIGPINTCRI---M---RDYKTGYSYGYAFVD-FTSEMDSQ--   59 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHH--------------HHTTSCEEEEEC---C---EETTTTEECSEEEEE-ESSHHHHH--
T ss_pred             ccEEEEeCCCCCCCHHHHHHH--------------HHhcCCeeEEEE---E---EeCCCCccceEEEEE-ECCHHHHH--
Confidence            35799999998 888888887              744333322111   1   122367799999999 55888888  


Q ss_pred             HHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE
Q 001991          225 DLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT  304 (985)
Q Consensus       225 ~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s  304 (985)
                      +|+..++|..+. +..+.+.....                    .....+.++|||+|||.++++++|+++|++||.|..
T Consensus        60 ~a~~~l~~~~~~-g~~l~v~~~~~--------------------~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~  118 (168)
T 1b7f_A           60 RAIKVLNGITVR-NKRLKVSYARP--------------------GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ  118 (168)
T ss_dssp             HHHHHHTTCEET-TEECEEEECCC--------------------CSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEE
T ss_pred             HHHHhcCCCEeC-CcEEEEEecCC--------------------CcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEE
Confidence            899889999997 44332222110                    112346789999999999999999999999999999


Q ss_pred             EEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccc--cccccccc
Q 001991          305 IYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYS  347 (985)
Q Consensus       305 Vki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a  347 (985)
                      +++     +++++|||||+|.+.++|.+|++.|+|..+.|  ++|.|.||
T Consensus       119 ~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            876     56678999999999999999999999999988  99999875

>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=99.76  E-value=4.8e-18  Score=168.11  Aligned_cols=130  Identities=18%  Similarity=0.273  Sum_probs=103.5

Q ss_pred             ccccceEEEEEeCCHHHHHHHHHHccCccccc-------ccccccccCCCCC--CCcccccccceeeecCCCCCCHHHHH
Q 001991          308 ACKHRGFVMISYYDIRAARNAMKALQNKPLRR-------RKLDIHYSIPKDN--PSEKDANQGTLVVFNLDSSVSTEELH  378 (985)
Q Consensus       308 tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G-------r~L~V~~a~pk~~--~~~~~~~~~tLfV~NLp~svTeedLr  378 (985)
                      ..+++|||||+|.+.++|++|++.+++.....       .............  .........+|||+|||..+++++|+
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            34689999999999999999999887643222       2222222111111  11223456799999999999999999


Q ss_pred             HHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          379 QIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       379 elFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ++|++||.|..|++..+     ++|||||+|.+.++|++|++.|||..|.|++|+|.+++++..
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            99999999999998754     678999999999999999999999999999999999987653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.76  E-value=4.1e-19  Score=182.21  Aligned_cols=174  Identities=13%  Similarity=0.254  Sum_probs=127.0

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      ..|||+||+. ++.+.|.+.              |+...++....+   +.+.   .++.++|||||. |.+.++|+  +
T Consensus        29 ~~l~V~nLp~~~t~~~l~~~--------------f~~~G~i~~v~i---~~~~---~~g~~~g~afV~-f~~~~~A~--~   85 (216)
T 2qfj_A           29 SRVYVGSIYYELGEDTIRQA--------------FAPFGPIKSIDM---SWDS---VTMKHKGFAFVE-YEVPEAAQ--L   85 (216)
T ss_dssp             TEEEEECCCTTCCHHHHHHH--------------HGGGSCEEEEEE---CCC----CC-CCCSEEEEE-ESSHHHHH--H
T ss_pred             CEEEEECCCCCCCHHHHHHH--------------HHhCCCEEEEEE---eecC---CCCccCceEEEE-eCCHHHHH--H
Confidence            4699999998 888888888              754444332221   1122   367899999999 56888888  8


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI  305 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV  305 (985)
                      |+..++|..+. +..+.+........        .. .............++|||+|||.++++++|+++|++||.|..|
T Consensus        86 A~~~l~~~~~~-g~~l~v~~~~~~~~--------~~-~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v  155 (216)
T 2qfj_A           86 ALEQMNSVMLG-GRNIKVGRPSNIGQ--------AQ-PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSA  155 (216)
T ss_dssp             HHHHHSSCCCC--CCCEEECCSCCGG--------GH-HHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEE
T ss_pred             HHHHccCCeeC-CeeEEEecCCCccc--------cc-hhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEE
Confidence            99989999887 44433322111000        00 0000000123466899999999999999999999999999999


Q ss_pred             Ee-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCC
Q 001991          306 YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP  353 (985)
Q Consensus       306 ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~  353 (985)
                      ++     +++++|||||+|.+.++|.+|++.|+|..|.|+.|.|.|+.++..+
T Consensus       156 ~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          156 TLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             EEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            76     4677999999999999999999999999999999999999877544

>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=99.76  E-value=5.4e-19  Score=175.01  Aligned_cols=158  Identities=15%  Similarity=0.239  Sum_probs=120.0

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCC---ChhhhhccCCCCeeeeecCCChhhhh
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLP---DEDDLFSGVTDDMGHNFQANTVDDLE  222 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILp---dedDL~sG~SkGfGFV~ff~t~Edae  222 (985)
                      ..|||+||+. ++.+.|.+.              |+...++    .|-+..   .-.++..+.++|||||+ |.+.++|+
T Consensus         5 ~~l~V~nLp~~~t~~~l~~~--------------F~~~g~~----~g~~~~~~~~v~~~~~~~~~g~afV~-f~~~~~A~   65 (172)
T 2g4b_A            5 RRLYVGNIPFGITEEAMMDF--------------FNAQMRL----GGLTQAPGNPVLAVQINQDKNFAFLE-FRSVDETT   65 (172)
T ss_dssp             GEEEEESCCTTCCHHHHHHH--------------HHHHHHH----TTCCSSSSCSEEEEEEETTTTEEEEE-ESSHHHHH
T ss_pred             cEEEEcCCCcccCHHHHHHH--------------HHHHhhh----cccccCCCCceeeeEecCCCCEEEEE-eCCHHHHH
Confidence            4799999998 888888877              7333111    121110   11233356689999999 55788878


Q ss_pred             hhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcE
Q 001991          223 DFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI  302 (985)
Q Consensus       223 e~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I  302 (985)
                        .|+ .++|..+. +..+.+.....                    .......++|||+|||.++++++|+++|++||+|
T Consensus        66 --~A~-~~~~~~~~-g~~i~v~~~~~--------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v  121 (172)
T 2g4b_A           66 --QAM-AFDGIIFQ-GQSLKIRRPHD--------------------YQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPL  121 (172)
T ss_dssp             --HHG-GGTTCEET-TEECEEECCSS--------------------CCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCE
T ss_pred             --HHH-HhCCcEec-CceeeecCCcc--------------------cCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCc
Confidence              788 89999997 44332221100                    1122347899999999999999999999999999


Q ss_pred             EEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          303 RTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       303 ~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..+++     +++++|||||+|.+.++|++|++.|+|..+.|++|.|.++
T Consensus       122 ~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          122 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             EEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             eEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99976     5677999999999999999999999999999999999987

>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=2.9e-19  Score=176.13  Aligned_cols=157  Identities=17%  Similarity=0.299  Sum_probs=117.6

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      ..|||+||+. ++.+.|.+.              |+...++....+   ..+.   .+|.++|||||. |.+.++|+  .
T Consensus         4 ~~l~v~nLp~~~t~~~l~~~--------------F~~~G~i~~v~i---~~~~---~~g~~~g~afV~-f~~~~~a~--~   60 (167)
T 2cjk_A            4 CKMFIGGLNWDTTEDNLREY--------------FGKYGTVTDLKI---MKDP---ATGRSRGFGFLS-FEKPSSVD--E   60 (167)
T ss_dssp             GEEEECSCCTTCCHHHHHHH--------------HTTTCCEEEEEC---CCCT---TTSSCCSCEEEE-ESSTHHHH--H
T ss_pred             cEEEEeCCCCCCCHHHHHHH--------------HHhCCCEEEEEE---EECC---CCCCccceEEEE-EccHHHHH--H
Confidence            4799999998 888888887              744433322111   1122   378899999999 55777777  6


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI  305 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV  305 (985)
                      |+..  +..+. +..+.+.....                    .....+.++|||+|||.++++++|+++|++||.|..+
T Consensus        61 A~~~--~~~~~-g~~i~v~~~~~--------------------~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~  117 (167)
T 2cjk_A           61 VVKT--QHILD-GKVIDPKRAIP--------------------RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA  117 (167)
T ss_dssp             HHHS--CCEET-TEECCCEECCC--------------------HHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEE
T ss_pred             HHhc--ccccC-CeEcccccccc--------------------hhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEE
Confidence            7774  44555 22221111110                    0112346799999999999999999999999999999


Q ss_pred             Ee-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          306 YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       306 ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ++     ++.++|||||+|.+.++|.+|++ +++..+.|++|.|.++.|+
T Consensus       118 ~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          118 QLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             ECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             EEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            75     47789999999999999999997 9999999999999999876

>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=99.74  E-value=2.8e-18  Score=168.21  Aligned_cols=157  Identities=19%  Similarity=0.287  Sum_probs=119.7

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhhH
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFD  225 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~~  225 (985)
                      ..||++||+. ++.+.|.+.              |+...++....+   +   .+..+|.++|||||+ |.+.++|+  .
T Consensus         3 ~~l~v~nlp~~~~~~~l~~~--------------f~~~G~i~~v~~---~---~~~~~~~~~g~afV~-f~~~~~A~--~   59 (167)
T 1fxl_A            3 TNLIVNYLPQNMTQEEFRSL--------------FGSIGEIESCKL---V---RDKITGQSLGYGFVN-YIDPKDAE--K   59 (167)
T ss_dssp             SEEEEESCCTTCCHHHHHHH--------------HHTTSCEEEEEE---E---ECTTTCCEEEEEEEE-ESSHHHHH--H
T ss_pred             ceEEEcCCCCCCCHHHHHHH--------------HHhcCCeEEEEE---E---eCCCCCcceeEEEEE-ECCHHHHH--H
Confidence            5799999998 888888877              744433322111   1   122367789999999 56888888  8


Q ss_pred             HHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE
Q 001991          226 LFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI  305 (985)
Q Consensus       226 ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV  305 (985)
                      |+..++|..+. +..+.+.....                    .......++|||+|||.++++++|+++|++||.|..+
T Consensus        60 a~~~l~~~~~~-g~~l~v~~~~~--------------------~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~  118 (167)
T 1fxl_A           60 AINTLNGLRLQ-TKTIKVSYARP--------------------SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS  118 (167)
T ss_dssp             HHHHHTTCEET-TEECEEEECCC--------------------CCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEE
T ss_pred             HHHHcCCCccC-CceEEEEecCC--------------------CcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEE
Confidence            99989999997 44332221110                    1123456899999999999999999999999999998


Q ss_pred             Ee-----ccccceEEEEEeCCHHHHHHHHHHccCccccccc--cccccc
Q 001991          306 YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK--LDIHYS  347 (985)
Q Consensus       306 ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~--L~V~~a  347 (985)
                      ++     ++.++|||||+|.+.++|.+|++.|+|..+.|+.  |.|.||
T Consensus       119 ~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            76     4667999999999999999999999999999976  666664

>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=99.74  E-value=3.7e-18  Score=161.41  Aligned_cols=103  Identities=16%  Similarity=0.315  Sum_probs=72.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ..++|||+|||+++|+++|+++|++||.|.+|++   .+.++|||||+|.+.++|++|++.|++..|.|++|.|.++.++
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            4678999999999999999999999999999976   4557899999999999999999999999999999999999876


Q ss_pred             CCCCc----ccccccceeeecCCCCCCHHH
Q 001991          351 DNPSE----KDANQGTLVVFNLDSSVSTEE  376 (985)
Q Consensus       351 ~~~~~----~~~~~~tLfV~NLp~svTeed  376 (985)
                      .....    ......+|||+|||+++|++.
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            65422    223445899999999999863

>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=99.73  E-value=4e-18  Score=168.68  Aligned_cols=162  Identities=13%  Similarity=0.186  Sum_probs=117.8

Q ss_pred             CcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhcc--CCCCeeeeecCCChhhhh
Q 001991          146 LSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSG--VTDDMGHNFQANTVDDLE  222 (985)
Q Consensus       146 l~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG--~SkGfGFV~ff~t~Edae  222 (985)
                      -..|||+||+. ++.+.|.+.              |+...++....+-   .+.   .++  .++|||||. |.+.++|+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~--------------F~~~G~i~~v~i~---~~~---~~~~~~~~g~afV~-f~~~~~A~   61 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLREL--------------FEQYGAVYEINVL---RDR---SQNPPQSKGCCFVT-FYTRKAAL   61 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHH--------------HHTTSCEEEEEEE---EEC---SSSSCEEEEEEEEE-ESSHHHHH
T ss_pred             ceEEEEeCCCCCCCHHHHHHH--------------HHhCCCEEEEEEE---ecC---CCCCCCcceEEEEE-ECCHHHHH
Confidence            35799999998 888888887              7443333211110   111   133  689999999 56788878


Q ss_pred             hhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcE
Q 001991          223 DFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI  302 (985)
Q Consensus       223 e~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I  302 (985)
                        +|+..++|..+.....    +.+.          .....   .......+.++|||+|||.++|+++|+++|++||.|
T Consensus        62 --~A~~~l~~~~~~~~~~----~~~~----------~~~~~---~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i  122 (175)
T 3nmr_A           62 --EAQNALHNMKVLPGMH----HPIQ----------MKPAD---SEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI  122 (175)
T ss_dssp             --HHHHHHTTTCCCTTCS----SCCE----------EEECG---GGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             --HHHHHhcCcEEccCCc----cceE----------Ecccc---ccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCE
Confidence              7898888877652211    1000          00000   111233467899999999999999999999999999


Q ss_pred             EEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccc---ccccccccc
Q 001991          303 RTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLR---RRKLDIHYS  347 (985)
Q Consensus       303 ~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~---Gr~L~V~~a  347 (985)
                      ..+++    +++++|||||+|.+.++|.+|++.|||..+.   +++|.|.|+
T Consensus       123 ~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             EEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             EEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            99976    4667999999999999999999999998776   499999987

>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=99.72  E-value=7.7e-18  Score=180.97  Aligned_cols=77  Identities=19%  Similarity=0.343  Sum_probs=71.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc-cccccccccC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHYSI  348 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~-Gr~L~V~~a~  348 (985)
                      ..+.++|||+|||.++++++|+++|++||.|..|++....+|||||+|.+.++|.+|++.|||..|. |+.|.|.|++
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            3467899999999999999999999999999999985555799999999999999999999999999 9999999985

>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=99.71  E-value=1.2e-17  Score=158.01  Aligned_cols=104  Identities=17%  Similarity=0.241  Sum_probs=72.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..+|||+|||.++|+++|+++|++||.|.+|+++.+   ++|||||+|.+.++|++|++.|||..|.|++|+|.+++++.
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            568999999999999999999999999999998754   47899999999999999999999999999999999999876


Q ss_pred             hhhhhhhhhhhccCCCcc-cCCCCCCCcc
Q 001991          437 ARRFMVQSEQEQDDLNLC-QIPFDDLSSG  464 (985)
Q Consensus       437 ~Rrl~qq~eq~q~e~nLy-kNlp~svt~e  464 (985)
                      .+. .+.....+...+|| +|||+++|++
T Consensus        85 ~~~-~~~~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           85 ERE-AELGARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             C----------------------------
T ss_pred             ccc-cccccccCCCCceEeCCCCCCcccc
Confidence            554 11223334456899 9999999876

>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=99.71  E-value=1.1e-17  Score=174.20  Aligned_cols=172  Identities=8%  Similarity=0.067  Sum_probs=118.4

Q ss_pred             cccccccCC-C-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhh
Q 001991          147 SDIFTRKMK-L-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDF  224 (985)
Q Consensus       147 ~~lFv~nL~-~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~  224 (985)
                      ..|||+||+ . ++.+.|++.              |        ..+|+|+...  +.. .++|||||+ |.+.++|+  
T Consensus         5 ~~l~V~nL~~~~~~~~~L~~~--------------F--------~~~G~v~~v~--i~~-~~~g~afV~-f~~~~~A~--   56 (205)
T 3tyt_A            5 PVLMVYGLDQSKMNCDRVFNV--------------F--------CLYGNVEKVK--FMK-SKPGAAMVE-MADGYAVD--   56 (205)
T ss_dssp             SEEEEECCCTTTCCHHHHHHH--------------H--------TTTSCEEEEE--ECT-TSTTCEEEE-ESSHHHHH--
T ss_pred             CEEEEeCCCcccCCHHHHHHH--------------H--------HhcCCeEEEE--Eec-CCCCEEEEE-ECCHHHHH--
Confidence            579999999 6 888889988              8        4455554411  000 158999999 56788888  


Q ss_pred             HHHhccCCeeEcCCcchhhhcccccc--cCCC----------CCCCCCC-CCcC----CCCCCCCCCCcEEEEecCCCCC
Q 001991          225 DLFSSGGGMELEGDDRLFAVQKNSDF--VGGV----------SNQGVSA-GSVV----GEHPYGEHPSRTLFVRNINSNV  287 (985)
Q Consensus       225 ~ai~~~nG~eLegd~~~~vg~~ls~l--~k~~----------~n~~~~~-~~~~----~e~~~~e~~srtLfVgNLP~~v  287 (985)
                      +|+..++|.+|. ++.+.+.......  .+..          +...... ....    ........++++|||+|||+++
T Consensus        57 ~Ai~~lng~~~~-g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~  135 (205)
T 3tyt_A           57 RAITHLNNNFMF-GQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEV  135 (205)
T ss_dssp             HHHHHHTTCEET-TEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTC
T ss_pred             HHHHHhCCCEEC-CceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCC
Confidence            899999999998 4544443322110  0000          0000000 0000    0000113467899999999999


Q ss_pred             CHHHHHHhhcccCcE--EEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccc----ccccccc
Q 001991          288 EDSELKALFEQFGDI--RTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR----KLDIHYS  347 (985)
Q Consensus       288 TEedLrelFs~fG~I--~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr----~L~V~~a  347 (985)
                      |+++|+++|++||.|  ..+++   .+..+|||||+|.+.++|.+|+..|||..|.|+    ++.|+++
T Consensus       136 t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          136 TEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            999999999999999  78876   234569999999999999999999999999886    4555543

>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=99.68  E-value=7.2e-17  Score=169.44  Aligned_cols=178  Identities=18%  Similarity=0.173  Sum_probs=124.5

Q ss_pred             CCCcccccccCCC--CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhh
Q 001991          144 SSLSDIFTRKMKL--SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDL  221 (985)
Q Consensus       144 Ssl~~lFv~nL~~--~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Eda  221 (985)
                      .....|||+||+.  ++.+.|.+.              |+        .+|.|....  +... .+|||||+ |.+.++|
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~--------------F~--------~~G~i~~v~--i~~~-~~g~afV~-F~~~~~A   85 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFIL--------------FG--------VYGDVQRVK--ILFN-KKENALVQ-MADGNQA   85 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHH--------------HH--------HHTCEEEEE--ECCT-TSCCEEEE-ESCHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHH--------------HH--------hCCCeEEEE--EEEC-CCCEEEEE-ECCHHHH
Confidence            4456799999985  777778877              73        344333310  0000 27899999 5588888


Q ss_pred             hhhHHHhccCCeeEcCCcchhhhccccccc---CCCCC-------CCCCCC-Cc----CCCCCCCCCCCcEEEEecCCCC
Q 001991          222 EDFDLFSSGGGMELEGDDRLFAVQKNSDFV---GGVSN-------QGVSAG-SV----VGEHPYGEHPSRTLFVRNINSN  286 (985)
Q Consensus       222 ee~~ai~~~nG~eLegd~~~~vg~~ls~l~---k~~~n-------~~~~~~-~~----~~e~~~~e~~srtLfVgNLP~~  286 (985)
                      +  +|+..++|..+. +..+.+........   +....       ...... ..    .........+.++|||+|||.+
T Consensus        86 ~--~Ai~~l~g~~~~-g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~  162 (229)
T 2adc_A           86 Q--LAMSHLNGHKLH-GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPS  162 (229)
T ss_dssp             H--HHHHHHTTCBCS-SSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTT
T ss_pred             H--HHHHHhCCCeEC-CeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCcc
Confidence            8  899999999997 44444433221100   00000       000000 00    0000112345799999999999


Q ss_pred             CCHHHHHHhhcccC-cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc-cccccccccCCC
Q 001991          287 VEDSELKALFEQFG-DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHYSIPK  350 (985)
Q Consensus       287 vTEedLrelFs~fG-~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~-Gr~L~V~~a~pk  350 (985)
                      +++++|+++|++|| .|..|++..+.+|||||+|.+.++|.+|++.|+|..+. |++|.|.|+.++
T Consensus       163 ~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          163 VSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99999999999999 99999985667999999999999999999999999999 999999999764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.67  E-value=1.2e-16  Score=162.78  Aligned_cols=175  Identities=18%  Similarity=0.184  Sum_probs=122.9

Q ss_pred             cccccccCCC--CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhhhh
Q 001991          147 SDIFTRKMKL--SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDF  224 (985)
Q Consensus       147 ~~lFv~nL~~--~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edaee~  224 (985)
                      ..||++||+.  ++.+.|.+.              |        ..+|.|....  +... .+|||||+ |.+.++|+  
T Consensus         4 ~~l~v~nlp~~~~~~~~l~~~--------------F--------~~~G~i~~v~--i~~~-~~g~afV~-f~~~~~a~--   55 (198)
T 1qm9_A            4 SVLLVSNLNPERVTPQSLFIL--------------F--------GVYGDVQRVK--ILFN-KKENALVQ-MADGNQAQ--   55 (198)
T ss_dssp             CEEEEECCCSSSCCHHHHHHH--------------H--------HTTCCCSEEE--CSTT-CSSCCEEE-CTTTHHHH--
T ss_pred             cEEEEeCCCcccCCHHHHHHH--------------H--------HhcCCEEEEE--EEeC-CCCEEEEE-ECCHHHHH--
Confidence            4799999985  677778877              7        4455444311  0000 27899999 55777778  


Q ss_pred             HHHhccCCeeEcCCcchhhhccccccc---CCCCC-------CCCCC-CCc----CCCCCCCCCCCcEEEEecCCCCCCH
Q 001991          225 DLFSSGGGMELEGDDRLFAVQKNSDFV---GGVSN-------QGVSA-GSV----VGEHPYGEHPSRTLFVRNINSNVED  289 (985)
Q Consensus       225 ~ai~~~nG~eLegd~~~~vg~~ls~l~---k~~~n-------~~~~~-~~~----~~e~~~~e~~srtLfVgNLP~~vTE  289 (985)
                      .|+..++|..+. +..+.+........   +....       ..... ...    .........++++|||+|||..+++
T Consensus        56 ~A~~~l~~~~~~-g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  134 (198)
T 1qm9_A           56 LAMSHLNGHKLH-GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSE  134 (198)
T ss_dssp             HHHHHHTTCCCS-SCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCH
T ss_pred             HHHHHhCCCeec-CeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCH
Confidence            799889999887 44444432221100   00000       00000 000    0000112346899999999999999


Q ss_pred             HHHHHhhcccC-cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc-cccccccccCCC
Q 001991          290 SELKALFEQFG-DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHYSIPK  350 (985)
Q Consensus       290 edLrelFs~fG-~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~-Gr~L~V~~a~pk  350 (985)
                      ++|+++|++|| .|..+++....+|||||+|.+.++|.+|++.|+|..+. |++|.|.|+.++
T Consensus       135 ~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          135 EDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            99999999999 99999986667999999999999999999999999999 999999998764

>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=99.66  E-value=1.4e-16  Score=170.55  Aligned_cols=153  Identities=18%  Similarity=0.177  Sum_probs=119.7

Q ss_pred             CCCcccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCChhhhhccCCCCeeeeecCCChhhhh
Q 001991          144 SSLSDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLE  222 (985)
Q Consensus       144 Ssl~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpdedDL~sG~SkGfGFV~ff~t~Edae  222 (985)
                      ..-..|||+||+. ++.+.|.+.              |..        +|.|...    .-..++|||||. |.+.++|+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~--------------F~~--------~G~i~~v----~i~~~kg~afV~-f~~~~~A~   72 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRL--------------FER--------YGEPSEV----FINRDRGFGFIR-LESRTLAE   72 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHH--------------TGG--------GCCCSEE----EEETTTTEEEEE-CSSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHH--------------HHh--------cCCEEEE----EEeCCCcEEEEE-ECCHHHHH
Confidence            4445799999998 888888888              843        4433321    123468999999 56888888


Q ss_pred             hhHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcE
Q 001991          223 DFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI  302 (985)
Q Consensus       223 e~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I  302 (985)
                        +|+..++|..+. +..+.+..                          ..+.++|||+|||..+|+++|+++|++||.|
T Consensus        73 --~A~~~l~g~~i~-g~~l~v~~--------------------------a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i  123 (261)
T 3sde_A           73 --IAKAELDGTILK-SRPLRIRF--------------------------ATHGAALTVKNLSPVVSNELLEQAFSQFGPV  123 (261)
T ss_dssp             --HHHHHHTTCEET-TEECEEEE--------------------------CCCSSEEEEESCCTTCCHHHHHHHHGGGSCE
T ss_pred             --HHHHHcCCcEEC-CceeEeee--------------------------cccCCcccccCCCCCCCHHHHHHHHHhcCCe
Confidence              899999999997 33322211                          1236799999999999999999999999999


Q ss_pred             EEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcc-cc---cccccccccCCCCC
Q 001991          303 RTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKP-LR---RRKLDIHYSIPKDN  352 (985)
Q Consensus       303 ~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~-I~---Gr~L~V~~a~pk~~  352 (985)
                      ..|++    +++++|||||+|.+.++|.+|++.|++.. +.   +++|.|.++.+...
T Consensus       124 ~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          124 EKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             EEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             EEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCc
Confidence            99876    57789999999999999999999996544 33   89999999876543

>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=99.62  E-value=1.5e-15  Score=150.13  Aligned_cols=83  Identities=25%  Similarity=0.464  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .....++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|||..|.|++|.|.
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456799999999999999999999999999999986     57789999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus       146 ~a~~~~~~  153 (158)
T 2kn4_A          146 MARYGRPP  153 (158)
T ss_dssp             EECCSSCC
T ss_pred             ECCCCCCC
Confidence            99876544

>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=99.60  E-value=6.2e-16  Score=145.15  Aligned_cols=103  Identities=26%  Similarity=0.407  Sum_probs=92.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ..+.++|||+|||.++++++|+++|++||.|..|.+  ++..+|||||+|.+.++|++|++.|||..+.|+.|.|.++.+
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            456799999999999999999999999999999987  567799999999999999999999999999999999999975


Q ss_pred             CCCCCcccccccceeeecCCCCCCHHHHHHHhhccCC
Q 001991          350 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE  386 (985)
Q Consensus       350 k~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~  386 (985)
                      +...            .+++...++++|.++|++||.
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            4322            567788899999999999984

>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=99.60  E-value=1.5e-15  Score=140.29  Aligned_cols=76  Identities=22%  Similarity=0.489  Sum_probs=71.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..++|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|.|++
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            4578999999999999999999999999999976     57889999999999999999999999999999999999997


Q ss_pred             C
Q 001991          349 P  349 (985)
Q Consensus       349 p  349 (985)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>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=99.60  E-value=1.7e-15  Score=140.01  Aligned_cols=76  Identities=26%  Similarity=0.441  Sum_probs=70.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||.++|+++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|++.|||..|.|++|+|+||+
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            3468999999999999999999999999999998643     46899999999999999999999999999999999998


Q ss_pred             C
Q 001991          434 P  434 (985)
Q Consensus       434 ~  434 (985)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>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=99.59  E-value=2e-15  Score=148.48  Aligned_cols=138  Identities=18%  Similarity=0.243  Sum_probs=103.1

Q ss_pred             CCCCeeeeecCCChhhhhhhHHHhcc-CCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecC
Q 001991          205 VTDDMGHNFQANTVDDLEDFDLFSSG-GGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNI  283 (985)
Q Consensus       205 ~SkGfGFV~ff~t~Edaee~~ai~~~-nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNL  283 (985)
                      ..+|+++|+ +.+.++|+  +++..+ +|.+++|  .+.+.........    .................+.++|||+||
T Consensus        11 ~l~G~~~ve-~~~~~~A~--~a~~~~~ng~~~~G--~~~~~~a~~~~~~----~~~~~~~~~~~~~~~~~~~~~l~V~nl   81 (150)
T 2i2y_A           11 TLKGETTTE-AVDAATAE--KVFKQYANDNGVDG--EWTYDDATKTFTV----TEGSHHHHHHMHRDSCPLDCKVYVGNL   81 (150)
T ss_dssp             SSCEEEEEE-CSSHHHHT--TTHHHHHHHHTCCC--EEEEETTTTEEEE----ECSSSSCCCCSCSSSSTTSCEEEEESC
T ss_pred             cccccceee-ecCHHHHH--HHHHHHhcCCCCCC--ceecccccCcccc----ccccccccccccccCCCCCCEEEEeCC
Confidence            367899988 55777778  788877 8888875  3222221110000    000000111122334567899999999


Q ss_pred             CCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          284 NSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       284 P~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      |+++++++|+++|++||+|..|++...++|||||+|.+.++|++|++.|+|..|.|++|.|.++.++.
T Consensus        82 ~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           82 GNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             CSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999999999999999999866689999999999999999999999999999999999998753

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.58  E-value=1.2e-15  Score=148.55  Aligned_cols=121  Identities=19%  Similarity=0.326  Sum_probs=77.6

Q ss_pred             eEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEE
Q 001991          313 GFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD  392 (985)
Q Consensus       313 GfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri  392 (985)
                      -++|++|.+...+..|+..+++....|+. .+.+..+    +......++|||+|||..+++++|+++|++||.|..|++
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            36888999999999999999987766653 2233322    233456789999999999999999999999999999998


Q ss_pred             cCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchh
Q 001991          393 TQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGAR  438 (985)
Q Consensus       393 ~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~R  438 (985)
                      ..+     .+|||||+|.+.++|++|++.|||..|.|++|+|.+++++..+
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            643     5789999999999999999999999999999999999876543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.56  E-value=5e-15  Score=135.82  Aligned_cols=94  Identities=22%  Similarity=0.364  Sum_probs=82.2

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE  355 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~  355 (985)
                      ++|||+|||.++++++|+++|++||+|..|++...++|||||+|.+.++|++|++.|++..+.|++|.|.++.++.....
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            58999999999999999999999999999988444799999999999999999999999999999999999988764322


Q ss_pred             c------cccccceeeecCC
Q 001991          356 K------DANQGTLVVFNLD  369 (985)
Q Consensus       356 ~------~~~~~tLfV~NLp  369 (985)
                      .      .....+|||+||+
T Consensus        81 ~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           81 FDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCCCccccCCCceecCCCC
Confidence            1      1235689999997

>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=9.6e-15  Score=137.60  Aligned_cols=82  Identities=21%  Similarity=0.287  Sum_probs=74.9

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .+.++|||+||+..+++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++|++.|||..|.|++|+|+++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34679999999999999999999999999999998643     5789999999999999999999999999999999999


Q ss_pred             cCcchhh
Q 001991          433 RPGGARR  439 (985)
Q Consensus       433 ~~k~~Rr  439 (985)
                      ..+..++
T Consensus        84 ~~~~~~~   90 (110)
T 3s8s_A           84 IKGQQRM   90 (110)
T ss_dssp             STTHHHH
T ss_pred             CCCcHHH
Confidence            8776554

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.55  E-value=6.8e-15  Score=133.84  Aligned_cols=76  Identities=16%  Similarity=0.158  Sum_probs=70.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..-|||+||++.+|+++|+++|.+||+|.++++.. ++|||||+|.+.++|++|++.||+..+.|++|+|.+|...+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e~~   82 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSENE   82 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCHHH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCHHH
Confidence            56799999999999999999999999999999876 69999999999999999999999999999999999995333

>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=99.55  E-value=7.6e-15  Score=147.07  Aligned_cols=123  Identities=17%  Similarity=0.273  Sum_probs=74.0

Q ss_pred             EEeCCHHHHHHHHHHccCcccc--cccccccccCCC----------------CCCCcccccccceeeecCCCCCCHHHHH
Q 001991          317 ISYYDIRAARNAMKALQNKPLR--RRKLDIHYSIPK----------------DNPSEKDANQGTLVVFNLDSSVSTEELH  378 (985)
Q Consensus       317 V~F~d~esA~kAi~~Lng~~I~--Gr~L~V~~a~pk----------------~~~~~~~~~~~tLfV~NLp~svTeedLr  378 (985)
                      .+|++.++|+.|+..+++....  |+..........                ...+......++|||+|||..+++++|+
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            6889999999999999887655  555554432110                0011223455689999999999999999


Q ss_pred             HHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchhh
Q 001991          379 QIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR  439 (985)
Q Consensus       379 elFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~Rr  439 (985)
                      ++|++||.|..|++..+     .+|||||+|.+.++|++||+.|||..|.|++|.|.|+.++..++
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            99999999999998755     47899999999999999999999999999999999998776554

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=8.4e-15  Score=137.61  Aligned_cols=80  Identities=18%  Similarity=0.212  Sum_probs=73.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCC--ceeCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR--SDVAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG--~~I~Gr~IkV~~A~~k  435 (985)
                      ...++|||+|||+++|+++|+++|++||+|.+|+++.+ +|||||+|.+.++|++|++.|++  ..|.|++|+|.|++++
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~   92 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            35679999999999999999999999999999999875 89999999999999999998864  7899999999999886


Q ss_pred             chh
Q 001991          436 GAR  438 (985)
Q Consensus       436 ~~R  438 (985)
                      ..+
T Consensus        93 ~~~   95 (105)
T 1sjq_A           93 ELK   95 (105)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.54  E-value=1.4e-14  Score=136.40  Aligned_cols=79  Identities=19%  Similarity=0.379  Sum_probs=73.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      +.+.++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|||..|.|+.|.|.+
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            357799999999999999999999999999999976     578999999999999999999999999999999999999


Q ss_pred             cCCC
Q 001991          347 SIPK  350 (985)
Q Consensus       347 a~pk  350 (985)
                      +...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8644

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.54  E-value=3.8e-15  Score=135.28  Aligned_cols=79  Identities=22%  Similarity=0.432  Sum_probs=71.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccC-cEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHcc-Cccccccccccccc
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFG-DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQ-NKPLRRRKLDIHYS  347 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG-~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Ln-g~~I~Gr~L~V~~a  347 (985)
                      +++|||+|||+++|+++|+++|++|| +|.+|++     +++++|||||+|.+.++|++|++.++ +..+.|++|.|.|+
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            57899999999999999999999999 8998875     57899999999999999999998874 56899999999999


Q ss_pred             CCCCCC
Q 001991          348 IPKDNP  353 (985)
Q Consensus       348 ~pk~~~  353 (985)
                      .|+...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            887654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.54  E-value=1.8e-14  Score=134.17  Aligned_cols=78  Identities=18%  Similarity=0.221  Sum_probs=72.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCce--eCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD--VAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~--I~Gr~IkV~~A~~k  435 (985)
                      .+.++|||+|||.++|+++|+++|++||.|.+|++++ .||||||+|.+.++|.+|++.||+..  |.|++|+|+|++++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            4567999999999999999999999999999999875 58999999999999999999999875  78999999999876


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      +
T Consensus        98 ~   98 (100)
T 3r27_A           98 K   98 (100)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.53  E-value=7.7e-15  Score=134.59  Aligned_cols=78  Identities=29%  Similarity=0.441  Sum_probs=73.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcchh
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGAR  438 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~R  438 (985)
                      ++|||+|||.++++++|+++|++||.|..|++..++++||||+|.+.++|++|++.|||..+.|++|+|.+++++..+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCc
Confidence            479999999999999999999999999999998778999999999999999999999999999999999999886633

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.53  E-value=3e-14  Score=130.03  Aligned_cols=82  Identities=23%  Similarity=0.389  Sum_probs=76.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            457899999999999999999999999999999987     577899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9887654

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=3.8e-14  Score=130.41  Aligned_cols=83  Identities=27%  Similarity=0.404  Sum_probs=75.6

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .....++|||+|||..+++++|+++|++||.|..|++..+   +++||||+|.+.++|++|++.|||..|.|++|+|.++
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 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            3456789999999999999999999999999999998764   5789999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2cqi_A           91 TTPSSQ   96 (103)
T ss_dssp             CCTTCC
T ss_pred             CCCccc
Confidence            986543

>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=5.1e-14  Score=129.55  Aligned_cols=85  Identities=18%  Similarity=0.394  Sum_probs=77.7

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....+.++|||+|||+++++++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567899999999999999999999999999999976   457899999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 001991          347 SIPKDNPS  354 (985)
Q Consensus       347 a~pk~~~~  354 (985)
                      +.++..+.
T Consensus        90 a~~~~~~~   97 (103)
T 2d9p_A           90 AQRKEERQ   97 (103)
T ss_dssp             CSSCCCCC
T ss_pred             ecccccCC
Confidence            98876653

>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=4.1e-14  Score=129.50  Aligned_cols=83  Identities=14%  Similarity=0.288  Sum_probs=76.0

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++    +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999976    46788999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 001991          346 YSIPKDN  352 (985)
Q Consensus       346 ~a~pk~~  352 (985)
                      ++.++..
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9987654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.52  E-value=6.1e-15  Score=133.92  Aligned_cols=76  Identities=16%  Similarity=0.337  Sum_probs=69.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccC-CEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhC-CceeCCceEEEEecc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLN-RSDVAGKQIKLEASR  433 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG-~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LN-G~~I~Gr~IkV~~A~  433 (985)
                      ++|||+|||.++|+++|+++|++|| +|.+|+++.+     ++|||||+|.+.++|++|++.++ +..++|++|+|+|++
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 8999988753     68999999999999999999874 568999999999998


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ++.
T Consensus        82 ~~~   84 (91)
T 2lxi_A           82 PKP   84 (91)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            865

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=4.5e-14  Score=130.41  Aligned_cols=83  Identities=19%  Similarity=0.422  Sum_probs=75.9

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHh-CCceeCCceEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTL-NRSDVAGKQIK  428 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~L-NG~~I~Gr~Ik  428 (985)
                      .....++|||+|||..+++++|+++|++||.|..|++..+      .+|||||+|.+.++|++|++.| |+..|.|++|+
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            4456789999999999999999999999999999999765      4899999999999999999999 99999999999


Q ss_pred             EEeccCcchh
Q 001991          429 LEASRPGGAR  438 (985)
Q Consensus       429 V~~A~~k~~R  438 (985)
                      |.+++++..+
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999986543

>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=4.5e-14  Score=129.25  Aligned_cols=82  Identities=20%  Similarity=0.322  Sum_probs=74.7

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      .....++|||+|||..+++++|+++|++||.|..|++..+    .+|||||+|.+.++|++|++.|||..|.|++|+|.+
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            3456789999999999999999999999999999998754    368999999999999999999999999999999999


Q ss_pred             ccCcch
Q 001991          432 SRPGGA  437 (985)
Q Consensus       432 A~~k~~  437 (985)
                      ++++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            998653

>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=99.52  E-value=4.4e-14  Score=128.88  Aligned_cols=81  Identities=22%  Similarity=0.337  Sum_probs=74.6

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..|.|++|+|.++
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            45679999999999999999999999999999998654     5799999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            987644

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.52  E-value=1.9e-14  Score=134.06  Aligned_cols=80  Identities=16%  Similarity=0.309  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcc--cccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP--LRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~--I~Gr~L~V~~a~  348 (985)
                      ...++++|||+|||.++|+++|+++|++||.|.+|++ .+.||||||+|++.++|.+|++.|++..  |.|++|+|.|++
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i-~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~   95 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV-MPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEE-EcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            4458899999999999999999999999999999988 4578999999999999999999999986  789999999998


Q ss_pred             CCC
Q 001991          349 PKD  351 (985)
Q Consensus       349 pk~  351 (985)
                      ++.
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            754

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=2.4e-14  Score=134.53  Aligned_cols=83  Identities=22%  Similarity=0.322  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccC--cccccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng--~~I~Gr~L~V~~a~  348 (985)
                      ...+.++|||+|||+++|+++|+++|++||+|.+|++. +.||||||+|.+.++|++|++.|++  ..|.|++|+|.|+.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~-~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~   90 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML-KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN   90 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcC
Confidence            44578999999999999999999999999999999983 3589999999999999999998864  78999999999998


Q ss_pred             CCCCCC
Q 001991          349 PKDNPS  354 (985)
Q Consensus       349 pk~~~~  354 (985)
                      ++....
T Consensus        91 ~~~~~~   96 (105)
T 1sjq_A           91 HKELKT   96 (105)
T ss_dssp             SSSCCC
T ss_pred             CCCCCc
Confidence            776543

>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=4.6e-14  Score=129.81  Aligned_cols=84  Identities=24%  Similarity=0.455  Sum_probs=77.0

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|.|
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 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            35567899999999999999999999999999999976     5678999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (103)
T 2cq0_A           90 EWAKPSTNS   98 (103)
T ss_dssp             EESSCCCCS
T ss_pred             EECCCCCCC
Confidence            999877654

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=5.1e-14  Score=131.10  Aligned_cols=81  Identities=19%  Similarity=0.194  Sum_probs=73.3

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh--CCceeCCceEEEEeccC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRP  434 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L--NG~~I~Gr~IkV~~A~~  434 (985)
                      ..+.++|||+|||..+++++|+++|++||.|.+|+++.+ +|||||+|.+.++|++|++.|  ++..+.|++|+|.|+++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   90 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   90 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCc
Confidence            345679999999999999999999999999999998875 899999999999999999987  56789999999999997


Q ss_pred             cchh
Q 001991          435 GGAR  438 (985)
Q Consensus       435 k~~R  438 (985)
                      +..+
T Consensus        91 ~~~~   94 (101)
T 2cq1_A           91 KELK   94 (101)
T ss_dssp             SSCC
T ss_pred             ccCc
Confidence            6543

>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=99.52  E-value=3.2e-14  Score=126.42  Aligned_cols=77  Identities=19%  Similarity=0.362  Sum_probs=70.1

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      +.++|||+|||..+++++|+++|++||.|.+|++..+     .+|||||+|.+.++|++|++.|||..+.|++|+|.+++
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            4679999999999999999999999999999998654     47899999999999999999999999999999999998


Q ss_pred             Cc
Q 001991          434 PG  435 (985)
Q Consensus       434 ~k  435 (985)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=4.8e-14  Score=129.97  Aligned_cols=84  Identities=17%  Similarity=0.299  Sum_probs=77.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|
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            45567899999999999999999999999999999986     5678999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999877544

>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=3.1e-14  Score=125.38  Aligned_cols=77  Identities=29%  Similarity=0.477  Sum_probs=71.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      +.+|||+|||.++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|+|..+.|++|.|.++.+
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            468999999999999999999999999999876     467799999999999999999999999999999999999987


Q ss_pred             CC
Q 001991          350 KD  351 (985)
Q Consensus       350 k~  351 (985)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.52  E-value=7e-14  Score=128.89  Aligned_cols=83  Identities=19%  Similarity=0.330  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccc---cccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR---RKLD  343 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G---r~L~  343 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.|   ++|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3456899999999999999999999999999999976    46679999999999999999999999999998   9999


Q ss_pred             ccccCCCCCC
Q 001991          344 IHYSIPKDNP  353 (985)
Q Consensus       344 V~~a~pk~~~  353 (985)
                      |.++.++..+
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999877654

>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=99.52  E-value=3e-14  Score=126.70  Aligned_cols=79  Identities=22%  Similarity=0.373  Sum_probs=72.6

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ..++|||+|||.++++++|+++|++||.|.+|++..+      .+|||||+|.+.++|++|++.|||..+.|++|+|+++
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            3578999999999999999999999999999998643      5789999999999999999999999999999999999


Q ss_pred             cCcch
Q 001991          433 RPGGA  437 (985)
Q Consensus       433 ~~k~~  437 (985)
                      .+...
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>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=6.6e-14  Score=131.30  Aligned_cols=84  Identities=20%  Similarity=0.407  Sum_probs=77.1

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|++..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            35567899999999999999999999999999999976     5667999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (115)
T 2dgo_A           90 NWATRKPPA   98 (115)
T ss_dssp             EESSCCCCC
T ss_pred             EEccCCCCC
Confidence            999887654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3.1e-14  Score=131.02  Aligned_cols=84  Identities=23%  Similarity=0.298  Sum_probs=76.3

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .....++|||+|||..+++++|+++|++||.|..|++..+   .++||||+|.+.++|++|++.|||..|.|++|+|.++
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            3456789999999999999999999999999999998753   5789999999999999999999999999999999999


Q ss_pred             cCcchhh
Q 001991          433 RPGGARR  439 (985)
Q Consensus       433 ~~k~~Rr  439 (985)
                      +++..++
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            9876543

>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=3.5e-14  Score=125.60  Aligned_cols=76  Identities=25%  Similarity=0.423  Sum_probs=70.8

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..+.|++|+|+++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45679999999999999999999999999999998644     5789999999999999999999999999999999998


Q ss_pred             c
Q 001991          433 R  433 (985)
Q Consensus       433 ~  433 (985)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.51  E-value=5.1e-14  Score=126.58  Aligned_cols=82  Identities=20%  Similarity=0.299  Sum_probs=75.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..+.++|||+|||.++++++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|++..+.|++|.|.++.
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            456799999999999999999999999999999976   56689999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 001991          349 PKDNP  353 (985)
Q Consensus       349 pk~~~  353 (985)
                      +....
T Consensus        85 ~~~~~   89 (92)
T 2dgv_A           85 NASGP   89 (92)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            76543

>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=99.51  E-value=4.2e-14  Score=124.54  Aligned_cols=76  Identities=17%  Similarity=0.229  Sum_probs=71.0

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      .+|||+|||.++++++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|++.|||..+.|++|+|.+++++
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            58999999999999999999999999999988644     3789999999999999999999999999999999999886


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      +
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.51  E-value=5.8e-14  Score=130.64  Aligned_cols=84  Identities=15%  Similarity=0.309  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ....+.++|||+|||.++++++|+++|++||.|..|++  ++.++|||||+|.+.++|++|++.|++..|.|++|.|.++
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            45567899999999999999999999999999999987  4567899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 001991          348 IPKDNP  353 (985)
Q Consensus       348 ~pk~~~  353 (985)
                      .++...
T Consensus        97 ~~~~~~  102 (109)
T 1x4a_A           97 RSGRGT  102 (109)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            876544

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=6.2e-14  Score=130.41  Aligned_cols=80  Identities=30%  Similarity=0.454  Sum_probs=73.8

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC--CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~--skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ....++|||+|||.++++++|+++|++||.|..|++..+  +++||||+|.+.++|++|++.||+..|.|++|+|+++++
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            445679999999999999999999999999999998654  578999999999999999999999999999999999987


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      +.
T Consensus        99 ~~  100 (109)
T 1x4a_A           99 GR  100 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=5.6e-14  Score=128.06  Aligned_cols=78  Identities=19%  Similarity=0.351  Sum_probs=73.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeC--CceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA--GKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~--Gr~IkV~~A~~k  435 (985)
                      ...++|||+|||..+++++|+++|++||.|.+|++..+ ++||||+|.+.++|++|++.|||..|.  |++|+|++++++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            34679999999999999999999999999999999875 899999999999999999999999999  999999999986


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      .
T Consensus        94 ~   94 (97)
T 1why_A           94 P   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=5.3e-14  Score=127.20  Aligned_cols=81  Identities=25%  Similarity=0.445  Sum_probs=75.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.++
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            46799999999999999999999999999999976     4678999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 001991          348 IPKDNP  353 (985)
Q Consensus       348 ~pk~~~  353 (985)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            877654

>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=7.3e-14  Score=128.50  Aligned_cols=83  Identities=20%  Similarity=0.342  Sum_probs=75.7

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .....++|||+|||..+++++|+++|++||.|..|++..+   .++||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3456789999999999999999999999999999998755   4789999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2cq3_A           91 TARVMT   96 (103)
T ss_dssp             CSSCCC
T ss_pred             ccCCCC
Confidence            886543

>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=6.9e-14  Score=127.74  Aligned_cols=82  Identities=23%  Similarity=0.485  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++ |++..|.|++|.|.
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            4457799999999999999999999999999999987     46689999999999999999998 99999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99887654

>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=99.51  E-value=2.9e-14  Score=126.66  Aligned_cols=78  Identities=21%  Similarity=0.430  Sum_probs=70.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|.|.++
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            35789999999999999999999999999999976     5668999999999999999999999999999999999999


Q ss_pred             CCC
Q 001991          348 IPK  350 (985)
Q Consensus       348 ~pk  350 (985)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            765

>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=99.51  E-value=5.2e-14  Score=128.46  Aligned_cols=79  Identities=20%  Similarity=0.361  Sum_probs=73.2

Q ss_pred             ccccceeeecCCCCCCHHHHH----HHhhccCCEEEEEEcCCC--CcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          358 ANQGTLVVFNLDSSVSTEELH----QIFGIYGEIREIRDTQHK--HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLr----elFs~fG~I~~Vri~~~s--kGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....+|||+|||..+++++|+    ++|++||.|.+|+++.+.  ++||||+|.+.++|++|++.|||..|.|++|+|++
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345799999999999999999    999999999999998553  88999999999999999999999999999999999


Q ss_pred             ccCcc
Q 001991          432 SRPGG  436 (985)
Q Consensus       432 A~~k~  436 (985)
                      ++++.
T Consensus        87 a~~~~   91 (96)
T 2dgx_A           87 ATGAS   91 (96)
T ss_dssp             CCCSS
T ss_pred             cCCCC
Confidence            98765

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.51  E-value=1.1e-14  Score=167.94  Aligned_cols=146  Identities=20%  Similarity=0.326  Sum_probs=105.5

Q ss_pred             HHHHhhcccCcEEEEEe-------ccccceEE-----EEEeCCHHHHHHHHHHccCccccccc-------------cccc
Q 001991          291 ELKALFEQFGDIRTIYT-------ACKHRGFV-----MISYYDIRAARNAMKALQNKPLRRRK-------------LDIH  345 (985)
Q Consensus       291 dLrelFs~fG~I~sVki-------tgksrGfA-----FV~F~d~esA~kAi~~Lng~~I~Gr~-------------L~V~  345 (985)
                      .|.++|.++|+|..|..       ..+..+|+     |+.|.....+..++..++......+.             ..+.
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~   87 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELK   87 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            37899999999988732       11233344     77887766655554433332222110             0111


Q ss_pred             ccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCc
Q 001991          346 YSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRS  420 (985)
Q Consensus       346 ~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~  420 (985)
                      ...+...........++|||+|||..+|+++|+++|++||.|+.|.|+.+     ++|||||+|.+.++|.+||..|||.
T Consensus        88 ~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  167 (437)
T 3pgw_S           88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK  167 (437)
T ss_pred             hcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC
Confidence            11222222223345679999999999999999999999999999998644     5899999999999999999999999


Q ss_pred             eeCCceEEEEeccCcc
Q 001991          421 DVAGKQIKLEASRPGG  436 (985)
Q Consensus       421 ~I~Gr~IkV~~A~~k~  436 (985)
                      .|.|++|.|.++.++.
T Consensus       168 ~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          168 KIDGRRVLVDVERGRT  183 (437)
T ss_pred             EECCEEEEEEEeCCCC
Confidence            9999999999998754

>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=3.9e-14  Score=130.28  Aligned_cols=84  Identities=24%  Similarity=0.381  Sum_probs=76.8

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|.|
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            35567899999999999999999999999999999986     3678999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2dnm_A           88 QVARYGRRD   96 (103)
T ss_dssp             EECSSCCSC
T ss_pred             EECCcCCCC
Confidence            999876544

>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=5.4e-14  Score=130.87  Aligned_cols=82  Identities=21%  Similarity=0.347  Sum_probs=75.0

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..|.|++|+|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            345679999999999999999999999999999998754     379999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus       103 a~~~~~~  109 (110)
T 1oo0_B          103 CFVKGPK  109 (110)
T ss_dssp             SEESSCC
T ss_pred             cccCCCC
Confidence            9877644

>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=4.2e-14  Score=132.22  Aligned_cols=79  Identities=19%  Similarity=0.205  Sum_probs=72.0

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCc--eeCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS--DVAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~--~I~Gr~IkV~~A~~k  435 (985)
                      .+.++|||+|||.++++++|+++|++||.|.+|+++++ +|||||+|.+.++|.+|++.|++.  .|.|++|+|+|++++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            45679999999999999999999999999999998764 899999999999999999998765  599999999999876


Q ss_pred             ch
Q 001991          436 GA  437 (985)
Q Consensus       436 ~~  437 (985)
                      ..
T Consensus        92 ~~   93 (104)
T 1wex_A           92 RI   93 (104)
T ss_dssp             SC
T ss_pred             cc
Confidence            53

>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=3.6e-14  Score=130.12  Aligned_cols=82  Identities=24%  Similarity=0.412  Sum_probs=75.2

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|+++.+     .++||||+|.+.++|++|++.|||..|.|++|+|.+
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            345679999999999999999999999999999998754     689999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9987644

>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=99.50  E-value=6.8e-14  Score=127.24  Aligned_cols=79  Identities=16%  Similarity=0.259  Sum_probs=73.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .++|||+|||..+++++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|++.|||..++|++|+|.++++
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            568999999999999999999999999999998754     479999999999999999999999999999999999998


Q ss_pred             cchh
Q 001991          435 GGAR  438 (985)
Q Consensus       435 k~~R  438 (985)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            7643

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.50  E-value=6.8e-14  Score=131.22  Aligned_cols=82  Identities=21%  Similarity=0.379  Sum_probs=75.0

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..|.|++|+|.+
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            346779999999999999999999999999999998754     368999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9987644

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=7.4e-14  Score=128.97  Aligned_cols=84  Identities=25%  Similarity=0.483  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe------ccccceEEEEEeCCHHHHHHHHHHc-cCcccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKL  342 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki------tgksrGfAFV~F~d~esA~kAi~~L-ng~~I~Gr~L  342 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++      +++++|||||+|.+.++|++|++.| ++..|.|++|
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            35567899999999999999999999999999999987      4557999999999999999999999 9999999999


Q ss_pred             cccccCCCCCC
Q 001991          343 DIHYSIPKDNP  353 (985)
Q Consensus       343 ~V~~a~pk~~~  353 (985)
                      .|.++.++...
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999887654

>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=5.8e-14  Score=131.29  Aligned_cols=84  Identities=17%  Similarity=0.252  Sum_probs=74.2

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCc--ccccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK--PLRRRKLDIHY  346 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~--~I~Gr~L~V~~  346 (985)
                      +....++++|||+|||.++++++|+++|++||.|..|.+ .+.||||||+|.+.++|++|++.|++.  .|.|++|+|.|
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 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE-ECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            345567899999999999999999999999999999987 345899999999999999999988765  49999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus        88 a~~~~~~   94 (104)
T 1wex_A           88 STSKRIT   94 (104)
T ss_dssp             CSSSSCC
T ss_pred             ccCcccc
Confidence            9876543

>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=99.50  E-value=3.8e-14  Score=128.96  Aligned_cols=79  Identities=22%  Similarity=0.428  Sum_probs=73.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ++++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++.
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            5789999999999999999999999999999986     46779999999999999999999999999999999999998


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7653

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=6.6e-14  Score=127.86  Aligned_cols=81  Identities=19%  Similarity=0.399  Sum_probs=74.3

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|+++.+     .+|||||+|.+.++|++|++ ||+..|.|++|+|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            345679999999999999999999999999999999754     57999999999999999999 999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9987644

>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=99.50  E-value=6e-14  Score=131.76  Aligned_cols=84  Identities=17%  Similarity=0.345  Sum_probs=76.9

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34557799999999999999999999999999999876     5778999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus       100 ~~a~~~~~~  108 (115)
T 2cpz_A          100 QLKRSKNDS  108 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EEcCCCCcC
Confidence            999887654

>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=127.28  Aligned_cols=84  Identities=21%  Similarity=0.385  Sum_probs=76.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++   ...++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            35567899999999999999999999999999999987   234689999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9887654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=4.7e-14  Score=130.26  Aligned_cols=81  Identities=17%  Similarity=0.444  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|.|.
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            4456799999999999999999999999999999986     37789999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 001991          346 YSIPKD  351 (985)
Q Consensus       346 ~a~pk~  351 (985)
                      ++.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            998764

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=5.6e-14  Score=126.31  Aligned_cols=78  Identities=28%  Similarity=0.408  Sum_probs=72.9

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ...++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|++++++..
T Consensus         6 ~~~~~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            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            456799999999999999999999999999999987   78999999999999999999999999999999999988654


Q ss_pred             h
Q 001991          438 R  438 (985)
Q Consensus       438 R  438 (985)
                      +
T Consensus        83 ~   83 (90)
T 2dnq_A           83 A   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.50  E-value=5.3e-14  Score=135.00  Aligned_cols=85  Identities=21%  Similarity=0.302  Sum_probs=75.6

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccC--cccccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIHY  346 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng--~~I~Gr~L~V~~  346 (985)
                      .....++++|||+|||+++++++|+++|++||.|..|++ .+.||||||+|++.++|++|++.+++  ..|.|++|+|.|
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i-~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~  103 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM-LKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF  103 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEE-EGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEE
Confidence            445567899999999999999999999999999999988 34589999999999999999998875  689999999999


Q ss_pred             cCCCCCCC
Q 001991          347 SIPKDNPS  354 (985)
Q Consensus       347 a~pk~~~~  354 (985)
                      +.++....
T Consensus       104 a~~k~~~~  111 (119)
T 2ad9_A          104 SNHKELKT  111 (119)
T ss_dssp             CSSSSCCC
T ss_pred             ccCCCCCc
Confidence            98776543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=8.3e-14  Score=125.75  Aligned_cols=78  Identities=21%  Similarity=0.391  Sum_probs=72.0

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .++||||+|.+.++|++|++.|||..|.|++|+|++
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            456789999999999999999999999999999998643     468999999999999999999999999999999999


Q ss_pred             ccC
Q 001991          432 SRP  434 (985)
Q Consensus       432 A~~  434 (985)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            875

>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=99.50  E-value=2.9e-14  Score=136.82  Aligned_cols=80  Identities=18%  Similarity=0.212  Sum_probs=73.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCC--ceeCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR--SDVAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG--~~I~Gr~IkV~~A~~k  435 (985)
                      .+.++|||+|||+++++++|+++|++||.|.+|+++.+ +|||||+|.+.++|++|++.|++  ..|.|++|+|.+++++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k  107 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCC
Confidence            45679999999999999999999999999999998875 89999999999999999999984  6899999999999887


Q ss_pred             chh
Q 001991          436 GAR  438 (985)
Q Consensus       436 ~~R  438 (985)
                      ..+
T Consensus       108 ~~~  110 (119)
T 2ad9_A          108 ELK  110 (119)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>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=99.50  E-value=3.2e-14  Score=132.90  Aligned_cols=78  Identities=18%  Similarity=0.218  Sum_probs=71.2

Q ss_pred             ccccceeeecCCC-CCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCc--eeCCceEEEEeccC
Q 001991          358 ANQGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS--DVAGKQIKLEASRP  434 (985)
Q Consensus       358 ~~~~tLfV~NLp~-svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~--~I~Gr~IkV~~A~~  434 (985)
                      .+.++|||+|||. ++++++|+++|++||.|.+|+++.+ ++||||+|.+.++|++|++.||+.  .|.|++|+|.+++.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            3567999999999 9999999999999999999999865 799999999999999999999864  59999999999986


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      +.
T Consensus        92 ~~   93 (102)
T 1x4d_A           92 YK   93 (102)
T ss_dssp             CT
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=99.50  E-value=7e-14  Score=126.41  Aligned_cols=80  Identities=25%  Similarity=0.341  Sum_probs=73.7

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+++++|+++|++||.|..|++..+     .++||||+|.+.++|++|++.|||..|.|++|+|.+++
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            4579999999999999999999999999999998754     47899999999999999999999999999999999998


Q ss_pred             Ccchh
Q 001991          434 PGGAR  438 (985)
Q Consensus       434 ~k~~R  438 (985)
                      ++..+
T Consensus        84 ~~~~~   88 (95)
T 2dnz_A           84 ERLDG   88 (95)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            86543

>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=99.50  E-value=6.3e-14  Score=129.19  Aligned_cols=82  Identities=21%  Similarity=0.311  Sum_probs=74.9

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..|.|++|+|.+
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            445679999999999999999999999999999998754     468999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus        92 a~~~~~~   98 (105)
T 1x5u_A           92 ASAHNKN   98 (105)
T ss_dssp             TTTTSCC
T ss_pred             CCCCCcC
Confidence            9886543

>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=8e-14  Score=129.59  Aligned_cols=85  Identities=22%  Similarity=0.479  Sum_probs=77.6

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHcc------Cccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQ------NKPL  337 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Ln------g~~I  337 (985)
                      +....+.++|||+|||.++++++|+++|++||+|..|++     ++.++|||||+|.+.++|++|++.|+      +..|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~   88 (111)
T 1x4h_A            9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   88 (111)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             CCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE
Confidence            345567899999999999999999999999999999986     36789999999999999999999999      9999


Q ss_pred             ccccccccccCCCCCC
Q 001991          338 RRRKLDIHYSIPKDNP  353 (985)
Q Consensus       338 ~Gr~L~V~~a~pk~~~  353 (985)
                      .|+.|.|.++.++...
T Consensus        89 ~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           89 DGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SSCEEEEECCCCCCCC
T ss_pred             cCEEEEEEECCCCccC
Confidence            9999999999887654

>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=7.5e-14  Score=130.67  Aligned_cols=82  Identities=23%  Similarity=0.459  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|.|
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            35567899999999999999999999999999999876     4678999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 001991          345 HYSIPKD  351 (985)
Q Consensus       345 ~~a~pk~  351 (985)
                      .++.++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.8e-14  Score=130.21  Aligned_cols=80  Identities=24%  Similarity=0.399  Sum_probs=73.5

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     ++|||||+|.+.++|++|++.|||..|.|++|+|.+
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            445679999999999999999999999999999998743     468999999999999999999999999999999999


Q ss_pred             ccCcc
Q 001991          432 SRPGG  436 (985)
Q Consensus       432 A~~k~  436 (985)
                      ++++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98765

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=7.5e-14  Score=130.14  Aligned_cols=78  Identities=18%  Similarity=0.238  Sum_probs=73.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCC-----ceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG-----KQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~G-----r~IkV~~A  432 (985)
                      ...++|||+|||.++++++|+++|++||.|..|++..+  +||||+|.+.++|++||+.|||..|.|     ++|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a   90 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   90 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeC
Confidence            45679999999999999999999999999999999876  999999999999999999999999999     99999999


Q ss_pred             cCcch
Q 001991          433 RPGGA  437 (985)
Q Consensus       433 ~~k~~  437 (985)
                      +++..
T Consensus        91 ~~~~~   95 (108)
T 1x4c_A           91 GPRSP   95 (108)
T ss_dssp             SCCSC
T ss_pred             CCCCC
Confidence            98653

>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=99.49  E-value=1.1e-13  Score=128.76  Aligned_cols=82  Identities=20%  Similarity=0.342  Sum_probs=75.3

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhC------CceeCCc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLN------RSDVAGK  425 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LN------G~~I~Gr  425 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.||      +..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            345679999999999999999999999999999998744     58899999999999999999999      9999999


Q ss_pred             eEEEEeccCcchh
Q 001991          426 QIKLEASRPGGAR  438 (985)
Q Consensus       426 ~IkV~~A~~k~~R  438 (985)
                      +|+|.++.++..+
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999999987644

>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=99.49  E-value=8.8e-14  Score=127.94  Aligned_cols=84  Identities=18%  Similarity=0.421  Sum_probs=76.0

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++   ...++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            35567899999999999999999999999999999987   234689999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9876544

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=7.2e-14  Score=127.24  Aligned_cols=81  Identities=27%  Similarity=0.463  Sum_probs=74.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEec--------cccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA--------CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkit--------gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      .+.++|||+|||.++++++|+++|++||+|..|++.        ++++|||||+|.+.++|++|++.|++..|.|++|.|
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            467999999999999999999999999999998762        277899999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876654

>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=99.49  E-value=5.5e-14  Score=124.36  Aligned_cols=77  Identities=29%  Similarity=0.484  Sum_probs=71.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..+.++|||+|||+++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|+|..+.|++|.|.+
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            356799999999999999999999999999999976     466899999999999999999999999999999999998


Q ss_pred             cC
Q 001991          347 SI  348 (985)
Q Consensus       347 a~  348 (985)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.49  E-value=4.9e-14  Score=132.34  Aligned_cols=82  Identities=16%  Similarity=0.341  Sum_probs=74.6

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||.++++++|+++|++||.|.+|++..+     .++||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999988654     358999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9987654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=5.8e-14  Score=129.17  Aligned_cols=82  Identities=20%  Similarity=0.310  Sum_probs=74.7

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..|.|++|+|.+
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            445789999999999999999999999999999998654     468999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9987643

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.4e-14  Score=129.59  Aligned_cols=81  Identities=26%  Similarity=0.489  Sum_probs=74.6

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|..|++..+     .++||||+|.+.++|++|++.||+..|.|++|+|.++
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 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45679999999999999999999999999999999764     5789999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 1x5s_A           90 GKSSDN   95 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            886643

>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=99.49  E-value=8.6e-14  Score=128.28  Aligned_cols=83  Identities=18%  Similarity=0.261  Sum_probs=75.1

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCC---ceEEE
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAG---KQIKL  429 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~G---r~IkV  429 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+    ++|||||+|.+.++|++|++.|||..+.|   ++|+|
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            345789999999999999999999999999999998754    36899999999999999999999999988   99999


Q ss_pred             EeccCcchhh
Q 001991          430 EASRPGGARR  439 (985)
Q Consensus       430 ~~A~~k~~Rr  439 (985)
                      .+++++..++
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9999876543

>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=99.49  E-value=7.2e-14  Score=130.15  Aligned_cols=80  Identities=20%  Similarity=0.303  Sum_probs=74.8

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ...++|||+|||..+++++|+++|++||.|..|++..+ ++||||+|.+.++|++|++.|||..|.|++|+|.|++++..
T Consensus        23 ~~~~~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           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            45679999999999999999999999999999999876 89999999999999999999999999999999999998664


Q ss_pred             h
Q 001991          438 R  438 (985)
Q Consensus       438 R  438 (985)
                      .
T Consensus       102 ~  102 (109)
T 1x4g_A          102 M  102 (109)
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=1.4e-13  Score=124.28  Aligned_cols=77  Identities=26%  Similarity=0.421  Sum_probs=71.4

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .++||||+|.+.++|++|++.|||..|.|++|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            345679999999999999999999999999999999754     468999999999999999999999999999999999


Q ss_pred             cc
Q 001991          432 SR  433 (985)
Q Consensus       432 A~  433 (985)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>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=99.49  E-value=4.9e-14  Score=131.49  Aligned_cols=95  Identities=17%  Similarity=0.289  Sum_probs=81.1

Q ss_pred             ccccccccccCCCCCCCcccccccceeeecCCCC-CCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHH
Q 001991          338 RRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT  416 (985)
Q Consensus       338 ~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~s-vTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~  416 (985)
                      .|..|.+..+.+.... ......++|||+|||.. +++++|+++|++||.|..|++   .++||||+|.+.++|++|++.
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 SGMSLKLQASNVTNKN-DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLG   81 (110)
T ss_dssp             CSCCCCCCCCCSCCSC-CCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHH
T ss_pred             CCcccccccCCCCCCC-CCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHH
Confidence            4567777766544332 22344579999999999 999999999999999999998   589999999999999999999


Q ss_pred             hCCceeCCceEEEEeccCcc
Q 001991          417 LNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       417 LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      |||..|.|++|+|++++++.
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            99999999999999998544

>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=6.2e-14  Score=130.92  Aligned_cols=80  Identities=15%  Similarity=0.154  Sum_probs=72.3

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCc--ccccccccccccC
Q 001991          272 EHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK--PLRRRKLDIHYSI  348 (985)
Q Consensus       272 e~~srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~--~I~Gr~L~V~~a~  348 (985)
                      ..++++|||+|||+ ++++++|+++|++||.|.+|++ -+.+|||||+|.+.++|++|++.|++.  .|.|++|+|.++.
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 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   90 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-CSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEE-EcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECC
Confidence            34789999999999 9999999999999999999998 456799999999999999999999875  4999999999998


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      ++..
T Consensus        91 ~~~~   94 (102)
T 1x4d_A           91 KYKR   94 (102)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            6543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=5.2e-14  Score=128.17  Aligned_cols=79  Identities=23%  Similarity=0.364  Sum_probs=72.6

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC--------CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--------HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~--------~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ..++|||+|||.++++++|+++|++||.|..|++..        ..++||||+|.+.++|++|++.|||..|.|++|+|.
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            457999999999999999999999999999998864        346899999999999999999999999999999999


Q ss_pred             eccCcch
Q 001991          431 ASRPGGA  437 (985)
Q Consensus       431 ~A~~k~~  437 (985)
                      +++++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9987653

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=1.2e-13  Score=128.69  Aligned_cols=83  Identities=25%  Similarity=0.341  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHcc--Cccccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ--NKPLRRRKLDIHYS  347 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Ln--g~~I~Gr~L~V~~a  347 (985)
                      ....++++|||+|||.++++++|+++|++||.|..|.+. +.||||||+|.+.++|++|++.|+  +..+.|++|+|.|+
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~-~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-CCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            345678999999999999999999999999999999873 459999999999999999999875  57799999999999


Q ss_pred             CCCCCC
Q 001991          348 IPKDNP  353 (985)
Q Consensus       348 ~pk~~~  353 (985)
                      .++...
T Consensus        89 ~~~~~~   94 (101)
T 2cq1_A           89 NHKELK   94 (101)
T ss_dssp             SCSSCC
T ss_pred             CcccCc
Confidence            876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=7.2e-14  Score=126.17  Aligned_cols=80  Identities=18%  Similarity=0.362  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567899999999999999999999999999999976     3678999999999999999999999999999999999


Q ss_pred             cccCC
Q 001991          345 HYSIP  349 (985)
Q Consensus       345 ~~a~p  349 (985)
                      .++.+
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99863

>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=99.48  E-value=1.4e-13  Score=125.32  Aligned_cols=81  Identities=28%  Similarity=0.492  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc--cccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR--RRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~--Gr~L~V~~a~  348 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++. ..+|||||+|.+.++|++|++.|++..|.  |++|.|.++.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe-CCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            34567999999999999999999999999999999983 34899999999999999999999999999  9999999998


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      ++..
T Consensus        92 ~~~~   95 (97)
T 1why_A           92 SGPS   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=4.4e-14  Score=127.99  Aligned_cols=81  Identities=22%  Similarity=0.457  Sum_probs=74.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE-Ee-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTI-YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV-ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .+.++|||+|||.++++++|+++|++||.|..+ ++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
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 65     466799999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9887654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=7e-14  Score=128.23  Aligned_cols=83  Identities=20%  Similarity=0.446  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.||+..|.|++|.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3457799999999999999999999999999999987     45688999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99876654

>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=4.4e-14  Score=128.00  Aligned_cols=80  Identities=18%  Similarity=0.330  Sum_probs=73.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEE-EEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~V-ri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ..++|||+|||..+++++|+++|++||.|..| ++..+     .++||||+|.+.++|++|++.|||..|.|++|+|.++
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            46799999999999999999999999999998 88764     5789999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            887644

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=9.3e-14  Score=125.35  Aligned_cols=78  Identities=23%  Similarity=0.432  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
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            4457799999999999999999999999999999987     36678999999999999999999999999999999999


Q ss_pred             ccC
Q 001991          346 YSI  348 (985)
Q Consensus       346 ~a~  348 (985)
                      +++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=1.3e-13  Score=126.83  Aligned_cols=83  Identities=20%  Similarity=0.380  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcc-cCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcc-cccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQ-FGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKP-LRRRKLDI  344 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~-fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~-I~Gr~L~V  344 (985)
                      ...+.++|||+|||.++++++|+++|++ ||.|..|++    +++++|||||+|.+.++|++|++.|++.. |.|++|.|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            4457799999999999999999999999 999999976    56789999999999999999999999999 99999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            999877654

>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=99.48  E-value=1.1e-13  Score=127.69  Aligned_cols=79  Identities=27%  Similarity=0.493  Sum_probs=73.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      .+.++|||+|||..+++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.||+..|.|++|+|.+++++..
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            456799999999999999999999999999999987   57999999999999999999999999999999999998764


Q ss_pred             hh
Q 001991          438 RR  439 (985)
Q Consensus       438 Rr  439 (985)
                      ++
T Consensus        86 ~~   87 (103)
T 2dgu_A           86 KR   87 (103)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.48  E-value=3e-14  Score=131.12  Aligned_cols=76  Identities=16%  Similarity=0.339  Sum_probs=68.3

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCC--EEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCc----eeCCceE
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGE--IREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRS----DVAGKQI  427 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~--I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~----~I~Gr~I  427 (985)
                      .-.||||+|||+.+|+++|+++|++||.  |.+|+++.+     ++|||||+|.+.++|++|++.|||.    .|+||+|
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            3468999999999999999999999995  567887654     6899999999999999999999997    5899999


Q ss_pred             EEEeccC
Q 001991          428 KLEASRP  434 (985)
Q Consensus       428 kV~~A~~  434 (985)
                      .|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999974

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=6.3e-14  Score=128.52  Aligned_cols=83  Identities=28%  Similarity=0.445  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3457899999999999999999999999999999986     46689999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99887654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=7.5e-14  Score=128.43  Aligned_cols=81  Identities=23%  Similarity=0.418  Sum_probs=74.1

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .++||||+|.+.++|++|++.|||..|.|++|+|.+
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 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            345679999999999999999999999999999998754     478999999999999999999999999999999999


Q ss_pred             ccCcch
Q 001991          432 SRPGGA  437 (985)
Q Consensus       432 A~~k~~  437 (985)
                      ++++..
T Consensus        90 a~~~~~   95 (103)
T 2dnm_A           90 ARYGRR   95 (103)
T ss_dssp             CSSCCS
T ss_pred             CCcCCC
Confidence            987653

>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=6.9e-14  Score=131.03  Aligned_cols=81  Identities=23%  Similarity=0.421  Sum_probs=73.2

Q ss_pred             cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       355 ~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ......++|||+|||..+++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..|.|++|+|.++++
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            344567899999999999999999999999999999987   89999999999999999999999999999999999988


Q ss_pred             cchh
Q 001991          435 GGAR  438 (985)
Q Consensus       435 k~~R  438 (985)
                      +..|
T Consensus       103 ~~~r  106 (108)
T 2jvo_A          103 PAKR  106 (108)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            6543

>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=99.48  E-value=1e-13  Score=122.74  Aligned_cols=76  Identities=32%  Similarity=0.443  Sum_probs=71.2

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh-CCceeCCceEEEEecc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL-NRSDVAGKQIKLEASR  433 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L-NG~~I~Gr~IkV~~A~  433 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++.. .+|||||+|.+.++|++|++.| ||..+.|++|+|+|++
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            45668999999999999999999999999999999886 4899999999999999999999 9999999999999985

>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=128.59  Aligned_cols=78  Identities=18%  Similarity=0.275  Sum_probs=66.2

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccC--cEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFG--DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG--~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      .+|||+|||.++++++|+++|++||  .|.++++     +++++|||||+|.+.++|++|++.|||..|.|++|.|.++.
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  8988875     67889999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 001991          349 PKDNP  353 (985)
Q Consensus       349 pk~~~  353 (985)
                      ++...
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            76543

>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=99.47  E-value=1e-13  Score=125.39  Aligned_cols=78  Identities=21%  Similarity=0.299  Sum_probs=72.0

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+    .++||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            345679999999999999999999999999999998754    3689999999999999999999999999999999998


Q ss_pred             cC
Q 001991          433 RP  434 (985)
Q Consensus       433 ~~  434 (985)
                      +.
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=9.2e-14  Score=127.09  Aligned_cols=81  Identities=26%  Similarity=0.481  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++ .+.+|||||+|.+.++|++|++.|++..|.|++|.|.++.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~-~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE-ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEE-ecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            4457799999999999999999999999999999998 466899999999999999999999999999999999999876


Q ss_pred             CC
Q 001991          351 DN  352 (985)
Q Consensus       351 ~~  352 (985)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpj_A           90 AS   91 (99)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.4e-13  Score=124.13  Aligned_cols=78  Identities=22%  Similarity=0.324  Sum_probs=72.5

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..|.|++|+|.+++++.
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            4557899999999999999999999999999999987   4599999999999999999999999999999999998765


Q ss_pred             h
Q 001991          437 A  437 (985)
Q Consensus       437 ~  437 (985)
                      .
T Consensus        84 ~   84 (92)
T 2dgt_A           84 R   84 (92)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.47  E-value=9.2e-14  Score=128.30  Aligned_cols=84  Identities=25%  Similarity=0.475  Sum_probs=76.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccc---cccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPL---RRRK  341 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I---~Gr~  341 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..+   .|++
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            35567899999999999999999999999999999986     467899999999999999999999999988   8999


Q ss_pred             ccccccCCCCCC
Q 001991          342 LDIHYSIPKDNP  353 (985)
Q Consensus       342 L~V~~a~pk~~~  353 (985)
                      |.|.++.++...
T Consensus        88 l~v~~a~~~~~~   99 (106)
T 2dgp_A           88 IQVKPADSESRG   99 (106)
T ss_dssp             CEEEECCCCSCC
T ss_pred             EEEEECCccccc
Confidence            999999876543

>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=9.7e-14  Score=130.14  Aligned_cols=80  Identities=16%  Similarity=0.302  Sum_probs=73.4

Q ss_pred             cccccceeeecCCCCCCHHHHH---HHhhccCCEEEEEEcCC--------CCcEEEEEEcCHHHHHHHHHHhCCceeCCc
Q 001991          357 DANQGTLVVFNLDSSVSTEELH---QIFGIYGEIREIRDTQH--------KHNHKFIEFYDIRAAETALRTLNRSDVAGK  425 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLr---elFs~fG~I~~Vri~~~--------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr  425 (985)
                      ....++|||+|||.++++++|+   ++|++||+|.+|+++.+        .+|||||+|.+.++|++|++.|||..|.|+
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   99999999999998754        347999999999999999999999999999


Q ss_pred             eEEEEeccCcc
Q 001991          426 QIKLEASRPGG  436 (985)
Q Consensus       426 ~IkV~~A~~k~  436 (985)
                      +|+|.++.++.
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            99999998865

>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=9e-14  Score=127.15  Aligned_cols=79  Identities=24%  Similarity=0.339  Sum_probs=73.6

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+ ++||||+|.+.++|++|++.|||..|.|++|+|.+++++.
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 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            345679999999999999999999999999999998764 8999999999999999999999999999999999998765

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.3e-13  Score=123.84  Aligned_cols=78  Identities=26%  Similarity=0.386  Sum_probs=72.4

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|||..+.|++|+|.+++++.
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            3456799999999999999999999999999999987   4599999999999999999999999999999999998765


Q ss_pred             h
Q 001991          437 A  437 (985)
Q Consensus       437 ~  437 (985)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.47  E-value=7e-14  Score=132.41  Aligned_cols=78  Identities=18%  Similarity=0.136  Sum_probs=71.5

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccC-CEEEEEEc-CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG-~I~~Vri~-~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ...+|||+|||.++++++|+++|++|| +|..+++. .+++|||||+|.+.++|++|++.|||..|.|++|+|++++.+.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            457999999999999999999999999 99999985 4679999999999999999999999999999999999997653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.4e-13  Score=123.68  Aligned_cols=79  Identities=22%  Similarity=0.390  Sum_probs=73.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      ..+.++|||+|||.++++++|+++|++||+|..|++.   +|||||+|.+.++|++|++.|++..+.|++|.|.++.++.
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            4577999999999999999999999999999999984   8999999999999999999999999999999999998776


Q ss_pred             CC
Q 001991          352 NP  353 (985)
Q Consensus       352 ~~  353 (985)
                      ..
T Consensus        82 ~~   83 (90)
T 2dnq_A           82 KA   83 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.47  E-value=1.1e-13  Score=127.91  Aligned_cols=83  Identities=16%  Similarity=0.320  Sum_probs=75.1

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCcee---CCceE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDV---AGKQI  427 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I---~Gr~I  427 (985)
                      .....++|||+|||..+++++|+++|++||.|.+|+++.+     .+|||||+|.+.++|++|++.|||..+   .|++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            3456789999999999999999999999999999998764     579999999999999999999999988   89999


Q ss_pred             EEEeccCcchh
Q 001991          428 KLEASRPGGAR  438 (985)
Q Consensus       428 kV~~A~~k~~R  438 (985)
                      +|.+++++..+
T Consensus        89 ~v~~a~~~~~~   99 (106)
T 2dgp_A           89 QVKPADSESRG   99 (106)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEECCccccc
Confidence            99999886543

>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=99.47  E-value=8e-14  Score=126.01  Aligned_cols=79  Identities=23%  Similarity=0.332  Sum_probs=72.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ....+.++|||+|||+++++++|+++|++||+|..|++    .++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            45567899999999999999999999999999999976    35679999999999999999999999999999999999


Q ss_pred             ccC
Q 001991          346 YSI  348 (985)
Q Consensus       346 ~a~  348 (985)
                      ++.
T Consensus        91 ~a~   93 (95)
T 2ywk_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            875

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.47  E-value=1.1e-13  Score=133.72  Aligned_cols=82  Identities=21%  Similarity=0.434  Sum_probs=75.8

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++.+|||||+|.+.++|++|++.|++..|.|++|.|
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            35567899999999999999999999999999999986     4678999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 001991          345 HYSIPKD  351 (985)
Q Consensus       345 ~~a~pk~  351 (985)
                      .++.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.47  E-value=1.5e-13  Score=133.06  Aligned_cols=83  Identities=23%  Similarity=0.366  Sum_probs=75.3

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      .....++|||+|||.++++++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|++.|||..|.|++|+|.
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            3445679999999999999999999999999999998644     47899999999999999999999999999999999


Q ss_pred             eccCcchh
Q 001991          431 ASRPGGAR  438 (985)
Q Consensus       431 ~A~~k~~R  438 (985)
                      +++++..+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99987644

>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=8.3e-14  Score=130.29  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=74.5

Q ss_pred             cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       355 ~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ......++|||+|||..+++++|+++|++||.|..|++..+   .+|||||+|.+.++|++|++.|||..|+|++|+|++
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            34456789999999999999999999999999999998754   479999999999999999999999999999999999


Q ss_pred             ccCc
Q 001991          432 SRPG  435 (985)
Q Consensus       432 A~~k  435 (985)
                      ++++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9875

>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=2.6e-13  Score=124.08  Aligned_cols=78  Identities=23%  Similarity=0.342  Sum_probs=72.3

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhcc--CCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIY--GEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~f--G~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ....++|||+|||..+++++|+++|++|  |.|..|++.   ++||||+|.+.++|++|++.|||..|.|++|+|.++++
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 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   88 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            3456799999999999999999999999  999999875   68999999999999999999999999999999999988


Q ss_pred             cch
Q 001991          435 GGA  437 (985)
Q Consensus       435 k~~  437 (985)
                      +..
T Consensus        89 ~~~   91 (99)
T 2cpd_A           89 VDK   91 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.47  E-value=5.7e-14  Score=131.70  Aligned_cols=80  Identities=21%  Similarity=0.433  Sum_probs=73.1

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|..|+++.     ..+|||||+|.+.++|++|+ .|||..|.|++|+|.++
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            4567999999999999999999999999999999974     35789999999999999999 89999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus       102 ~~~~~~  107 (114)
T 2cq4_A          102 QAEKNR  107 (114)
T ss_dssp             HHHHHH
T ss_pred             CCCccC
Confidence            876544

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.47  E-value=7.3e-14  Score=126.70  Aligned_cols=82  Identities=24%  Similarity=0.400  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..+..+++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.++
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            45578999999999999999999999999999988667889999999999999999999999999999999999999876


Q ss_pred             CC
Q 001991          351 DN  352 (985)
Q Consensus       351 ~~  352 (985)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.46  E-value=9.5e-14  Score=129.21  Aligned_cols=83  Identities=19%  Similarity=0.390  Sum_probs=75.7

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|.|
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            34556799999999999999999999999999999986     4677999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 001991          345 HYSIPKDN  352 (985)
Q Consensus       345 ~~a~pk~~  352 (985)
                      .++.++..
T Consensus       101 ~~a~~~~~  108 (110)
T 1oo0_B          101 DWCFVKGP  108 (110)
T ss_dssp             EESEESSC
T ss_pred             EEcccCCC
Confidence            99987643

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.46  E-value=6.7e-14  Score=128.30  Aligned_cols=76  Identities=14%  Similarity=0.224  Sum_probs=71.6

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ..++|||+|||..+++++|+++|++||.|.+|++. ..+|||||+|.+.++|++|++.|||..+.|++|+|.|++++
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            45799999999999999999999999999999987 46899999999999999999999999999999999999864

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.46  E-value=8.1e-14  Score=125.26  Aligned_cols=80  Identities=19%  Similarity=0.246  Sum_probs=73.5

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ...++|||+|||..+++++|+++|++||.|..|++..+   .++||||+|.+.++|++|++.|||..+.|++|+|.++++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   85 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRN   85 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            45679999999999999999999999999999988753   478999999999999999999999999999999999987


Q ss_pred             cch
Q 001991          435 GGA  437 (985)
Q Consensus       435 k~~  437 (985)
                      +..
T Consensus        86 ~~~   88 (92)
T 2dgv_A           86 ASG   88 (92)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            653

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.8e-13  Score=126.31  Aligned_cols=83  Identities=17%  Similarity=0.369  Sum_probs=75.3

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----c-cccceEEEEEeCCHHHHHHHHHHccCcccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----A-CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  342 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----t-gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L  342 (985)
                      +....+.++|||+|||.++++++|+++|++|| |..|++     + ++++|||||+|.+.++|++|+ .|++..|.|++|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            34556789999999999999999999999999 999986     2 678999999999999999999 999999999999


Q ss_pred             cccccCCCCCC
Q 001991          343 DIHYSIPKDNP  353 (985)
Q Consensus       343 ~V~~a~pk~~~  353 (985)
                      .|.++.++...
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999887654

>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=99.46  E-value=1e-13  Score=123.29  Aligned_cols=78  Identities=13%  Similarity=0.325  Sum_probs=71.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEec------cccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA------CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkit------gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..++|||+|||.++++++|+++|++||.|..+++.      ++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++
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            46899999999999999999999999999999861      238999999999999999999999999999999999999


Q ss_pred             CCCC
Q 001991          348 IPKD  351 (985)
Q Consensus       348 ~pk~  351 (985)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.46  E-value=4.5e-14  Score=129.98  Aligned_cols=79  Identities=15%  Similarity=0.335  Sum_probs=70.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCc--EEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCc----cccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGD--IRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNK----PLRR  339 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~--I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~----~I~G  339 (985)
                      .+..-.+|||+|||+++|+++|+++|++||.  |.+|++     ++++||||||+|.+.++|++|++.|||.    .|.|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3456689999999999999999999999995  556664     5789999999999999999999999997    4899


Q ss_pred             ccccccccCC
Q 001991          340 RKLDIHYSIP  349 (985)
Q Consensus       340 r~L~V~~a~p  349 (985)
                      ++|.|.|++.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999863

>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=99.46  E-value=1.2e-13  Score=122.30  Aligned_cols=78  Identities=23%  Similarity=0.414  Sum_probs=71.8

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHc-cCcccccccccccccC
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKLDIHYSI  348 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~L-ng~~I~Gr~L~V~~a~  348 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++ .+.+|||||+|.+.++|++|++.| ++..+.|++|.|.|++
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~-~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITV-VQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEE-EGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEE-ECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            34567899999999999999999999999999999998 457899999999999999999989 9999999999999873

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.3e-13  Score=124.31  Aligned_cols=81  Identities=20%  Similarity=0.379  Sum_probs=74.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ....+.++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..|.|+.|.|.++.+
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            345678999999999999999999999999999999983   66999999999999999999999999999999999987


Q ss_pred             CCCC
Q 001991          350 KDNP  353 (985)
Q Consensus       350 k~~~  353 (985)
                      +...
T Consensus        82 ~~~~   85 (92)
T 2dgt_A           82 RLRT   85 (92)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7554

>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=4.9e-14  Score=129.54  Aligned_cols=83  Identities=22%  Similarity=0.372  Sum_probs=75.5

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      +...++|||+|||..+++++|+++|++||.|..|++..+     ++|||||+|.+.++|++|++.|||..+.|++|+|.+
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            345679999999999999999999999999999988644     378999999999999999999999999999999999


Q ss_pred             ccCcchhh
Q 001991          432 SRPGGARR  439 (985)
Q Consensus       432 A~~k~~Rr  439 (985)
                      +.++..++
T Consensus        85 a~~~~~~~   92 (104)
T 1p1t_A           85 AASEKNKE   92 (104)
T ss_dssp             TTCTTHHH
T ss_pred             CCCccchh
Confidence            99877654

>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=2.4e-13  Score=124.75  Aligned_cols=77  Identities=29%  Similarity=0.388  Sum_probs=71.8

Q ss_pred             cccccceeeecCCC-CCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          357 DANQGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       357 ~~~~~tLfV~NLp~-svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ....++|||+|||. .+++++|+++|++||.|.+|++.   +|||||+|.+.++|++|++.|||..+.|++|+|++++++
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            34678999999998 99999999999999999999984   899999999999999999999999999999999999875


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      .
T Consensus        96 ~   96 (97)
T 2xnq_A           96 A   96 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.3e-13  Score=127.16  Aligned_cols=80  Identities=21%  Similarity=0.335  Sum_probs=72.7

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ....++|||+|||..+++++|+++|++|| |..|+++.+      .+|||||+|.+.++|++|+ .||+..|.|++|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            34568999999999999999999999999 999998743      4789999999999999999 899999999999999


Q ss_pred             eccCcchh
Q 001991          431 ASRPGGAR  438 (985)
Q Consensus       431 ~A~~k~~R  438 (985)
                      +++++..+
T Consensus        90 ~a~~~~~~   97 (104)
T 1wi8_A           90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99987644

>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=3e-13  Score=126.46  Aligned_cols=82  Identities=20%  Similarity=0.227  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++    +++++|||||+|.+.++|++|++.|++..|.|+.|.|.+
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            4457899999999999999999999999999999876    456789999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 001991          347 SIPKDN  352 (985)
Q Consensus       347 a~pk~~  352 (985)
                      +.+...
T Consensus        91 a~~~~~   96 (114)
T 2do0_A           91 DERALP   96 (114)
T ss_dssp             CSCCCC
T ss_pred             cccCCC
Confidence            875443

>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=130.24  Aligned_cols=78  Identities=19%  Similarity=0.259  Sum_probs=72.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ...++|||+|||..+++++|+++|++||.|..|++.. .++||||+|.+.++|++|++.|||..|.|++|+|+|++...
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            3467999999999999999999999999999999875 68999999999999999999999999999999999997643

>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=99.46  E-value=1.7e-13  Score=129.86  Aligned_cols=82  Identities=24%  Similarity=0.444  Sum_probs=75.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..|.|+.|.|.++
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            456799999999999999999999999999999976    5678899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 001991          348 IPKDNP  353 (985)
Q Consensus       348 ~pk~~~  353 (985)
                      .++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.2e-13  Score=125.93  Aligned_cols=80  Identities=13%  Similarity=0.380  Sum_probs=73.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEE-EEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccc----
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIR-TIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK----  341 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~-sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~----  341 (985)
                      ..+.++|||+|||+++++++|+++|++||+|. .|++     +++++|||||+|.+.++|++|++.||+..+.|+.    
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 8875     5678899999999999999999999999999999    


Q ss_pred             ccccccCCCC
Q 001991          342 LDIHYSIPKD  351 (985)
Q Consensus       342 L~V~~a~pk~  351 (985)
                      |+|.|+.+..
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

>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=125.26  Aligned_cols=82  Identities=20%  Similarity=0.417  Sum_probs=74.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++|| |..|++     +++++|||||+|.+.++|++|+ .|++..|.|++|.|
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            4556789999999999999999999999997 999876     4678999999999999999999 89999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2dng_A           88 DIAEGRKQD   96 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEecCCCCC
Confidence            999877654

>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=8.8e-14  Score=126.23  Aligned_cols=82  Identities=28%  Similarity=0.619  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH----HhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLr----elFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ...++++|||+|||.++++++|+    ++|++||.|..|++  +++++|||||+|.+.++|++|++.|+|..+.|+.|.|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34578999999999999999999    99999999999987  4578899999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 001991          345 HYSIPKDN  352 (985)
Q Consensus       345 ~~a~pk~~  352 (985)
                      .++.++..
T Consensus        84 ~~a~~~~~   91 (97)
T 1nu4_A           84 QYAKTDSD   91 (97)
T ss_dssp             EECSSCCT
T ss_pred             EEccCCCc
Confidence            99987653

>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=1.3e-13  Score=127.29  Aligned_cols=84  Identities=19%  Similarity=0.392  Sum_probs=76.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|.|
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            35567899999999999999999999999999999876     467889999999999999999988 999999999999


Q ss_pred             cccCCCCCCC
Q 001991          345 HYSIPKDNPS  354 (985)
Q Consensus       345 ~~a~pk~~~~  354 (985)
                      .++.++....
T Consensus        90 ~~a~~~~~~~   99 (105)
T 2dh8_A           90 KPCTPRGMQP   99 (105)
T ss_dssp             CCSCCSSCCT
T ss_pred             EEccCCCCCC
Confidence            9998876543

>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=1.6e-13  Score=125.40  Aligned_cols=79  Identities=23%  Similarity=0.379  Sum_probs=72.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE--------EEe-----ccccceEEEEEeCCHHHHHHHHHHccCcc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--------IYT-----ACKHRGFVMISYYDIRAARNAMKALQNKP  336 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s--------Vki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~  336 (985)
                      ....+.++|||+|||.++++++|+++|++||.|..        +++     +++++|||||+|.+.++|++|++.|+|..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999999998        765     46789999999999999999999999999


Q ss_pred             cccccccccccC
Q 001991          337 LRRRKLDIHYSI  348 (985)
Q Consensus       337 I~Gr~L~V~~a~  348 (985)
                      +.|++|+|.+++
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999873

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.46  E-value=1.6e-13  Score=129.29  Aligned_cols=77  Identities=17%  Similarity=0.345  Sum_probs=70.8

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||.++++++|+++|++||.|.+|++..+     .+|||||+|.+.++|++|++.|||..|+|++|+|++
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            445679999999999999999999999999999998754     478999999999999999999999999999999999


Q ss_pred             cc
Q 001991          432 SR  433 (985)
Q Consensus       432 A~  433 (985)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            75

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.3e-13  Score=122.38  Aligned_cols=76  Identities=20%  Similarity=0.340  Sum_probs=70.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .+.++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|||..|.|+.|++.+.
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            46799999999999999999999999999999975     4677999999999999999999999999999999999875


Q ss_pred             C
Q 001991          348 I  348 (985)
Q Consensus       348 ~  348 (985)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.46  E-value=1e-13  Score=127.00  Aligned_cols=77  Identities=25%  Similarity=0.376  Sum_probs=72.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...++|||+|||.++++++|+++|++||.|..+++ .+++|||||+|.+.++|++|++.|+|..+.|++|.|.++.++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH-YPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEE-ecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            45689999999999999999999999999999998 478999999999999999999999999999999999998764

>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=99.45  E-value=1.6e-13  Score=132.66  Aligned_cols=80  Identities=21%  Similarity=0.370  Sum_probs=73.8

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||.++++++|+++|++||+|..|++..     ..+|||||+|.+.++|++|++.|||..|.|++|+|++
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999864     3578999999999999999999999999999999999


Q ss_pred             ccCcc
Q 001991          432 SRPGG  436 (985)
Q Consensus       432 A~~k~  436 (985)
                      ++++.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            98765

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.45  E-value=1.5e-13  Score=133.15  Aligned_cols=82  Identities=27%  Similarity=0.392  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH----HhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLr----elFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ...+.++|||+|||+.+++++|+    ++|++||+|..|.+  +++++|||||+|.+.++|++|++.|||..|.|++|.|
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            34568999999999999999876    69999999999987  5688999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 001991          345 HYSIPKDN  352 (985)
Q Consensus       345 ~~a~pk~~  352 (985)
                      .|+.++..
T Consensus       105 ~~a~~~~~  112 (127)
T 2a3j_A          105 TFSETPQS  112 (127)
T ss_dssp             EECCCCCH
T ss_pred             EEccCcch
Confidence            99987643

>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=99.45  E-value=1.1e-13  Score=131.52  Aligned_cols=81  Identities=15%  Similarity=0.175  Sum_probs=73.3

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccC--cccccccccccccC
Q 001991          272 EHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIHYSI  348 (985)
Q Consensus       272 e~~srtLfVgNLP~~-vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng--~~I~Gr~L~V~~a~  348 (985)
                      ..++++|||+|||++ +++++|+++|++||+|..|++ .+.||||||+|.+.++|++|++.|++  ..|.|++|+|.|+.
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            567899999999998 999999999999999999998 56799999999999999999998865  56999999999998


Q ss_pred             CCCCC
Q 001991          349 PKDNP  353 (985)
Q Consensus       349 pk~~~  353 (985)
                      ++...
T Consensus       101 ~~~~~  105 (112)
T 1x4f_A          101 KYKKL  105 (112)
T ss_dssp             SCSSS
T ss_pred             ccccc
Confidence            76543

>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=6.4e-14  Score=136.43  Aligned_cols=85  Identities=26%  Similarity=0.471  Sum_probs=77.2

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      +....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.
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            345567899999999999999999999999999999986     567899999999999999999999999999999999


Q ss_pred             ccccCCCCCC
Q 001991          344 IHYSIPKDNP  353 (985)
Q Consensus       344 V~~a~pk~~~  353 (985)
                      |.++.++..+
T Consensus       121 V~~a~~~~~~  130 (135)
T 2lea_A          121 VQMARYGRPP  130 (135)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876554

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=2.4e-13  Score=127.82  Aligned_cols=83  Identities=25%  Similarity=0.394  Sum_probs=75.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ..+.+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.+++ .|.|++|.|
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            45667899999999999999999999999999999986     467899999999999999999999998 899999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++..+
T Consensus        91 ~~a~~~~~~   99 (116)
T 2cqd_A           91 NLAYLGAKP   99 (116)
T ss_dssp             EESTTTCCC
T ss_pred             EEcccCCCc
Confidence            999776544

>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=99.45  E-value=1.7e-13  Score=128.20  Aligned_cols=81  Identities=27%  Similarity=0.357  Sum_probs=73.9

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      .....++|||+|||..+++++|+++|++||.|..|++..+     ++|||||+|.+.++|++|++.|||..|.|++|+|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456679999999999999999999999999999998643     46899999999999999999999999999999999


Q ss_pred             eccCcc
Q 001991          431 ASRPGG  436 (985)
Q Consensus       431 ~A~~k~  436 (985)
                      +++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=1.5e-13  Score=125.45  Aligned_cols=79  Identities=18%  Similarity=0.246  Sum_probs=70.9

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEE-cCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri-~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ....++|||+|||..+++++|+++|++||.|. +++ ....+|||||+|.+.++|++|++.|||..|.|++|+|.+++++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            34567999999999999999999999999996 443 3457899999999999999999999999999999999999876


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      .
T Consensus        95 ~   95 (97)
T 2e5j_A           95 R   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.45  E-value=1.3e-13  Score=131.32  Aligned_cols=82  Identities=23%  Similarity=0.387  Sum_probs=74.7

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|+++.+     ++|||||+|.+.++|++|++.|||..|.|++|+|++
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            345679999999999999999999999999999998755     388999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      +.++..+
T Consensus        99 a~~~~~~  105 (126)
T 3ex7_B           99 CFVRGPP  105 (126)
T ss_dssp             SEESSSC
T ss_pred             ecCCCCC
Confidence            9876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.4e-13  Score=128.65  Aligned_cols=84  Identities=23%  Similarity=0.352  Sum_probs=75.9

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEE--------EEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIR--------TIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKP  336 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~--------sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~  336 (985)
                      ....+.++|||+|||.++++++|+++|++||.|.        .|++     +++++|||||+|.+.++|++|++.|++..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            3556789999999999999999999999999998        4665     46789999999999999999999999999


Q ss_pred             cccccccccccCCCCCC
Q 001991          337 LRRRKLDIHYSIPKDNP  353 (985)
Q Consensus       337 I~Gr~L~V~~a~pk~~~  353 (985)
                      |.|++|.|.++.++...
T Consensus        90 ~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             cCCCEEEEEECCCCCCC
Confidence            99999999999887654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.45  E-value=4.9e-14  Score=129.87  Aligned_cols=78  Identities=13%  Similarity=0.184  Sum_probs=71.8

Q ss_pred             cccceeeecCCC------CCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCC-ce
Q 001991          359 NQGTLVVFNLDS------SVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAG-KQ  426 (985)
Q Consensus       359 ~~~tLfV~NLp~------svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~G-r~  426 (985)
                      ..++|||+|||.      ++++++|+++|++||.|.+|+++.     .++|||||+|.+.++|++|++.|||..|.| ++
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            356899999999      999999999999999999999874     357999999999999999999999999999 99


Q ss_pred             EEEEeccCcc
Q 001991          427 IKLEASRPGG  436 (985)
Q Consensus       427 IkV~~A~~k~  436 (985)
                      |+|.++.+++
T Consensus        85 l~V~~a~~~~   94 (100)
T 3ns6_A           85 LFLYTMKDVE   94 (100)
T ss_dssp             CEEEESHHHH
T ss_pred             EEEEECchhh
Confidence            9999998744

>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=5.9e-14  Score=128.96  Aligned_cols=81  Identities=25%  Similarity=0.460  Sum_probs=74.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      +.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|.|.+
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            345689999999999999999999999999999876     467799999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 001991          347 SIPKDN  352 (985)
Q Consensus       347 a~pk~~  352 (985)
                      +.++..
T Consensus        85 a~~~~~   90 (104)
T 1p1t_A           85 AASEKN   90 (104)
T ss_dssp             TTCTTH
T ss_pred             CCCccc
Confidence            987643

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.45  E-value=8.1e-14  Score=126.78  Aligned_cols=73  Identities=21%  Similarity=0.294  Sum_probs=69.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .+.-|||+||++.+||++|+++|.+||+|.++++ ..+||||||+|.+.++|++|++.||+..+.|++|+|+++
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            4678999999999999999999999999999998 558999999999999999999999999999999999887

>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=2.1e-13  Score=132.09  Aligned_cols=84  Identities=20%  Similarity=0.402  Sum_probs=77.0

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            35567799999999999999999999999999999976     4678999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++..+
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999887654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=9.3e-14  Score=127.83  Aligned_cols=82  Identities=21%  Similarity=0.251  Sum_probs=75.0

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhc-cCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCce-eCCceEEEEe
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGI-YGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSD-VAGKQIKLEA  431 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~-fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~-I~Gr~IkV~~  431 (985)
                      ....+|||+|||..+++++|+++|++ ||.|.+|+++.+    ++|||||+|.+.++|++|++.|||.. |.|++|+|.+
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 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            45679999999999999999999999 999999998654    57899999999999999999999999 9999999999


Q ss_pred             ccCcchhh
Q 001991          432 SRPGGARR  439 (985)
Q Consensus       432 A~~k~~Rr  439 (985)
                      +.++..++
T Consensus        87 a~~~~~~~   94 (104)
T 2dhg_A           87 AIPKASRV   94 (104)
T ss_dssp             CCCCCSCC
T ss_pred             ccCCCcCC
Confidence            98876543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.45  E-value=1.7e-13  Score=129.13  Aligned_cols=79  Identities=18%  Similarity=0.341  Sum_probs=72.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|
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            45567899999999999999999999999999999986     4677999999999999999999999999999999999


Q ss_pred             cccC
Q 001991          345 HYSI  348 (985)
Q Consensus       345 ~~a~  348 (985)
                      .+++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9863

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=1.9e-13  Score=125.33  Aligned_cols=83  Identities=19%  Similarity=0.398  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..++. +++++|||||+|.+.++|++|++.|++..|.|+.|.|.++.+
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            4567899999999999999999999999999954443 677899999999999999999999999999999999999988


Q ss_pred             CCCC
Q 001991          350 KDNP  353 (985)
Q Consensus       350 k~~~  353 (985)
                      +...
T Consensus        91 ~~~~   94 (101)
T 2fc9_A           91 RGSP   94 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.45  E-value=5.9e-14  Score=129.34  Aligned_cols=78  Identities=18%  Similarity=0.273  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCC------CCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccc-c
Q 001991          273 HPSRTLFVRNINS------NVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR-R  340 (985)
Q Consensus       273 ~~srtLfVgNLP~------~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G-r  340 (985)
                      ...++|||+|||.      ++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|||..|.| +
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      9999999999999999999986     47899999999999999999999999999999 9


Q ss_pred             cccccccCCC
Q 001991          341 KLDIHYSIPK  350 (985)
Q Consensus       341 ~L~V~~a~pk  350 (985)
                      .|.|.++.++
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998754

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.1e-13  Score=129.51  Aligned_cols=82  Identities=22%  Similarity=0.414  Sum_probs=74.8

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .....+.++|||+|||.++++++|+++|++||+|..|++   .+.++|||||+|.+.++|++|++.|+|..|.|++|.|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345567899999999999999999999999999999987   34578999999999999999999999999999999999


Q ss_pred             ccCCC
Q 001991          346 YSIPK  350 (985)
Q Consensus       346 ~a~pk  350 (985)
                      ++.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99765

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.44  E-value=1.1e-13  Score=125.58  Aligned_cols=81  Identities=23%  Similarity=0.333  Sum_probs=73.5

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ....++|||+|||..+++++|+++|++||.|..+.....++|||||+|.+.++|++|++.|||..|.|++|+|.+++++.
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            44668999999999999999999999999998885555578999999999999999999999999999999999998765


Q ss_pred             h
Q 001991          437 A  437 (985)
Q Consensus       437 ~  437 (985)
                      .
T Consensus        93 ~   93 (96)
T 1fjc_A           93 G   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=2e-13  Score=124.50  Aligned_cols=81  Identities=22%  Similarity=0.291  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      .....++|||+|||.++++++|+++|++||.|....++++++|||||+|.+.++|++|++.|||..|.|++|.|.++.++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            34567899999999999999999999999999633345788999999999999999999999999999999999999876


Q ss_pred             C
Q 001991          351 D  351 (985)
Q Consensus       351 ~  351 (985)
                      .
T Consensus        95 ~   95 (97)
T 2e5j_A           95 R   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.44  E-value=1.9e-13  Score=121.98  Aligned_cols=76  Identities=28%  Similarity=0.388  Sum_probs=70.4

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+++++|+++|++||.|..|++..+     ++|||||+|.+.++|++|+ .|||..+.|++|+|.+++
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            4579999999999999999999999999999988644     4889999999999999999 899999999999999998


Q ss_pred             Cc
Q 001991          434 PG  435 (985)
Q Consensus       434 ~k  435 (985)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.44  E-value=1.9e-13  Score=128.16  Aligned_cols=81  Identities=19%  Similarity=0.283  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH---HhhcccCcEEEEEec--------cccceEEEEEeCCHHHHHHHHHHccCccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELK---ALFEQFGDIRTIYTA--------CKHRGFVMISYYDIRAARNAMKALQNKPLRR  339 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLr---elFs~fG~I~sVkit--------gksrGfAFV~F~d~esA~kAi~~Lng~~I~G  339 (985)
                      .....++|||+|||+++++++|+   ++|++||+|..|++.        ++++|||||+|.+.++|++|++.||+..|.|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            44567899999999999999999   999999999999862        2456999999999999999999999999999


Q ss_pred             ccccccccCCCC
Q 001991          340 RKLDIHYSIPKD  351 (985)
Q Consensus       340 r~L~V~~a~pk~  351 (985)
                      ++|.|.++.++.
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999998775

>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=99.44  E-value=1.8e-13  Score=130.31  Aligned_cols=84  Identities=18%  Similarity=0.448  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||.|..|.+     +++++|||||+|.+.++|++|++.|++..|.|+.|.|
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            34556799999999999999999999999999999986     5677999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999876544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2.3e-13  Score=127.91  Aligned_cols=80  Identities=23%  Similarity=0.294  Sum_probs=73.3

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      .+...++|||+|||..+++++|+++|++||.|..|++..+     +++||||+|.+.++|++|++.||+ .|.|++|+|.
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            4456789999999999999999999999999999999764     578999999999999999999998 8999999999


Q ss_pred             eccCcc
Q 001991          431 ASRPGG  436 (985)
Q Consensus       431 ~A~~k~  436 (985)
                      ++.++.
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            998754

>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=99.44  E-value=2.6e-13  Score=125.15  Aligned_cols=80  Identities=26%  Similarity=0.520  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..|++   .++||||+|.+.++|++|++.|++..|.|++|.|.++.++
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~---~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK---LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEE---CSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE---ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            3456799999999999999999999999999999988   3789999999999999999999999999999999999887


Q ss_pred             CCC
Q 001991          351 DNP  353 (985)
Q Consensus       351 ~~~  353 (985)
                      ...
T Consensus        84 ~~~   86 (103)
T 2dgu_A           84 DQK   86 (103)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=2.7e-13  Score=126.79  Aligned_cols=79  Identities=16%  Similarity=0.183  Sum_probs=72.6

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...++|||+|||..+++++|+++|++||.|.+|++..+    .++||||+|.+.++|++|++.|||..|.|++|+|.+++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   92 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE   92 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcc
Confidence            45679999999999999999999999999999988754    36799999999999999999999999999999999997


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ...
T Consensus        93 ~~~   95 (114)
T 2do0_A           93 RAL   95 (114)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=2.3e-13  Score=125.89  Aligned_cols=79  Identities=24%  Similarity=0.421  Sum_probs=72.9

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ....+.++|||+|||+.+++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999999999876    56789999999999999999999999999999999999


Q ss_pred             ccC
Q 001991          346 YSI  348 (985)
Q Consensus       346 ~a~  348 (985)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            874

>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=99.44  E-value=2e-13  Score=123.87  Aligned_cols=81  Identities=21%  Similarity=0.411  Sum_probs=74.1

Q ss_pred             ccccceeeecCCCCCCHHHHH----HHhhccCCEEEEEEcC--CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          358 ANQGTLVVFNLDSSVSTEELH----QIFGIYGEIREIRDTQ--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLr----elFs~fG~I~~Vri~~--~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      .+.++|||+|||..+++++|+    ++|++||.|..|++..  ..+|||||+|.+.++|++|++.|||..+.|++|+|.+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   85 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456799999999999999999    9999999999999863  3579999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++...
T Consensus        86 a~~~~~~   92 (97)
T 1nu4_A           86 AKTDSDI   92 (97)
T ss_dssp             CSSCCTH
T ss_pred             ccCCCcc
Confidence            9987644

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.44  E-value=2.5e-13  Score=131.51  Aligned_cols=82  Identities=15%  Similarity=0.251  Sum_probs=73.8

Q ss_pred             ccccceeeecCCCCCCHHHHH----HHhhccCCEEEEEEcC--CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          358 ANQGTLVVFNLDSSVSTEELH----QIFGIYGEIREIRDTQ--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLr----elFs~fG~I~~Vri~~--~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      .+.++|||+|||..+++++|+    ++|++||.|.+|.+..  .++|||||+|.+.++|.+|++.|||..|.|++|+|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            446799999999999999876    6999999999998864  4789999999999999999999999999999999999


Q ss_pred             ccCcchhh
Q 001991          432 SRPGGARR  439 (985)
Q Consensus       432 A~~k~~Rr  439 (985)
                      ++++..+.
T Consensus       107 a~~~~~~~  114 (127)
T 2a3j_A          107 SETPQSQV  114 (127)
T ss_dssp             CCCCCHHH
T ss_pred             ccCcchhc
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=99.44  E-value=2.1e-13  Score=127.53  Aligned_cols=82  Identities=20%  Similarity=0.328  Sum_probs=74.3

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEE--------EEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIR--------EIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~--------~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                      ....++|||+|||..+++++|+++|++||.|.        .|++..+     .+|||||+|.+.++|++|++.|||..|.
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            45678999999999999999999999999998        5888654     4789999999999999999999999999


Q ss_pred             CceEEEEeccCcchh
Q 001991          424 GKQIKLEASRPGGAR  438 (985)
Q Consensus       424 Gr~IkV~~A~~k~~R  438 (985)
                      |++|+|.+++++..+
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999987643

>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=99.44  E-value=1.8e-13  Score=129.68  Aligned_cols=79  Identities=25%  Similarity=0.415  Sum_probs=73.0

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...++|||+|||.++++++|+++|++||.|..|++..+    .+|||||+|.+.++|++|++.|||..|.|++|+|++++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            34579999999999999999999999999999998754    47899999999999999999999999999999999998


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ++.
T Consensus        85 ~~~   87 (116)
T 2fy1_A           85 KPS   87 (116)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            765

>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=99.43  E-value=4.4e-14  Score=127.32  Aligned_cols=77  Identities=16%  Similarity=0.168  Sum_probs=65.5

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccC--CEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG--~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      .+|||+|||.++++++|+++|++||  .|.+|+++.+     ++|||||+|.+.++|++|++.|||..+.|++|+|.++.
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  9999988653     47899999999999999999999999999999999998


Q ss_pred             Ccch
Q 001991          434 PGGA  437 (985)
Q Consensus       434 ~k~~  437 (985)
                      ++..
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=4.8e-13  Score=122.30  Aligned_cols=80  Identities=21%  Similarity=0.402  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhccc--CcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQF--GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~f--G~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ...+.++|||+|||.++++++|+++|++|  |.|..|++   .+|||||+|.+.++|++|++.|++..|.|++|.|.++.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK---IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   87 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE---CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE---eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            44578999999999999999999999999  99999987   57899999999999999999999999999999999998


Q ss_pred             CCCCC
Q 001991          349 PKDNP  353 (985)
Q Consensus       349 pk~~~  353 (985)
                      ++...
T Consensus        88 ~~~~~   92 (99)
T 2cpd_A           88 PVDKD   92 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.43  E-value=2.4e-13  Score=124.26  Aligned_cols=77  Identities=21%  Similarity=0.317  Sum_probs=70.7

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEE--------EEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVA  423 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~--------Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~  423 (985)
                      ....++|||+|||.++++++|+++|++||.|.+        |++..+     .+|||||+|.+.++|++|++.|||..+.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            455789999999999999999999999999998        888654     4689999999999999999999999999


Q ss_pred             CceEEEEecc
Q 001991          424 GKQIKLEASR  433 (985)
Q Consensus       424 Gr~IkV~~A~  433 (985)
                      |++|+|++|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999974

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=2.8e-13  Score=121.76  Aligned_cols=80  Identities=18%  Similarity=0.372  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..+.|++|.|.++.++
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   81 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV---KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG   81 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCC
Confidence            34567999999999999999999999999999999983   669999999999999999999999999999999999876


Q ss_pred             CCC
Q 001991          351 DNP  353 (985)
Q Consensus       351 ~~~  353 (985)
                      ...
T Consensus        82 ~~~   84 (90)
T 2dnp_A           82 QKK   84 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.43  E-value=3.3e-13  Score=124.29  Aligned_cols=80  Identities=18%  Similarity=0.251  Sum_probs=72.2

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++|| |..|+++.+     .+|||||+|.+.++|++|+ .|||..|.|++|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34567999999999999999999999997 999998754     3689999999999999999 7999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9886543

>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=99.43  E-value=2.8e-13  Score=126.81  Aligned_cols=83  Identities=20%  Similarity=0.384  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcE----EEEEe-ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI----RTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I----~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++|+++|+++|++||.|    ..+++ +++++|||||+|.+.++|++|++.|++..|.|++|.|.
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            34578999999999999999999999999998    45543 78899999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpx_A          101 FGKNKKQR  108 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EccCCCCC
Confidence            99887654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.43  E-value=1.8e-13  Score=132.04  Aligned_cols=84  Identities=17%  Similarity=0.364  Sum_probs=75.4

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE--EEe-----ccccceEEEEEeCCHHHHHHHHHHccCc----cc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--IYT-----ACKHRGFVMISYYDIRAARNAMKALQNK----PL  337 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s--Vki-----tgksrGfAFV~F~d~esA~kAi~~Lng~----~I  337 (985)
                      +....+.++|||+|||+++|+++|+++|++||.|..  |++     +++++|||||+|.+. +|.+|++.|++.    .|
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  654     678999999999999 999999999999    99


Q ss_pred             ccccccccccCCCCCC
Q 001991          338 RRRKLDIHYSIPKDNP  353 (985)
Q Consensus       338 ~Gr~L~V~~a~pk~~~  353 (985)
                      .|++|.|.++.++...
T Consensus        96 ~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           96 DGKTINVEFAKGSKRD  111 (131)
T ss_dssp             GGCCCCCEECCCSCCC
T ss_pred             CCEEEEEEECCCCCCC
Confidence            9999999999886543

>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=5.8e-13  Score=124.67  Aligned_cols=80  Identities=16%  Similarity=0.316  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccc--------c
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPL--------R  338 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I--------~  338 (985)
                      .+.+.++|||+|||.++++++|+++|++||+|..|++    ++.++|||||+|.+.++|++|++.|||..|        .
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            4557799999999999999999999999999999976    467899999999999999999999999999        5


Q ss_pred             cccccccccCCC
Q 001991          339 RRKLDIHYSIPK  350 (985)
Q Consensus       339 Gr~L~V~~a~pk  350 (985)
                      +++|.|.|+.|+
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            677888888754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.43  E-value=1.7e-13  Score=124.92  Aligned_cols=77  Identities=29%  Similarity=0.407  Sum_probs=71.4

Q ss_pred             ccccceeeecCCC-CCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          358 ANQGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       358 ~~~~tLfV~NLp~-svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      .+.++|||+|||. .+++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|||..+.|++|+|++++++.
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            4577999999998 99999999999999999999984   7999999999999999999999999999999999998765


Q ss_pred             h
Q 001991          437 A  437 (985)
Q Consensus       437 ~  437 (985)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
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=99.43  E-value=3.7e-13  Score=123.40  Aligned_cols=83  Identities=22%  Similarity=0.442  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ...+.++|||+|||.++++++|+++|+.|+.|..+..  +++++|||||+|.+.++|++|++.|++..|.|+.|.|.++.
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            4567899999999999999999999999988777753  67889999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 001991          349 PKDNP  353 (985)
Q Consensus       349 pk~~~  353 (985)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87654

>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=2.5e-13  Score=126.06  Aligned_cols=80  Identities=16%  Similarity=0.308  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEecCCCCC------CHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccc-
Q 001991          271 GEHPSRTLFVRNINSNV------EDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR-  340 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~v------TEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr-  340 (985)
                      .....++|||+|||..+      ++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|||..|.|+ 
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            44567999999999999      78999999999999999987   567899999999999999999999999999999 


Q ss_pred             cccccccCCC
Q 001991          341 KLDIHYSIPK  350 (985)
Q Consensus       341 ~L~V~~a~pk  350 (985)
                      +|.|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998654

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.43  E-value=2e-13  Score=124.42  Aligned_cols=80  Identities=24%  Similarity=0.392  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          271 GEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       271 ~e~~srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ...+.++|||+|||. ++++++|+++|++||+|..|++   .+|||||+|.+.++|++|++.|++..+.|++|.|.++.+
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   82 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSS   82 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEEC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCc
Confidence            345789999999998 9999999999999999999998   489999999999999999999999999999999999987


Q ss_pred             CCCC
Q 001991          350 KDNP  353 (985)
Q Consensus       350 k~~~  353 (985)
                      +..+
T Consensus        83 ~~~~   86 (96)
T 2kvi_A           83 NARP   86 (96)
T ss_dssp             CCC-
T ss_pred             CCCC
Confidence            6544

>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=99.43  E-value=4.9e-13  Score=124.61  Aligned_cols=81  Identities=14%  Similarity=0.206  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccc-----cccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR-----RKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~G-----r~L~V~  345 (985)
                      .....++|||+|||.++++++|+++|++||+|..|++...  |||||+|.+.++|++||+.||+..|.|     +.|.|.
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            3456799999999999999999999999999999988333  999999999999999999999999999     999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (108)
T 1x4c_A           89 VDGPRSPS   96 (108)
T ss_dssp             ESSCCSCC
T ss_pred             eCCCCCCC
Confidence            99887644

>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=99.43  E-value=2e-13  Score=125.56  Aligned_cols=79  Identities=19%  Similarity=0.396  Sum_probs=69.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe------ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki------tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      .....++|||+|||.++++++|+++|++|| |..|++      +++++|||||+|.+.++|++|+ .|+|..|.|+.|.|
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            455679999999999999999999999999 999986      4667999999999999999999 89999999999999


Q ss_pred             cccCCCC
Q 001991          345 HYSIPKD  351 (985)
Q Consensus       345 ~~a~pk~  351 (985)
                      .++.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9998754

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.43  E-value=5.3e-14  Score=133.67  Aligned_cols=78  Identities=21%  Similarity=0.336  Sum_probs=71.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|+ .|||..|.|++|+|.++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            34679999999999999999999999999999988643     5789999999999999999 79999999999999999


Q ss_pred             cCcc
Q 001991          433 RPGG  436 (985)
Q Consensus       433 ~~k~  436 (985)
                      ++..
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8644

>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=99.43  E-value=2.8e-13  Score=123.66  Aligned_cols=81  Identities=15%  Similarity=0.274  Sum_probs=72.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHH----HhhcccCcEEEEEec--cccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLr----elFs~fG~I~sVkit--gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ...++|||+|||.++++++|+    ++|++||+|..|++.  ...+|||||+|.+.++|++|++.|||..|.|++|+|.+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            356899999999999999999    999999999999872  22289999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++..+
T Consensus        87 a~~~~~~   93 (96)
T 2dgx_A           87 ATGASGP   93 (96)
T ss_dssp             CCCSSCC
T ss_pred             cCCCCCC
Confidence            9876543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.43  E-value=3.1e-13  Score=131.57  Aligned_cols=76  Identities=21%  Similarity=0.333  Sum_probs=71.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcE-EEEEEcCHHHHHHHHHHhCCceeCC--ceEEEEeccCcc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNH-KFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPGG  436 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGf-aFVeF~d~edA~kAI~~LNG~~I~G--r~IkV~~A~~k~  436 (985)
                      -.|||+||+..+|+++|+++|++||+|.+|++..+.++| |||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            468899999999999999999999999999988777888 9999999999999999999999988  999999999864

>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=99.43  E-value=1.3e-13  Score=124.47  Aligned_cols=79  Identities=24%  Similarity=0.314  Sum_probs=70.9

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCC-EEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCC-ceeCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDTQHKHNHKFIEFYDIRAAETALRTLNR-SDVAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~-I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG-~~I~Gr~IkV~~A~~k  435 (985)
                      ...++|||+|||.++++++|+++|++||. |..+.+.  +++||||+|.+.++|++|++.||| ..|.|++|+|.+++++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE--ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc--CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            35679999999999999999999999999 6655553  589999999999999999999999 9999999999999987


Q ss_pred             chh
Q 001991          436 GAR  438 (985)
Q Consensus       436 ~~R  438 (985)
                      ..+
T Consensus        84 ~~~   86 (93)
T 2cqh_A           84 KLR   86 (93)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            644

>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=6.7e-13  Score=121.04  Aligned_cols=77  Identities=22%  Similarity=0.375  Sum_probs=71.1

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ...++|||+||  ++++++|+++|++||.|..|++. ..++||||+|.+.++|++|++.|||..|.|++|+|.+++++..
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            45679999996  89999999999999999999985 5789999999999999999999999999999999999988654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.42  E-value=2e-13  Score=120.42  Aligned_cols=70  Identities=19%  Similarity=0.385  Sum_probs=65.4

Q ss_pred             CcEEEEecCCCCC------CHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccc-cccc
Q 001991          275 SRTLFVRNINSNV------EDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR-KLDI  344 (985)
Q Consensus       275 srtLfVgNLP~~v------TEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr-~L~V  344 (985)
                      +++|||+|||..+      ++++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|||..|.|+ +|+|
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            4789999999999      77999999999999999986   567899999999999999999999999999999 8887

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.42  E-value=6.9e-13  Score=126.30  Aligned_cols=80  Identities=16%  Similarity=0.258  Sum_probs=73.5

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+    .+|||||+|.+.++|++|++.|||..|.|++|+|+++
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            345679999999999999999999999999999998754    5789999999999999999999999999999999999


Q ss_pred             cCcc
Q 001991          433 RPGG  436 (985)
Q Consensus       433 ~~k~  436 (985)
                      .+..
T Consensus       112 ~~~~  115 (124)
T 2kt5_A          112 ASQI  115 (124)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            8754

>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=99.42  E-value=2.5e-13  Score=121.16  Aligned_cols=76  Identities=22%  Similarity=0.454  Sum_probs=70.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|+ .|++..+.|++|.|.++.
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            3589999999999999999999999999999976     5678999999999999999999 899999999999999987


Q ss_pred             CC
Q 001991          349 PK  350 (985)
Q Consensus       349 pk  350 (985)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.42  E-value=3.5e-13  Score=125.52  Aligned_cols=82  Identities=15%  Similarity=0.310  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      .....++|||+|||.++++++|+++|++||.|..|++. ..+|||||+|.+.++|++|++.|++..|.|+.|.|.++.++
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   99 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   99 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCC
Confidence            34567999999999999999999999999999999983 34899999999999999999999999999999999999876


Q ss_pred             CCC
Q 001991          351 DNP  353 (985)
Q Consensus       351 ~~~  353 (985)
                      ...
T Consensus       100 ~~~  102 (109)
T 1x4g_A          100 PDM  102 (109)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            544

>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=99.42  E-value=4.3e-13  Score=132.68  Aligned_cols=81  Identities=23%  Similarity=0.303  Sum_probs=74.1

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|..|+++.+     .++||||+|.+.++|++||+.||+..|.|++|+|+|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45679999999999999999999999999999998644     4689999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus       117 ~~~~~~  122 (156)
T 1h2v_Z          117 AGFKEG  122 (156)
T ss_dssp             SCCCTT
T ss_pred             CCCCCc
Confidence            876543

>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=99.42  E-value=3.8e-13  Score=123.34  Aligned_cols=77  Identities=25%  Similarity=0.396  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          271 GEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       271 ~e~~srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ...+.++|||+|||. ++++++|+++|++||.|..|++   .+|||||+|.+.++|++|++.|+|..+.|++|.|.++.+
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            455789999999998 9999999999999999999998   489999999999999999999999999999999999876


Q ss_pred             C
Q 001991          350 K  350 (985)
Q Consensus       350 k  350 (985)
                      +
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.42  E-value=3.9e-13  Score=124.29  Aligned_cols=76  Identities=20%  Similarity=0.349  Sum_probs=70.6

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...++|||+|||..+++++|+++|++||.|.+|++..+    .+|||||+|.+.++|++|++.|||..|.|++|+|.++.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            45679999999999999999999999999999988744    47899999999999999999999999999999999985

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.42  E-value=2.3e-13  Score=127.43  Aligned_cols=81  Identities=26%  Similarity=0.517  Sum_probs=73.2

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ...+.+.++|||+|||.++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|+|..|.|+.|.|.++.
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  101 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK  101 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCS
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            3456678999999999999999999999999999999984   8999999999999999999999999999999999998


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      ++..
T Consensus       102 ~~~~  105 (108)
T 2jvo_A          102 LPAK  105 (108)
T ss_dssp             CCC-
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=99.42  E-value=1.5e-13  Score=129.19  Aligned_cols=77  Identities=13%  Similarity=0.279  Sum_probs=71.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...++|||+|||.++++++|+++|++||.|..|.+ .+.+|||||+|.+.++|++|++.|||..|.|++|.|.|+...
T Consensus         8 ~~~~~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            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            35689999999999999999999999999999998 468999999999999999999999999999999999998653

>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=99.42  E-value=1.6e-13  Score=123.85  Aligned_cols=80  Identities=20%  Similarity=0.351  Sum_probs=72.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCc-EEEEEeccccceEEEEEeCCHHHHHHHHHHccC-cccccccccccccCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGD-IRTIYTACKHRGFVMISYYDIRAARNAMKALQN-KPLRRRKLDIHYSIP  349 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~-I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng-~~I~Gr~L~V~~a~p  349 (985)
                      ..+.++|||+|||.++++++|+++|++||. |..+.+  .++|||||+|.+.++|++|++.||+ ..|.|++|.|.++.+
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            346789999999999999999999999999 666665  5689999999999999999999999 999999999999988


Q ss_pred             CCCC
Q 001991          350 KDNP  353 (985)
Q Consensus       350 k~~~  353 (985)
                      +...
T Consensus        83 ~~~~   86 (93)
T 2cqh_A           83 KKLR   86 (93)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            7654

>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=3.2e-13  Score=120.25  Aligned_cols=76  Identities=21%  Similarity=0.414  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .+.+.++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++ +++..|.|++|.|+
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            4567899999999999999999999999999999976     47789999999999999999995 68889999999998


Q ss_pred             cc
Q 001991          346 YS  347 (985)
Q Consensus       346 ~a  347 (985)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            65

>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=99.42  E-value=3.3e-13  Score=126.53  Aligned_cols=80  Identities=26%  Similarity=0.380  Sum_probs=73.2

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC--CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~--~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..++|||+|||..+++++|+++|++||.|..|++..  ..+|||||+|.+.++|.+|++.|||..+.|+.|+|.++.++.
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            457999999999999999999999999999999864  357999999999999999999999999999999999998755


Q ss_pred             hh
Q 001991          437 AR  438 (985)
Q Consensus       437 ~R  438 (985)
                      .+
T Consensus        87 ~~   88 (115)
T 3lqv_A           87 AF   88 (115)
T ss_dssp             HT
T ss_pred             hh
Confidence            33

>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=2.2e-13  Score=123.97  Aligned_cols=80  Identities=19%  Similarity=0.242  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .....++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
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            3456799999999999999999999999999864432     56789999999999999999999999999999999999


Q ss_pred             ccCCC
Q 001991          346 YSIPK  350 (985)
Q Consensus       346 ~a~pk  350 (985)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98643

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.42  E-value=4.1e-13  Score=124.66  Aligned_cols=79  Identities=16%  Similarity=0.216  Sum_probs=71.7

Q ss_pred             cccccceeeecCCCCC------CHHHHHHHhhccCCEEEEEEcC---CCCcEEEEEEcCHHHHHHHHHHhCCceeCCc-e
Q 001991          357 DANQGTLVVFNLDSSV------STEELHQIFGIYGEIREIRDTQ---HKHNHKFIEFYDIRAAETALRTLNRSDVAGK-Q  426 (985)
Q Consensus       357 ~~~~~tLfV~NLp~sv------TeedLrelFs~fG~I~~Vri~~---~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr-~  426 (985)
                      ....++|||+|||..+      ++++|+++|++||.|..|++..   .++|||||+|.+.++|++|++.|||..|.|+ +
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            3446799999999999      7899999999999999999873   3579999999999999999999999999999 9


Q ss_pred             EEEEeccCc
Q 001991          427 IKLEASRPG  435 (985)
Q Consensus       427 IkV~~A~~k  435 (985)
                      |+|.++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999999754

>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=99.42  E-value=3.6e-13  Score=124.96  Aligned_cols=80  Identities=21%  Similarity=0.254  Sum_probs=72.7

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCC-EEEEEEcC------CCCcEEEEEEcCHHHHHHHHHHhC--CceeCCceEE
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDTQ------HKHNHKFIEFYDIRAAETALRTLN--RSDVAGKQIK  428 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~-I~~Vri~~------~skGfaFVeF~d~edA~kAI~~LN--G~~I~Gr~Ik  428 (985)
                      ...++|||+|||..+++++|+++|++||. |.+|+++.      .++|||||+|.+.++|++|++.||  +..+.|++|+
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            35679999999999999999999999998 99999872      468999999999999999999996  5899999999


Q ss_pred             EEeccCcch
Q 001991          429 LEASRPGGA  437 (985)
Q Consensus       429 V~~A~~k~~  437 (985)
                      |.|++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999998664

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.41  E-value=1.3e-13  Score=131.01  Aligned_cols=79  Identities=18%  Similarity=0.163  Sum_probs=71.5

Q ss_pred             ccccceeeecCCCC-CCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCC--ceeCCceEEEEeccC
Q 001991          358 ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR--SDVAGKQIKLEASRP  434 (985)
Q Consensus       358 ~~~~tLfV~NLp~s-vTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG--~~I~Gr~IkV~~A~~  434 (985)
                      .+.++|||+|||.+ +++++|+++|++||+|.+|++.+ .+|||||+|.+.++|++|++.||+  ..|.|++|+|.++++
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            45679999999998 99999999999999999999875 589999999999999999998864  569999999999987


Q ss_pred             cch
Q 001991          435 GGA  437 (985)
Q Consensus       435 k~~  437 (985)
                      +..
T Consensus       102 ~~~  104 (112)
T 1x4f_A          102 YKK  104 (112)
T ss_dssp             CSS
T ss_pred             ccc
Confidence            653

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=4.2e-13  Score=124.44  Aligned_cols=81  Identities=20%  Similarity=0.313  Sum_probs=73.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCc-EEEEEec------cccceEEEEEeCCHHHHHHHHHHcc--Cccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGD-IRTIYTA------CKHRGFVMISYYDIRAARNAMKALQ--NKPLRRRKLD  343 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~-I~sVkit------gksrGfAFV~F~d~esA~kAi~~Ln--g~~I~Gr~L~  343 (985)
                      .+.++|||+|||.++++++|+++|++||. |..|.+.      ++++|||||+|.+.++|++|++.|+  +..+.|++|.
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 9999863      4789999999999999999999996  5899999999


Q ss_pred             ccccCCCCCC
Q 001991          344 IHYSIPKDNP  353 (985)
Q Consensus       344 V~~a~pk~~~  353 (985)
                      |.++.++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999887654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=2.2e-13  Score=128.13  Aligned_cols=81  Identities=11%  Similarity=0.261  Sum_probs=73.6

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|+++.+     .+|||||+|.+.++|++||+. ++..|.|++|+|.+
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            445679999999999999999999999999999998754     478999999999999999997 99999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus       103 a~~~~~~  109 (116)
T 1x4b_A          103 AVAREES  109 (116)
T ss_dssp             CSSCCCC
T ss_pred             CCCCccC
Confidence            9987643

>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=99.41  E-value=5.1e-13  Score=132.12  Aligned_cols=82  Identities=26%  Similarity=0.394  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            4457899999999999999999999999999999987     56789999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 001991          346 YSIPKDN  352 (985)
Q Consensus       346 ~a~pk~~  352 (985)
                      ++.+...
T Consensus       115 ~a~~~~~  121 (156)
T 1h2v_Z          115 WDAGFKE  121 (156)
T ss_dssp             EESCCCT
T ss_pred             ECCCCCC
Confidence            9987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=2.9e-13  Score=123.99  Aligned_cols=82  Identities=29%  Similarity=0.450  Sum_probs=70.9

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEE-cCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri-~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .....++|||+|||..+++++|+++|++||.|.-++. ....++||||+|.+.++|++|++.|||..|.|++|+|.++++
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            3456789999999999999999999999998843322 123689999999999999999999999999999999999988


Q ss_pred             cch
Q 001991          435 GGA  437 (985)
Q Consensus       435 k~~  437 (985)
                      +..
T Consensus        91 ~~~   93 (101)
T 2fc9_A           91 RGS   93 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=1.5e-13  Score=124.29  Aligned_cols=77  Identities=18%  Similarity=0.226  Sum_probs=68.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            345699999999999999999999999999875543     567899999999999999999999999999999999998


Q ss_pred             cC
Q 001991          347 SI  348 (985)
Q Consensus       347 a~  348 (985)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
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=99.41  E-value=9.6e-13  Score=121.00  Aligned_cols=82  Identities=17%  Similarity=0.318  Sum_probs=73.8

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++  ++..|.|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEE
Confidence            34567899999999999999999999999999999976     47789999999999999999997  477899999999


Q ss_pred             cccCCCCCC
Q 001991          345 HYSIPKDNP  353 (985)
Q Consensus       345 ~~a~pk~~~  353 (985)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqg_A           88 KLPNSKQSQ   96 (103)
T ss_dssp             ECCCTTCCC
T ss_pred             EecCCCCcC
Confidence            999887654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=3.7e-13  Score=125.42  Aligned_cols=78  Identities=9%  Similarity=0.156  Sum_probs=71.6

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ....++|||+|||.++|+++|+++|++||.|.+|+++.+    ++|||||+|.+.++|++|+. +||..|.|+.|.|.++
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            345689999999999999999999999999999998753    68999999999999999999 9999999999999998


Q ss_pred             cCc
Q 001991          433 RPG  435 (985)
Q Consensus       433 ~~k  435 (985)
                      ..-
T Consensus        87 ~~~   89 (103)
T 1s79_A           87 DDY   89 (103)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            653

>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=99.41  E-value=1.6e-13  Score=126.15  Aligned_cols=78  Identities=21%  Similarity=0.331  Sum_probs=69.5

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ....++|||+|||.++++++|+++|++|| |.+|++..+      ++|||||+|.+.++|++|+ .|||..|+|++|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34567999999999999999999999999 999998754      3789999999999999999 899999999999999


Q ss_pred             eccCcc
Q 001991          431 ASRPGG  436 (985)
Q Consensus       431 ~A~~k~  436 (985)
                      +++++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998754

>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=8.2e-13  Score=119.76  Aligned_cols=79  Identities=15%  Similarity=0.138  Sum_probs=71.8

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEE-EcCC-CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQH-KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vr-i~~~-skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ...++|||+|||..+++++|+++|++||.|.+|+ ++.+ ..+.|||+|.+.++|++|++.|||..|.|++|+|.++.++
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            3467999999999999999999999999999995 6654 3456999999999999999999999999999999999987


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      +
T Consensus        93 ~   93 (96)
T 2e44_A           93 M   93 (96)
T ss_dssp             C
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=5.4e-13  Score=119.95  Aligned_cols=79  Identities=11%  Similarity=0.240  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .....++|||+|||.++++++|+++|++| .|..|++    +++++|||||+|.+.++|++|++ |++..|.|+.|.|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            34567999999999999999999999999 8988876    56789999999999999999999 999999999999999


Q ss_pred             cCCCC
Q 001991          347 SIPKD  351 (985)
Q Consensus       347 a~pk~  351 (985)
                      +.++.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.41  E-value=2.1e-13  Score=129.16  Aligned_cols=79  Identities=11%  Similarity=0.100  Sum_probs=72.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccC-cEEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFG-DIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG-~I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ....++|||+|||+++++++|+++|++|| +|..+++ ..+++|||||+|.+.++|++|++.|||..|.|++|.|.++..
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            34568999999999999999999999999 9999988 467899999999999999999999999999999999999864


Q ss_pred             C
Q 001991          350 K  350 (985)
Q Consensus       350 k  350 (985)
                      .
T Consensus       105 ~  105 (111)
T 2jvr_A          105 P  105 (111)
T ss_dssp             -
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=99.41  E-value=5.6e-13  Score=122.16  Aligned_cols=84  Identities=20%  Similarity=0.359  Sum_probs=71.9

Q ss_pred             cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc--CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       355 ~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~--~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ......++|||+|||..+++++|+++|+.|+.|.-++..  ...++||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            344567899999999999999999999999765554432  234789999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2fc8_A           90 KPKGEG   95 (102)
T ss_dssp             CCCCSS
T ss_pred             cCCCCC
Confidence            987654

>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=1.3e-13  Score=123.63  Aligned_cols=77  Identities=23%  Similarity=0.425  Sum_probs=67.9

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.+ |++|++.|+|..+.|++|.|.++.++
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            68999999999999999999999999999986     3678999999999999 99999999999999999999999876


Q ss_pred             CCC
Q 001991          351 DNP  353 (985)
Q Consensus       351 ~~~  353 (985)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=9.6e-13  Score=120.00  Aligned_cols=80  Identities=18%  Similarity=0.313  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|||+||  ++++++|+++|++||+|..|++ .+++|||||+|.+.++|++|++.|++..|.|++|.|.++.++
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            4457799999996  8999999999999999999998 688999999999999999999999999999999999999876


Q ss_pred             CCC
Q 001991          351 DNP  353 (985)
Q Consensus       351 ~~~  353 (985)
                      ...
T Consensus        88 ~~~   90 (97)
T 1x5p_A           88 PML   90 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=2.4e-13  Score=123.95  Aligned_cols=79  Identities=22%  Similarity=0.349  Sum_probs=72.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEE-EEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCce----E
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIR-EIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQ----I  427 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~-~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~----I  427 (985)
                      ...++|||+|||..+++++|+++|++||.|. +|+++.+     ++|||||+|.+.++|++|++.|||..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            4567999999999999999999999999999 9988654     4589999999999999999999999999999    9


Q ss_pred             EEEeccCcc
Q 001991          428 KLEASRPGG  436 (985)
Q Consensus       428 kV~~A~~k~  436 (985)
                      +|.|+++..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999998754

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.40  E-value=3.4e-13  Score=134.77  Aligned_cols=81  Identities=10%  Similarity=0.159  Sum_probs=72.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccC--CEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG--~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ..++|||+|||..+++++|+++|++||  .|.+|+++.+     ++|||||+|.+.++|++||+.|||..|.|++|+|.+
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            356999999999999999999999999  9999998644     578999999999999999999999999999999999


Q ss_pred             ccCcchhh
Q 001991          432 SRPGGARR  439 (985)
Q Consensus       432 A~~k~~Rr  439 (985)
                      +.++..++
T Consensus       134 a~~~~~~~  141 (156)
T 3n9u_C          134 ATRQNLSQ  141 (156)
T ss_dssp             CCHHHHHH
T ss_pred             cCCCcchh
Confidence            98766443

>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=99.40  E-value=7.2e-13  Score=119.87  Aligned_cols=77  Identities=22%  Similarity=0.382  Sum_probs=64.8

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCce--eCCceEEEEeccC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD--VAGKQIKLEASRP  434 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~--I~Gr~IkV~~A~~  434 (985)
                      .....+|||+|||.++|+++|+++|++||.|.+|+++.+++|||||+|.+.++|++    |++..  +.|++|.|.++.+
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            34567999999999999999999999999999999998899999999999999983    56665  4699999999998


Q ss_pred             cch
Q 001991          435 GGA  437 (985)
Q Consensus       435 k~~  437 (985)
                      +..
T Consensus        84 k~~   86 (89)
T 3d2w_A           84 KHN   86 (89)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>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=99.40  E-value=5.5e-13  Score=124.36  Aligned_cols=78  Identities=23%  Similarity=0.477  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEecCCCC-CCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          271 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~-vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .....++|||+|||.+ +++++|+++|++||+|..|++   .+|||||+|.+.++|++|++.|++..|.|+.|.|.++.+
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            3445689999999999 999999999999999999999   789999999999999999999999999999999999975


Q ss_pred             CC
Q 001991          350 KD  351 (985)
Q Consensus       350 k~  351 (985)
                      ..
T Consensus       100 ~~  101 (110)
T 1wf1_A          100 PK  101 (110)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=3.3e-13  Score=125.72  Aligned_cols=77  Identities=13%  Similarity=0.319  Sum_probs=70.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .+...++|||+|||+++|+++|+++|++||+|.+|++    .+.++|||||+|.+.++|++|++ +++..|.|+.|.|.+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999986    36789999999999999999998 999999999999987


Q ss_pred             cC
Q 001991          347 SI  348 (985)
Q Consensus       347 a~  348 (985)
                      +.
T Consensus        86 ~~   87 (103)
T 1s79_A           86 KD   87 (103)
T ss_dssp             HH
T ss_pred             ch
Confidence            64

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.40  E-value=6.1e-13  Score=126.65  Aligned_cols=83  Identities=24%  Similarity=0.414  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++    +++++|||||+|.+.++|++|++.|++..|.|+.|.|.+
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            4567799999999999999999999999999999976    466899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.+....
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9876543

>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=5.8e-13  Score=124.66  Aligned_cols=82  Identities=21%  Similarity=0.362  Sum_probs=70.7

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|++.+ +..|.|++|+|.
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            3446679999999999999999999999999999999754     4789999999999999999976 599999999999


Q ss_pred             eccCcchh
Q 001991          431 ASRPGGAR  438 (985)
Q Consensus       431 ~A~~k~~R  438 (985)
                      ++.++..+
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99987643

>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=99.40  E-value=2.4e-13  Score=123.79  Aligned_cols=78  Identities=19%  Similarity=0.203  Sum_probs=69.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|..++++.     ..+|||||+|.+.++|++|++.|||..|.|++|+|+++
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            4567899999999999999999999999997654432     25789999999999999999999999999999999998


Q ss_pred             cCc
Q 001991          433 RPG  435 (985)
Q Consensus       433 ~~k  435 (985)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            764

>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=99.40  E-value=3.9e-13  Score=125.87  Aligned_cols=82  Identities=23%  Similarity=0.296  Sum_probs=72.8

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCE----EEEEEc-CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEI----REIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I----~~Vri~-~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|    ..+++. ...+|||||+|.+.++|++|++.|||..|.|++|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3456799999999999999999999999998    455543 45789999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9987644

>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=99.40  E-value=7e-13  Score=118.06  Aligned_cols=75  Identities=21%  Similarity=0.359  Sum_probs=68.1

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++|++ +++..|.|++|+|++
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            346779999999999999999999999999999998644     47899999999999999996 688999999999987


Q ss_pred             c
Q 001991          432 S  432 (985)
Q Consensus       432 A  432 (985)
                      |
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=99.40  E-value=2.9e-13  Score=135.27  Aligned_cols=78  Identities=14%  Similarity=0.267  Sum_probs=71.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccC--cEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG--~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...++|||+|||.++++++|+++|++||  +|..|++     +++++|||||+|.+.++|++||+.|+|..|.|+.|.|.
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  9999876     67899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 001991          346 YSIPK  350 (985)
Q Consensus       346 ~a~pk  350 (985)
                      ++.++
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=4.8e-13  Score=123.40  Aligned_cols=81  Identities=26%  Similarity=0.414  Sum_probs=73.8

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|+++.+     .+|||||+|.+.++|++|++. |+..|.|++|+|.+
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            456789999999999999999999999999999998754     358999999999999999998 99999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++..+
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9987644

>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=4.3e-13  Score=125.58  Aligned_cols=82  Identities=16%  Similarity=0.395  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.+ +..|.|+.|.|.
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            4557799999999999999999999999999999986     4778999999999999999999865 599999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99877543

>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=99.39  E-value=3.9e-13  Score=120.58  Aligned_cols=75  Identities=15%  Similarity=0.319  Sum_probs=70.2

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ..++|||+|||..+++++|+++|++| .|.+|++. .++|||||+|.+.++|++|++.|||..+.|++|+|+++..+
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            45789999999999999999999999 99999885 67899999999999999999999999999999999998764

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.39  E-value=1.1e-12  Score=126.50  Aligned_cols=76  Identities=25%  Similarity=0.410  Sum_probs=70.1

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..|.|++|+|++
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            345679999999999999999999999999999998654     589999999999999999999999999999999998


Q ss_pred             c
Q 001991          432 S  432 (985)
Q Consensus       432 A  432 (985)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.39  E-value=2.9e-13  Score=117.25  Aligned_cols=70  Identities=19%  Similarity=0.427  Sum_probs=65.6

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +|||+|||+++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ +++..+.|++|.|+++
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     56789999999999999999997 9999999999999875

>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=1e-12  Score=121.78  Aligned_cols=80  Identities=13%  Similarity=0.212  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE-EEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT-IYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s-Vki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .....++|||+|||+++++++|+++|++||.|.. |.+    +++++|||||+|.+.++|++|++. ++..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            3456799999999999999999999999999987 665    678899999999999999999986 9999999999999


Q ss_pred             ccCCCC
Q 001991          346 YSIPKD  351 (985)
Q Consensus       346 ~a~pk~  351 (985)
                      ++.++.
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            887654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1.5e-13  Score=121.87  Aligned_cols=76  Identities=20%  Similarity=0.300  Sum_probs=69.7

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+++++|+++|++||.|..|++..+     .+|||||+|.+.++|++|++.|||..+.|+.|+|.+++
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            4679999999999999999999999999999998654     47899999999999999999999999999999988765


Q ss_pred             C
Q 001991          434 P  434 (985)
Q Consensus       434 ~  434 (985)
                      .
T Consensus        84 s   84 (85)
T 1x4e_A           84 S   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.39  E-value=1e-12  Score=126.65  Aligned_cols=78  Identities=28%  Similarity=0.471  Sum_probs=71.6

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....+.++|||+|||.++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|++..|.|++|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567899999999999999999999999999999986     4678999999999999999999999999999999999


Q ss_pred             ccc
Q 001991          345 HYS  347 (985)
Q Consensus       345 ~~a  347 (985)
                      .++
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

>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=99.38  E-value=9.5e-13  Score=123.22  Aligned_cols=79  Identities=16%  Similarity=0.269  Sum_probs=71.7

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCcee--------CC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDV--------AG  424 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I--------~G  424 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+    ++|||||+|.+.++|++|++.|||..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            345679999999999999999999999999999998754    468999999999999999999999999        57


Q ss_pred             ceEEEEeccCc
Q 001991          425 KQIKLEASRPG  435 (985)
Q Consensus       425 r~IkV~~A~~k  435 (985)
                      ++|.|.|+.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999999875

>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=99.38  E-value=2.3e-13  Score=123.05  Aligned_cols=76  Identities=20%  Similarity=0.242  Sum_probs=67.5

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+++++|+++|++||.|..++++.     ..++||||+|.+.++|++|++.|||..|.|++|+|+++.
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            457999999999999999999999999997665543     357899999999999999999999999999999999986


Q ss_pred             C
Q 001991          434 P  434 (985)
Q Consensus       434 ~  434 (985)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=6.6e-13  Score=133.95  Aligned_cols=77  Identities=21%  Similarity=0.311  Sum_probs=70.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-CCcEEEEEEcCHHHHHHHHHHhCCceeCC--ceEEEEeccCcc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-KHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPGG  436 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-skGfaFVeF~d~edA~kAI~~LNG~~I~G--r~IkV~~A~~k~  436 (985)
                      ..+|||+||+..+|+++|+++|++||+|++|++..+ +++||||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
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            457999999999999999999999999999998644 57899999999999999999999999955  999999999753

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.38  E-value=3.4e-13  Score=116.78  Aligned_cols=70  Identities=13%  Similarity=0.276  Sum_probs=65.4

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      +|||+|||.++++++|+++|++||.|.+|++..+     ++|||||+|.+.++|++|++ |||..++|++|+|.+|
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            5899999999999999999999999999988654     47899999999999999998 9999999999999875

>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=99.38  E-value=6.8e-13  Score=125.36  Aligned_cols=76  Identities=18%  Similarity=0.264  Sum_probs=67.4

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCce-----EEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ-----IKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~-----IkV~~A~  433 (985)
                      ...+|||.|||.++++++|+++|++||+|..|.++.+  +||||+|.+.++|++||+.|||..|.|++     |+|..+.
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            4579999999999999999999999999999999876  99999999999999999999999999998     7777766


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ++.
T Consensus        93 ~~~   95 (115)
T 3beg_B           93 PRS   95 (115)
T ss_dssp             ---
T ss_pred             CCC
Confidence            544

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.38  E-value=1.1e-12  Score=126.74  Aligned_cols=74  Identities=22%  Similarity=0.299  Sum_probs=68.3

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcE-EEEEEcCHHHHHHHHHHhCCceeCC--ceEEEEeccCcc
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNH-KFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPGG  436 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGf-aFVeF~d~edA~kAI~~LNG~~I~G--r~IkV~~A~~k~  436 (985)
                      .|||+||+..+++++|+++|++||.|.+|++..+ .|| |||+|.+.++|.+|++.|||..|.|  ++|+|.+|+++.
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            5789999999999999999999999999998764 586 9999999999999999999999987  699999999865

>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=99.37  E-value=7.2e-13  Score=126.24  Aligned_cols=77  Identities=19%  Similarity=0.204  Sum_probs=70.1

Q ss_pred             ccccceee--ecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCcee-----CCceEEEE
Q 001991          358 ANQGTLVV--FNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV-----AGKQIKLE  430 (985)
Q Consensus       358 ~~~~tLfV--~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I-----~Gr~IkV~  430 (985)
                      .+..+|||  +||+..+++++|+++|++||.|.+|.+.. .+|||||+|.+.++|++|++.|||+++     .|++|+|.
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~  101 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN  101 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEE
Confidence            34678999  66999999999999999999999998875 489999999999999999999999998     79999999


Q ss_pred             eccCc
Q 001991          431 ASRPG  435 (985)
Q Consensus       431 ~A~~k  435 (985)
                      |++..
T Consensus       102 ~a~~~  106 (114)
T 2cq2_A          102 FVEKV  106 (114)
T ss_dssp             EESCC
T ss_pred             ecccC
Confidence            98753

>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=99.37  E-value=1.8e-13  Score=122.60  Aligned_cols=75  Identities=20%  Similarity=0.415  Sum_probs=67.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ++|||+|||..+++++|+++|++||.|.+|++..+     ++|||||+|.+.+ |++|++.|||..++|++|+|++|.++
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            57999999999999999999999999999998744     5789999999999 99999999999999999999999875


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.37  E-value=2.7e-13  Score=124.20  Aligned_cols=82  Identities=16%  Similarity=0.238  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE----eccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk----itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..+.    .+++++|||||+|.+.++|++|++ |++..|.|+.|.|.+
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            344679999999999999999999999999876621    257889999999999999999998 999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus        92 a~~~~~~   98 (101)
T 1fj7_A           92 PKGRDGT   98 (101)
T ss_dssp             CSCCCCS
T ss_pred             cCCCCCC
Confidence            9876543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=6.9e-13  Score=124.68  Aligned_cols=81  Identities=17%  Similarity=0.431  Sum_probs=73.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|.|.+
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            345699999999999999999999999999999876     467899999999999999999986 99999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus       103 a~~~~~~  109 (116)
T 1x4b_A          103 AVAREES  109 (116)
T ss_dssp             CSSCCCC
T ss_pred             CCCCccC
Confidence            9887654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.37  E-value=4.7e-13  Score=118.07  Aligned_cols=69  Identities=17%  Similarity=0.275  Sum_probs=64.1

Q ss_pred             cceeeecCCCCC------CHHHHHHHhhccCCEEEEEEcC---CCCcEEEEEEcCHHHHHHHHHHhCCceeCCc-eEEE
Q 001991          361 GTLVVFNLDSSV------STEELHQIFGIYGEIREIRDTQ---HKHNHKFIEFYDIRAAETALRTLNRSDVAGK-QIKL  429 (985)
Q Consensus       361 ~tLfV~NLp~sv------TeedLrelFs~fG~I~~Vri~~---~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr-~IkV  429 (985)
                      ++|||+|||..+      ++++|+++|++||.|.+|++.+   .++|||||+|.+.++|++|++.|||..+.|+ +|+|
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      7899999999999999999874   3589999999999999999999999999999 8876

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.37  E-value=3e-13  Score=130.47  Aligned_cols=80  Identities=19%  Similarity=0.358  Sum_probs=72.5

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEE--EEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCc----eeCC
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--IRDTQH-----KHNHKFIEFYDIRAAETALRTLNRS----DVAG  424 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~--Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~----~I~G  424 (985)
                      .....++|||+|||..+|+++|+++|++||.|..  |+++.+     ++|||||+|.+. +|.+|++.|||.    .|.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3455679999999999999999999999999977  888654     579999999999 999999999999    9999


Q ss_pred             ceEEEEeccCcc
Q 001991          425 KQIKLEASRPGG  436 (985)
Q Consensus       425 r~IkV~~A~~k~  436 (985)
                      ++|+|.+++++.
T Consensus        98 r~l~V~~a~~~~  109 (131)
T 2m2b_A           98 KTINVEFAKGSK  109 (131)
T ss_dssp             CCCCCEECCCSC
T ss_pred             EEEEEEECCCCC
Confidence            999999998764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.37  E-value=3.2e-13  Score=117.18  Aligned_cols=71  Identities=17%  Similarity=0.430  Sum_probs=66.4

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ++|||+|||.++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.++ ..+.|++|.|.++
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            57999999999999999999999999998876     46789999999999999999999998 9999999999876

>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=99.37  E-value=1.8e-13  Score=128.25  Aligned_cols=79  Identities=18%  Similarity=0.398  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .+...++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+ .|++..|.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   99 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ   99 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEE
Confidence            3345689999999999999999999999999999987     3778999999999999999999 999999999999999


Q ss_pred             ccCCC
Q 001991          346 YSIPK  350 (985)
Q Consensus       346 ~a~pk  350 (985)
                      ++.++
T Consensus       100 ~a~~~  104 (114)
T 2cq4_A          100 ASQAE  104 (114)
T ss_dssp             EHHHH
T ss_pred             ecCCC
Confidence            98754

>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=1.1e-12  Score=131.48  Aligned_cols=85  Identities=20%  Similarity=0.409  Sum_probs=75.3

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       269 ~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      +....+.++|||+|||..+++++|+++|++||+|..|.+     ++.++|||||+|.+.++|++||+.|+|..|.|+.|.
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            344567789999999999999999999999999999976     566899999999999999999999999999999999


Q ss_pred             ccccCCCCCC
Q 001991          344 IHYSIPKDNP  353 (985)
Q Consensus       344 V~~a~pk~~~  353 (985)
                      |.|+.++...
T Consensus       146 V~~a~~~~~~  155 (165)
T 1rk8_A          146 VDWCFVKGPK  155 (165)
T ss_dssp             EEESEECC--
T ss_pred             EEEecCCCCC
Confidence            9999876544

>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=99.37  E-value=2.3e-12  Score=118.45  Aligned_cols=79  Identities=14%  Similarity=0.322  Sum_probs=71.1

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||..+++++|+++|++||.|..|+++.+     ++|||||+|.+.++|++|++  ++..|.|++|+|.+
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            445679999999999999999999999999999998654     36899999999999999999  57899999999999


Q ss_pred             ccCcch
Q 001991          432 SRPGGA  437 (985)
Q Consensus       432 A~~k~~  437 (985)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            988654

>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=99.37  E-value=5.8e-13  Score=119.47  Aligned_cols=76  Identities=16%  Similarity=0.367  Sum_probs=70.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...++|||+|||+++++++|+++|++| +|..+++. +++|||||+|.+.++|++|++.|+|..+.|++|+|.++..+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            356899999999999999999999999 99999884 88999999999999999999999999999999999998543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.36  E-value=2.9e-13  Score=124.07  Aligned_cols=79  Identities=22%  Similarity=0.251  Sum_probs=70.0

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|++||.|.. .++     ..++|||||+|.+.++|++|++ |||..|.|++|+|.++
T Consensus        15 ~~~~~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           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            35679999999999999999999999998766 222     3468999999999999999999 9999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++..+
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            987644

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=1.9e-12  Score=117.30  Aligned_cols=80  Identities=23%  Similarity=0.303  Sum_probs=71.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE-e-ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-T-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk-i-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ....++|||+|||+++++++|+++|++||.|..|+ + ..+..+.|||+|.+.++|++|++.|+|..|.|++|.|.++.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            34578999999999999999999999999999994 4 444556699999999999999999999999999999999987


Q ss_pred             CC
Q 001991          350 KD  351 (985)
Q Consensus       350 k~  351 (985)
                      +.
T Consensus        92 ~~   93 (96)
T 2e44_A           92 EM   93 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            74

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=1e-12  Score=118.10  Aligned_cols=77  Identities=18%  Similarity=0.267  Sum_probs=70.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ....+|||+|||.++++++|+++|++| .|..|+++.+    ++|||||+|.+.++|++|++ |||..|+|++|+|.+++
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            456799999999999999999999999 9999988654    46799999999999999999 99999999999999998


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ++.
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            754

>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=9.5e-13  Score=125.42  Aligned_cols=79  Identities=14%  Similarity=0.277  Sum_probs=71.3

Q ss_pred             CCCCCcEEEE--ecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccc-----cccccc
Q 001991          271 GEHPSRTLFV--RNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL-----RRRKLD  343 (985)
Q Consensus       271 ~e~~srtLfV--gNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I-----~Gr~L~  343 (985)
                      ...++++|||  +||+.++++++|+++|++||+|..|.+ ...||||||+|.+.++|++|++.|||+.+     .|++|+
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 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   99 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC-CTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEE-eCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEE
Confidence            4457899999  669999999999999999999999988 34689999999999999999999999988     789999


Q ss_pred             ccccCCC
Q 001991          344 IHYSIPK  350 (985)
Q Consensus       344 V~~a~pk  350 (985)
                      |.|+...
T Consensus       100 v~~a~~~  106 (114)
T 2cq2_A          100 LNFVEKV  106 (114)
T ss_dssp             EEEESCC
T ss_pred             EEecccC
Confidence            9998644

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=3e-12  Score=116.01  Aligned_cols=80  Identities=18%  Similarity=0.311  Sum_probs=69.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      ...++|||+|||.++++++|+++|++||+|..|........||||+|.+.++|++|++ |++..|.|+.|.|.++.++..
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            4568999999999999999999999999999985432222299999999999999999 999999999999999876654


Q ss_pred             C
Q 001991          353 P  353 (985)
Q Consensus       353 ~  353 (985)
                      .
T Consensus        85 ~   85 (94)
T 2e5g_A           85 Q   85 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=6e-13  Score=125.33  Aligned_cols=82  Identities=11%  Similarity=0.128  Sum_probs=73.4

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCE-EEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I-~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ....++|||+|||.++++++|+++|++||.| ..|+++.+    .+|||||+|.+.++|++||+. |+..|.|++|+|.+
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            3456799999999999999999999999999 78888643    689999999999999999996 99999999999999


Q ss_pred             ccCcchhh
Q 001991          432 SRPGGARR  439 (985)
Q Consensus       432 A~~k~~Rr  439 (985)
                      +.++..++
T Consensus        91 a~~~~~~~   98 (114)
T 2cpy_A           91 VTLEDMRE   98 (114)
T ss_dssp             ECHHHHHH
T ss_pred             CCHHHHHH
Confidence            98876554

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=1.5e-12  Score=118.04  Aligned_cols=77  Identities=16%  Similarity=0.307  Sum_probs=68.1

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..++|||+|||..+++++|+++|++||.|.+|.+......||||+|.+.++|++|++ |||..|.|++|+|.++.++.
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            456999999999999999999999999999984433322299999999999999999 99999999999999987655

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.35  E-value=1.3e-12  Score=124.05  Aligned_cols=77  Identities=19%  Similarity=0.378  Sum_probs=71.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      +.++|||+|||.++++++|+++|++||+|..|++     ++.++|||||+|.+.++|++|+ .|+|..|.|+.|.|.++.
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            4689999999999999999999999999999876     5778999999999999999999 799999999999999987


Q ss_pred             CCC
Q 001991          349 PKD  351 (985)
Q Consensus       349 pk~  351 (985)
                      +..
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.35  E-value=5e-13  Score=127.57  Aligned_cols=79  Identities=11%  Similarity=0.228  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE-E----eccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI-Y----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV-k----itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .....++|||+|||+++|+++|+++|++||.|..+ .    .+++++|||||+|.+.++|++||+ |++..|.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34567999999999999999999999999998652 2    267889999999999999999998 99999999999999


Q ss_pred             ccCCC
Q 001991          346 YSIPK  350 (985)
Q Consensus       346 ~a~pk  350 (985)
                      ++.++
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.35  E-value=4.8e-13  Score=116.06  Aligned_cols=71  Identities=20%  Similarity=0.369  Sum_probs=66.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ++|||+|||.++++++|+++|++||.|..|++..+     ++|||||+|.+.++|++|++.++ ..+.|++|+|.+|
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            47999999999999999999999999999988654     47899999999999999999999 9999999999987

>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=99.34  E-value=1.7e-12  Score=120.28  Aligned_cols=78  Identities=22%  Similarity=0.288  Sum_probs=70.5

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEE-EEEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~-Vri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ....+|||+|||.++++++|+++|++||.|.. |+++.    .++|||||+|.+.++|++||+. |+..|+|+.|+|.++
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            45679999999999999999999999999987 87753    3579999999999999999996 999999999999998


Q ss_pred             cCcc
Q 001991          433 RPGG  436 (985)
Q Consensus       433 ~~k~  436 (985)
                      .+++
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7655

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.34  E-value=2.3e-12  Score=125.44  Aligned_cols=80  Identities=25%  Similarity=0.359  Sum_probs=72.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceE-EEEEeCCHHHHHHHHHHccCccccc--ccccccccCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIP  349 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGf-AFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~p  349 (985)
                      ..--.|||+||+..+|+++|+++|++||+|..|++..+.+|| |||+|.+.++|++|++.|||..|.|  +.|+|+|+++
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            344667799999999999999999999999999886667888 9999999999999999999999988  8999999987


Q ss_pred             CCC
Q 001991          350 KDN  352 (985)
Q Consensus       350 k~~  352 (985)
                      +..
T Consensus       106 ~~l  108 (130)
T 3zzy_A          106 TSL  108 (130)
T ss_dssp             SSC
T ss_pred             Cce
Confidence            654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.34  E-value=6.1e-13  Score=126.36  Aligned_cols=80  Identities=14%  Similarity=0.139  Sum_probs=71.5

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCC---EEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGE---IREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~---I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ...++|||+|||.++|+++|+++|+.||.   |..|+++.+    ++|||||+|.+.++|++||+ ||+..|+|+.|+|.
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            45678999999999999999999999999   888887643    57899999999999999999 99999999999999


Q ss_pred             eccCcchh
Q 001991          431 ASRPGGAR  438 (985)
Q Consensus       431 ~A~~k~~R  438 (985)
                      ++.+++..
T Consensus        94 ~a~~~~~~  101 (118)
T 2db1_A           94 KSHRTEMD  101 (118)
T ss_dssp             EECHHHHH
T ss_pred             ECCHHHHH
Confidence            99866533

>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=99.34  E-value=5.9e-13  Score=130.41  Aligned_cols=80  Identities=14%  Similarity=0.118  Sum_probs=71.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCC---EEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGE---IREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~---I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ....+|||+|||.++|+++|+++|++||.   |.+|+++.+    ++|||||+|.+.++|++||+ ||+..|+|+.|+|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            34678999999999999999999999999   778887643    57899999999999999999 99999999999999


Q ss_pred             eccCcchh
Q 001991          431 ASRPGGAR  438 (985)
Q Consensus       431 ~A~~k~~R  438 (985)
                      ++.+++..
T Consensus       121 ~a~~~e~~  128 (136)
T 2hgl_A          121 KSHRTEMD  128 (136)
T ss_dssp             ECCHHHHH
T ss_pred             ECChHHHH
Confidence            99766543

>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=99.33  E-value=2.1e-12  Score=125.99  Aligned_cols=82  Identities=20%  Similarity=0.380  Sum_probs=73.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE--------EE--eccccceEEEEEeCCHHHHHHHHHHccCccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--------IY--TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  341 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s--------Vk--itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~  341 (985)
                      ..++++|||+|||+++|+++|+++|++||.|..        ++  .+++++|||||+|.+.++|.+|++.|||..|.|+.
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            457799999999999999999999999998865        32  36889999999999999999999999999999999


Q ss_pred             ccccccCCCCCC
Q 001991          342 LDIHYSIPKDNP  353 (985)
Q Consensus       342 L~V~~a~pk~~~  353 (985)
                      |.|.++.+....
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999775443

>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=2.2e-12  Score=119.68  Aligned_cols=79  Identities=10%  Similarity=0.219  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .....++|||+|||+++|+++|+++|++||.| .|++    +++++|||||+|.+.++|++|| .+++..|.|+.|.|..
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEE
Confidence            34567899999999999999999999999955 7765    5788999999999999999999 5899999999999998


Q ss_pred             cCCCC
Q 001991          347 SIPKD  351 (985)
Q Consensus       347 a~pk~  351 (985)
                      +.+..
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=2.2e-12  Score=118.60  Aligned_cols=76  Identities=17%  Similarity=0.321  Sum_probs=67.6

Q ss_pred             CCCcE-EEEecCCCCCCHHH----HHHhhccc-CcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          273 HPSRT-LFVRNINSNVEDSE----LKALFEQF-GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       273 ~~srt-LfVgNLP~~vTEed----LrelFs~f-G~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .|+.+ |||+|||.++++++    |+++|++| |+|.+|  ++   |+|||.|.+.++|++|++.|+|..+.||+|+|.|
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 599988  23   9999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +..+.+.
T Consensus        81 A~~~sd~   87 (96)
T 2diu_A           81 TPKNREL   87 (96)
T ss_dssp             SCCSCCC
T ss_pred             cCCCcce
Confidence            9877654

>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=99.32  E-value=9.2e-13  Score=124.03  Aligned_cols=80  Identities=14%  Similarity=0.173  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcE-EEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI-RTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I-~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++|+++|+++|++||.| ..|++    +++++|||||+|.+.++|++|++. ++..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            34567999999999999999999999999999 66665    577899999999999999999976 9999999999999


Q ss_pred             ccCCCC
Q 001991          346 YSIPKD  351 (985)
Q Consensus       346 ~a~pk~  351 (985)
                      ++.++.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            986543

>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=99.32  E-value=3.5e-12  Score=113.19  Aligned_cols=72  Identities=19%  Similarity=0.367  Sum_probs=67.1

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhcc----C-------CEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCce
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIY----G-------EIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  426 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~f----G-------~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~  426 (985)
                      ...++|||+|||.++++++|+++|++|    |       .|.++++..+ +|||||+|.+.++|++|+ .|||..+.|++
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 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-KNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-SSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-CcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            346799999999999999999999999    8       9999998765 899999999999999999 89999999999


Q ss_pred             EEEEe
Q 001991          427 IKLEA  431 (985)
Q Consensus       427 IkV~~  431 (985)
                      |+|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99974

>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=5.8e-13  Score=122.26  Aligned_cols=81  Identities=20%  Similarity=0.483  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++  ++..+.|+.|.|.+
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            4456799999999999999999999999999999976    56789999999999999999997  99999999999999


Q ss_pred             cCCCCCC
Q 001991          347 SIPKDNP  353 (985)
Q Consensus       347 a~pk~~~  353 (985)
                      +.++...
T Consensus        83 a~~~~~~   89 (102)
T 2xs2_A           83 AIRKQNL   89 (102)
T ss_dssp             EEECC--
T ss_pred             CCcCcch
Confidence            8876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.00  E-value=1.3e-13  Score=129.71  Aligned_cols=83  Identities=22%  Similarity=0.370  Sum_probs=75.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEE--------EEe-----ccccceEEEEEeCCHHHHHHHHHHccCccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--------IYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPL  337 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~s--------Vki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I  337 (985)
                      ...+.++|||+|||.++++++|+++|++||.|..        |++     +++++|||||+|.+.++|++|++.|++..|
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            3457799999999999999999999999999988        654     467899999999999999999999999999


Q ss_pred             ccccccccccCCCCCC
Q 001991          338 RRRKLDIHYSIPKDNP  353 (985)
Q Consensus       338 ~Gr~L~V~~a~pk~~~  353 (985)
                      .|++|.|.++.++...
T Consensus        83 ~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           83 SGNPIKVSFATRRADF   98 (116)
Confidence            9999999999887654

>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=99.32  E-value=3.6e-12  Score=128.64  Aligned_cols=82  Identities=22%  Similarity=0.295  Sum_probs=73.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccccC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSI  348 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~  348 (985)
                      .....+|||+||++.+|+++|+++|++||+|..|++ .+..+|||||+|.+.++|++|++.|||..|.|  ++|+|.|++
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            334567999999999999999999999999999987 34568999999999999999999999999965  999999998


Q ss_pred             CCCCC
Q 001991          349 PKDNP  353 (985)
Q Consensus       349 pk~~~  353 (985)
                      ++...
T Consensus       123 ~~~l~  127 (164)
T 1sjr_A          123 LTSLN  127 (164)
T ss_dssp             SSSCC
T ss_pred             CCccc
Confidence            87543

>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=99.32  E-value=2.4e-12  Score=116.36  Aligned_cols=78  Identities=22%  Similarity=0.467  Sum_probs=63.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcc--cccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP--LRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~--I~Gr~L~V~~a~  348 (985)
                      ...+..+|||+|||+++|+++|+++|++||+|.+|++...+||||||+|.+.++|++    +++..  +.|++|.|.++.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcC
Confidence            456789999999999999999999999999999999876789999999999999984    45554  458999999998


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      ++..
T Consensus        83 ~k~~   86 (89)
T 3d2w_A           83 PKHN   86 (89)
T ss_dssp             ----
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=99.32  E-value=7.9e-13  Score=118.28  Aligned_cols=76  Identities=16%  Similarity=0.310  Sum_probs=67.7

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCc--eeCCceEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS--DVAGKQIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~--~I~Gr~IkV~~A~~k~  436 (985)
                      ..++|||+|||.++++++|+++|++||.|.+|++..+++|||||+|.+.++|++|    ++.  .+.|++|+|.++.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSL----CGEDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEECCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEEecCCCC
Confidence            4579999999999999999999999999999999988999999999999999864    444  4589999999998876


Q ss_pred             hh
Q 001991          437 AR  438 (985)
Q Consensus       437 ~R  438 (985)
                      .+
T Consensus        80 ~~   81 (88)
T 1wf0_A           80 NS   81 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.32  E-value=3.2e-12  Score=124.60  Aligned_cols=81  Identities=26%  Similarity=0.359  Sum_probs=71.1

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEE--------EEE--cCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~--------Vri--~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                      ...++|||+|||..+|+++|+++|++||.|..        |++  .+..+|||||+|.+.++|.+|++.|||..|.|++|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            45679999999999999999999999998865        332  35678999999999999999999999999999999


Q ss_pred             EEEeccCcchh
Q 001991          428 KLEASRPGGAR  438 (985)
Q Consensus       428 kV~~A~~k~~R  438 (985)
                      +|.++++...+
T Consensus       123 ~V~~a~~~~~~  133 (143)
T 3egn_A          123 VVQFARSARPK  133 (143)
T ss_dssp             EEEECCCSCC-
T ss_pred             EEEECCCCCCc
Confidence            99999876544

>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=7e-13  Score=123.49  Aligned_cols=81  Identities=12%  Similarity=0.082  Sum_probs=72.7

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCC---EEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGE---IREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~---I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ....+|||+|||.++|+++|+++|+.||.   |..|+++.+    ++|||||+|.+.++|++||+ +|+..|+|+.|+|.
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            45678999999999999999999999998   888888643    57899999999999999999 99999999999999


Q ss_pred             eccCcchhh
Q 001991          431 ASRPGGARR  439 (985)
Q Consensus       431 ~A~~k~~Rr  439 (985)
                      ++.+++..+
T Consensus        88 ~a~~~~~~~   96 (107)
T 2lmi_A           88 EINNEDVDA   96 (107)
T ss_dssp             ECCHHHHHH
T ss_pred             ECCHHHHHH
Confidence            998766444

>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=9.3e-13  Score=113.86  Aligned_cols=70  Identities=20%  Similarity=0.476  Sum_probs=64.8

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +|||+|||.++++++|+++|++||+|..+.+     +++++|||||+|.+.++|++|++ +++..+.|++|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            5999999999999999999999999999976     46789999999999999999997 5899999999999864

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.98  E-value=1.8e-13  Score=128.87  Aligned_cols=81  Identities=20%  Similarity=0.279  Sum_probs=73.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEE--------EEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCC
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAG  424 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~--------Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~G  424 (985)
                      ...++|||+|||..+++++|+++|++||.|..        |+++.+     .+|||||+|.+.++|++|++.|||..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            45679999999999999999999999999998        777643     47899999999999999999999999999


Q ss_pred             ceEEEEeccCcchh
Q 001991          425 KQIKLEASRPGGAR  438 (985)
Q Consensus       425 r~IkV~~A~~k~~R  438 (985)
                      ++|+|.+++++..+
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999999886543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.31  E-value=1.1e-12  Score=124.73  Aligned_cols=77  Identities=8%  Similarity=0.114  Sum_probs=69.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCc---EEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~---I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ....++|||+|||.++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++|++ +++..|.|+.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            346789999999999999999999999998   777765    47789999999999999999998 9999999999999


Q ss_pred             cccCC
Q 001991          345 HYSIP  349 (985)
Q Consensus       345 ~~a~p  349 (985)
                      .++.+
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=3.4e-12  Score=117.37  Aligned_cols=72  Identities=21%  Similarity=0.329  Sum_probs=64.9

Q ss_pred             ccceeeecCCCCCCHHH----HHHHhhcc-CCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEE----LHQIFGIY-GEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeed----LrelFs~f-G~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .+.|||.|||..+++++    |+++|++| |+|.+|.     .|+|||+|.+.++|++|++.|||..+.||+|+|.+|+.
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt-----gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT-----GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC-----TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe-----cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            33499999999999888    55899999 5999982     39999999999999999999999999999999999987


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      +.
T Consensus        84 ~s   85 (96)
T 2diu_A           84 NR   85 (96)
T ss_dssp             SC
T ss_pred             Cc
Confidence            54

>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=99.30  E-value=1.6e-12  Score=121.07  Aligned_cols=79  Identities=10%  Similarity=0.053  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCc---EEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~---I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      .....++|||+|||+++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++|++ +++..|.|+.|.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3456799999999999999999999999998   788775    46789999999999999999998 999999999999


Q ss_pred             ccccCCC
Q 001991          344 IHYSIPK  350 (985)
Q Consensus       344 V~~a~pk  350 (985)
                      |.++.++
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9988653

>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=99.30  E-value=2.5e-12  Score=114.12  Aligned_cols=72  Identities=18%  Similarity=0.393  Sum_probs=67.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhccc----C-------cEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQF----G-------DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  341 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~f----G-------~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~  341 (985)
                      .+.++|||+|||+++++++|+++|++|    |       +|..+++ .+.+|||||+|.+.++|++|+ .|++..+.|++
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~-~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~   81 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-CSSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEe-cCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            467999999999999999999999999    8       9999998 456999999999999999999 99999999999


Q ss_pred             ccccc
Q 001991          342 LDIHY  346 (985)
Q Consensus       342 L~V~~  346 (985)
                      |.|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99864

>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=99.30  E-value=6.7e-13  Score=130.53  Aligned_cols=120  Identities=10%  Similarity=0.047  Sum_probs=69.8

Q ss_pred             eEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCCCCcccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEE
Q 001991          313 GFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD  392 (985)
Q Consensus       313 GfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri  392 (985)
                      |+|+.+|..++.+..++..+... ..|...--.+...  ..........+|||+|||.++|+++|+++|++|| |.+|++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~--~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i   77 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDS--EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHI   77 (139)
T ss_dssp             ----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEEC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCc--ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE
Confidence            67888888888777777654433 2232221111111  1112234567999999999999999999999999 668888


Q ss_pred             cCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          393 TQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       393 ~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      +.+    ++|||||+|.+.++|++|| .+|+..|+|+.|+|.++.+++.
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            754    5789999999999999999 6999999999999999987653

>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=99.30  E-value=3.3e-12  Score=120.63  Aligned_cols=71  Identities=14%  Similarity=0.185  Sum_probs=62.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...++|||+|||.++++++|+++|++||+|..|++...  |||||+|.+.++|++||+.||+..|.|++|.|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~   84 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   84 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeE
Confidence            45689999999999999999999999999999998433  999999999999999999999999999994443

>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=5.5e-13  Score=127.26  Aligned_cols=81  Identities=11%  Similarity=0.117  Sum_probs=70.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEE-EEc----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~V-ri~----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ....+|||+|||.++|+++|+++|++||.|..+ .+.    +..+|||||+|.+.++|++||+ |||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            345799999999999999999999999998763 222    2357899999999999999999 9999999999999999


Q ss_pred             cCcchhh
Q 001991          433 RPGGARR  439 (985)
Q Consensus       433 ~~k~~Rr  439 (985)
                      .+++..+
T Consensus       102 ~~~~~~~  108 (124)
T 1wel_A          102 TKKGMLE  108 (124)
T ss_dssp             CHHHHHH
T ss_pred             CHHHHHH
Confidence            8766433

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.30  E-value=3.7e-12  Score=120.06  Aligned_cols=75  Identities=11%  Similarity=0.178  Sum_probs=68.3

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ...+|||+|||.++++++|+++|+.| .|..|+++.+    ++|||||+|.+.++|++|| .||+..|+|+.|.|..+.+
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            45699999999999999999999999 8999998743    5899999999999999999 5999999999999998865


Q ss_pred             c
Q 001991          435 G  435 (985)
Q Consensus       435 k  435 (985)
                      +
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            4

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.30  E-value=3.7e-12  Score=135.98  Aligned_cols=105  Identities=17%  Similarity=0.189  Sum_probs=78.9

Q ss_pred             cCcccccccccccccCCCCCCCcccccccceeeecCCCCC---------CHHHHHHHhhccCCEEEEEEcCCCCcEEEEE
Q 001991          333 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSV---------STEELHQIFGIYGEIREIRDTQHKHNHKFIE  403 (985)
Q Consensus       333 ng~~I~Gr~L~V~~a~pk~~~~~~~~~~~tLfV~NLp~sv---------TeedLrelFs~fG~I~~Vri~~~skGfaFVe  403 (985)
                      +...+.|+.....+..............++|||+||+..+         ++++|+++|++||+|.+|+++. .+|||||+
T Consensus       107 ~~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-~kG~AFV~  185 (240)
T 3u1l_A          107 EVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-SKNCGFVK  185 (240)
T ss_dssp             SSBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-GGTEEEEE
T ss_pred             cCcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-CCCEEEEE
Confidence            3344556655554443322222234567899999999998         7999999999999999999886 58999999


Q ss_pred             EcCHHHHHHHHHHhCCcee------------CCceEEEEeccCcchh
Q 001991          404 FYDIRAAETALRTLNRSDV------------AGKQIKLEASRPGGAR  438 (985)
Q Consensus       404 F~d~edA~kAI~~LNG~~I------------~Gr~IkV~~A~~k~~R  438 (985)
                      |.+.++|++|+++|+|..|            .|+.|.|.||+.+...
T Consensus       186 F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          186 FKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             ESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             eCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence            9999999999999999999            8999999999876543

>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=99.29  E-value=2e-12  Score=136.90  Aligned_cols=76  Identities=17%  Similarity=0.262  Sum_probs=70.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccC--cEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG--~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..++|||+|||.++|+++|+++|++||  +|..|++     ++++||||||+|.+.++|++||+.||++.|.|++|+|.+
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  9999976     678999999999999999999999999999999999999


Q ss_pred             cCC
Q 001991          347 SIP  349 (985)
Q Consensus       347 a~p  349 (985)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>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=99.29  E-value=1.9e-12  Score=115.82  Aligned_cols=79  Identities=22%  Similarity=0.449  Sum_probs=68.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      .++++|||+|||.++++++|+++|++||+|..|++...++|||||+|.+.++|++|+.  ....+.|++|.|.++.++..
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 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCCCC
Confidence            3579999999999999999999999999999999866789999999999999986542  13456899999999988765


Q ss_pred             C
Q 001991          353 P  353 (985)
Q Consensus       353 ~  353 (985)
                      .
T Consensus        81 ~   81 (88)
T 1wf0_A           81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.29  E-value=1.8e-12  Score=126.97  Aligned_cols=78  Identities=8%  Similarity=0.089  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCc---EEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~---I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      .....++|||+|||+++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++|++ +++..|.|+.|.
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            3456789999999999999999999999999   677654    47789999999999999999998 999999999999


Q ss_pred             ccccCC
Q 001991          344 IHYSIP  349 (985)
Q Consensus       344 V~~a~p  349 (985)
                      |.++.+
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            988753

>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=99.28  E-value=1.7e-12  Score=137.37  Aligned_cols=80  Identities=14%  Similarity=0.152  Sum_probs=72.1

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccC--CEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG--~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ..++|||+||+..+|+++|+++|++||  .|++|+|+.+     ++|||||+|.+.++|++||+.||+..|.|++|+|.+
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  9999998654     578999999999999999999999999999999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      ++++...
T Consensus       147 a~~~~~~  153 (229)
T 3q2s_C          147 VNKQFLS  153 (229)
T ss_dssp             CCHHHHH
T ss_pred             CCCCccc
Confidence            9876533

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.28  E-value=7.9e-12  Score=120.70  Aligned_cols=76  Identities=20%  Similarity=0.273  Sum_probs=68.0

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceE-EEEEeCCHHHHHHHHHHccCccccc--ccccccccCCCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIPKDN  352 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGf-AFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~pk~~  352 (985)
                      ..|||+||+..+++++|+++|++||+|..|++..+ .|| |||+|.+.++|++|++.|||..|.|  +.|+|.|+.++..
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            34679999999999999999999999999987433 486 9999999999999999999999987  6899999987754

>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=99.28  E-value=1.4e-12  Score=112.69  Aligned_cols=70  Identities=17%  Similarity=0.339  Sum_probs=64.9

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      +|||+|||.++++++|+++|++||.|..|++..+     ++|||||+|.+.++|++|++ +++..+.|++|+|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            6899999999999999999999999999988643     57899999999999999999 5999999999999875

>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=2.1e-12  Score=118.53  Aligned_cols=79  Identities=19%  Similarity=0.375  Sum_probs=71.3

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ....++|||+|||..+++++|+++|++||.|..|++..+    .+|||||+|.+.++|++|++  ++..+.|++|.|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            345679999999999999999999999999999998754    56899999999999999999  999999999999999


Q ss_pred             cCcch
Q 001991          433 RPGGA  437 (985)
Q Consensus       433 ~~k~~  437 (985)
                      .++..
T Consensus        84 ~~~~~   88 (102)
T 2xs2_A           84 IRKQN   88 (102)
T ss_dssp             EECC-
T ss_pred             CcCcc
Confidence            87653

>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=99.28  E-value=2.8e-12  Score=118.98  Aligned_cols=77  Identities=10%  Similarity=0.161  Sum_probs=68.6

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ....+|||+|||.++|+++|+++|++||.| +|+++.+    ++|||||+|.+.++|++||+ +|+..|+|+.|+|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            456799999999999999999999999955 8887643    47899999999999999995 89999999999999988


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      +.+
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            655

>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=99.28  E-value=9.7e-12  Score=128.25  Aligned_cols=113  Identities=13%  Similarity=0.178  Sum_probs=88.3

Q ss_pred             CHHHHHHHHHHc--cCcccccccccccccCCCCCCCc-----ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc
Q 001991          321 DIRAARNAMKAL--QNKPLRRRKLDIHYSIPKDNPSE-----KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT  393 (985)
Q Consensus       321 d~esA~kAi~~L--ng~~I~Gr~L~V~~a~pk~~~~~-----~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~  393 (985)
                      +.+.+..|++..  ....+.+....|.....+..+..     .....++|||+|||.++++++|+++|++||.|..|++.
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            567788888776  45556666666655422221111     23356799999999999999999999999999999987


Q ss_pred             C----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          394 Q----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       394 ~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .    ..+|||||+|.+.++|++|++.+ +..+.|++|.|.+++.
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4    35789999999999999999855 4599999999999765

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.28  E-value=5.2e-12  Score=128.65  Aligned_cols=80  Identities=25%  Similarity=0.446  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ...+.++|||+|||.++++++|+++|++||+|..|.+    ++.++|||||+|.+.++|++|++.|++..|.|++|.|.+
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            3456799999999999999999999999999999987    367899999999999999999999999999999999999


Q ss_pred             cCCC
Q 001991          347 SIPK  350 (985)
Q Consensus       347 a~pk  350 (985)
                      +.+.
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.25  E-value=9.7e-12  Score=126.62  Aligned_cols=79  Identities=16%  Similarity=0.273  Sum_probs=72.9

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...++|||+|||..+++++|+++|++||.|..|++..+    ++|||||+|.+.++|++|++.|||..|.|++|+|+++.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            34679999999999999999999999999999998754    57899999999999999999999999999999999998


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            644

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.25  E-value=5.3e-12  Score=119.02  Aligned_cols=75  Identities=7%  Similarity=0.176  Sum_probs=67.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ...++|||+|||.++|+++|+++|++| .|..|++    .++++|||||+|.+.++|++|+ .+++..|.|+.|.|..+.
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            345899999999999999999999999 8888876    4678999999999999999999 699999999999997764


Q ss_pred             C
Q 001991          349 P  349 (985)
Q Consensus       349 p  349 (985)
                      +
T Consensus        92 ~   92 (109)
T 2dnn_A           92 E   92 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=3.8e-12  Score=125.18  Aligned_cols=80  Identities=9%  Similarity=0.190  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .....++|||+|||.++|+++|+++|++|| |..|++    .++++|||||+|.+.++|++|| .+++..|.|+.|.|.+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            445678999999999999999999999999 668875    4678999999999999999999 7999999999999998


Q ss_pred             cCCCCC
Q 001991          347 SIPKDN  352 (985)
Q Consensus       347 a~pk~~  352 (985)
                      +.++..
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            876543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.23  E-value=3.2e-11  Score=112.88  Aligned_cols=77  Identities=17%  Similarity=0.162  Sum_probs=67.7

Q ss_pred             ccccceeeecCCC-----CCCHHHHHHHhhccCCEEEEEEcC------CCCcEEEEEEcCHHHHHHHHHHhCCceeCCce
Q 001991          358 ANQGTLVVFNLDS-----SVSTEELHQIFGIYGEIREIRDTQ------HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  426 (985)
Q Consensus       358 ~~~~tLfV~NLp~-----svTeedLrelFs~fG~I~~Vri~~------~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~  426 (985)
                      .+.++|+|.||..     +-++++|+++|++||.|.+|+++.      .++|||||+|.+.++|.+|++.|||+.+.||+
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            3567999999953     236899999999999999998864      35899999999999999999999999999999


Q ss_pred             EEEEeccC
Q 001991          427 IKLEASRP  434 (985)
Q Consensus       427 IkV~~A~~  434 (985)
                      |+|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999975

>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=1.1e-11  Score=119.90  Aligned_cols=77  Identities=14%  Similarity=0.207  Sum_probs=67.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEE--EEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIR--TIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~--sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      .....++|||+|||+++|+++|+++|++| .|.  .|++    .++++|||||+|.+.++|++|++ +++..|.|+.|.|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            34567899999999999999999999999 566  7765    47789999999999999999997 5789999999999


Q ss_pred             cccCC
Q 001991          345 HYSIP  349 (985)
Q Consensus       345 ~~a~p  349 (985)
                      .++.+
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=3.4e-12  Score=122.94  Aligned_cols=82  Identities=22%  Similarity=0.232  Sum_probs=70.6

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCE----EEEEEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEI----REIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I----~~Vri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ...+|||+|||.++|+++|+++|++||.|    ..|+++.    .++|||||+|.+.++|++||+. |+..|+|+.|.|.
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            45689999999999999999999999975    4676653    3578999999999999999995 9999999999999


Q ss_pred             eccCcchhhhh
Q 001991          431 ASRPGGARRFM  441 (985)
Q Consensus       431 ~A~~k~~Rrl~  441 (985)
                      .+.+++.++.+
T Consensus       101 ~a~~~e~~~~~  111 (123)
T 2dha_A          101 RSTAAEVQQVL  111 (123)
T ss_dssp             EECHHHHHHHH
T ss_pred             ECCHHHHHHHH
Confidence            99876655433

>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=8.9e-12  Score=120.64  Aligned_cols=77  Identities=25%  Similarity=0.273  Sum_probs=68.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEE--EEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIR--EIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~--~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ...++|||+|||.++|+++|+++|++| .|.  .|+++.+    ++|||||+|.+.++|++||+ +++..|+|+.|+|.+
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            346789999999999999999999999 676  8888743    58999999999999999999 588999999999999


Q ss_pred             ccCcc
Q 001991          432 SRPGG  436 (985)
Q Consensus       432 A~~k~  436 (985)
                      +.+++
T Consensus       118 a~~~e  122 (126)
T 2hgm_A          118 SSQEE  122 (126)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            87544

>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=5.3e-12  Score=121.62  Aligned_cols=76  Identities=18%  Similarity=0.231  Sum_probs=66.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcE----EEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDI----RTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I----~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ...++|||+|||+++|+++|+++|++||.|    ..|++    +++++|||||+|.+.++|++|++. +++.|.|+.|.|
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            457899999999999999999999999975    35543    678899999999999999999975 999999999999


Q ss_pred             cccCC
Q 001991          345 HYSIP  349 (985)
Q Consensus       345 ~~a~p  349 (985)
                      ..+.+
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.20  E-value=1.7e-11  Score=130.93  Aligned_cols=81  Identities=21%  Similarity=0.380  Sum_probs=71.6

Q ss_pred             CCCCcEEEEecCCCCC---------CHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccc-----
Q 001991          272 EHPSRTLFVRNINSNV---------EDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL-----  337 (985)
Q Consensus       272 e~~srtLfVgNLP~~v---------TEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I-----  337 (985)
                      ....++|||+||+..+         ++++|+++|++||+|.+|++ ..++|||||+|.+.++|+.|+++|+|+.|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v-~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY-VESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEE-EGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEE-ECCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            4578999999999998         79999999999999999998 46799999999999999999999999999     


Q ss_pred             -------ccccccccccCCCCCC
Q 001991          338 -------RRRKLDIHYSIPKDNP  353 (985)
Q Consensus       338 -------~Gr~L~V~~a~pk~~~  353 (985)
                             .|+.|.|.|+..+.++
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

>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=5.7e-11  Score=111.52  Aligned_cols=83  Identities=16%  Similarity=0.276  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEecCCCCCC-----------HHHHHHhhcccCcEEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCcccc
Q 001991          271 GEHPSRTLFVRNINSNVE-----------DSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLR  338 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vT-----------EedLrelFs~fG~I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~  338 (985)
                      ...++++|+|+||....+           +++|+++|++||+|..|.+ ...++|||||+|.+.++|++|++.|||..|.
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            556889999999954332           6899999999999999976 4557999999999999999999999999999


Q ss_pred             cccccccccCCCCCC
Q 001991          339 RRKLDIHYSIPKDNP  353 (985)
Q Consensus       339 Gr~L~V~~a~pk~~~  353 (985)
                      |++|.|.++.++...
T Consensus        91 gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           91 GRQITAQAWDGTTDY  105 (112)
T ss_dssp             TEECEEEECCSCCCS
T ss_pred             CcEEEEEEeCCCCCc
Confidence            999999999876543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=2.9e-11  Score=113.76  Aligned_cols=72  Identities=17%  Similarity=0.322  Sum_probs=61.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----c---cccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----A---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----t---gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ...++|||+|||+++++++|+++|++||+|. +.+     +   ++++|||||+|.+.++|++|++.|++  +.|+.+.+
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 554     2   57899999999999999999998843  66666666


Q ss_pred             ccc
Q 001991          345 HYS  347 (985)
Q Consensus       345 ~~a  347 (985)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            544

>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=99.19  E-value=6.1e-11  Score=111.30  Aligned_cols=80  Identities=20%  Similarity=0.273  Sum_probs=69.5

Q ss_pred             cccccceeeecCCCCCC-----------HHHHHHHhhccCCEEEEEEc-CCCCcEEEEEEcCHHHHHHHHHHhCCceeCC
Q 001991          357 DANQGTLVVFNLDSSVS-----------TEELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAG  424 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svT-----------eedLrelFs~fG~I~~Vri~-~~skGfaFVeF~d~edA~kAI~~LNG~~I~G  424 (985)
                      ....++|+|.||....+           +++|+++|++||.|.+|.+. +.++|||||+|.+.++|++|++.|||..|.|
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   91 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   91 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            34678999999954432           58999999999999999764 3468999999999999999999999999999


Q ss_pred             ceEEEEeccCcc
Q 001991          425 KQIKLEASRPGG  436 (985)
Q Consensus       425 r~IkV~~A~~k~  436 (985)
                      ++|+|.++.++.
T Consensus        92 r~l~v~~a~~~~  103 (112)
T 2dit_A           92 RQITAQAWDGTT  103 (112)
T ss_dssp             EECEEEECCSCC
T ss_pred             cEEEEEEeCCCC
Confidence            999999998765

>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=99.17  E-value=2.9e-11  Score=139.53  Aligned_cols=80  Identities=28%  Similarity=0.449  Sum_probs=74.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..+.++|||+|||..+|+++|+++|++||.|..|.+     +++++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
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            456789999999999999999999999999999976     577899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 001991          347 SIPKD  351 (985)
Q Consensus       347 a~pk~  351 (985)
                      +.++.
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            98654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=4.6e-11  Score=112.41  Aligned_cols=77  Identities=13%  Similarity=0.178  Sum_probs=65.9

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC--------CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--------HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~--------~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ..++|||+|||.++++++|+++|++||.|. +.++.        .++|||||+|.+.++|++|++.|+  .+.|+.|.+.
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            467999999999999999999999999999 76653        458999999999999999999994  4788888888


Q ss_pred             eccCcchh
Q 001991          431 ASRPGGAR  438 (985)
Q Consensus       431 ~A~~k~~R  438 (985)
                      .+.+...+
T Consensus        84 ~~~~~~~~   91 (114)
T 2dnl_A           84 SSPTIKDK   91 (114)
T ss_dssp             CCSSSCSE
T ss_pred             cCCCcCCC
Confidence            76654433

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.14  E-value=8.1e-11  Score=110.14  Aligned_cols=77  Identities=14%  Similarity=0.228  Sum_probs=68.0

Q ss_pred             CCCcEEEEecCCC-----CCCHHHHHHhhcccCcEEEEEec------cccceEEEEEeCCHHHHHHHHHHccCccccccc
Q 001991          273 HPSRTLFVRNINS-----NVEDSELKALFEQFGDIRTIYTA------CKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  341 (985)
Q Consensus       273 ~~srtLfVgNLP~-----~vTEedLrelFs~fG~I~sVkit------gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~  341 (985)
                      .++++|+|+||..     +-++++|++.|++||+|.+|++.      ++++|||||+|.+.++|.+|++.|||+.+.|+.
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            5789999999963     23789999999999999999761      467999999999999999999999999999999


Q ss_pred             ccccccCC
Q 001991          342 LDIHYSIP  349 (985)
Q Consensus       342 L~V~~a~p  349 (985)
                      |.|.++.+
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999853

>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=99.13  E-value=9.8e-11  Score=109.51  Aligned_cols=78  Identities=17%  Similarity=0.308  Sum_probs=67.4

Q ss_pred             ccccceeeecC--CCCCC--------HHHHHHHhhccCCEEEEEEcCC-------CCcEEEEEEcCHHHHHHHHHHhCCc
Q 001991          358 ANQGTLVVFNL--DSSVS--------TEELHQIFGIYGEIREIRDTQH-------KHNHKFIEFYDIRAAETALRTLNRS  420 (985)
Q Consensus       358 ~~~~tLfV~NL--p~svT--------eedLrelFs~fG~I~~Vri~~~-------skGfaFVeF~d~edA~kAI~~LNG~  420 (985)
                      .+.+.|.|.|+  +..+.        +++|+++|++||.|.+|+++.+       ++|+|||+|.+.++|.+|++.|||+
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            35678999998  33443        3799999999999999998753       4799999999999999999999999


Q ss_pred             eeCCceEEEEeccCc
Q 001991          421 DVAGKQIKLEASRPG  435 (985)
Q Consensus       421 ~I~Gr~IkV~~A~~k  435 (985)
                      .++||+|+|.++...
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998653

>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=99.08  E-value=1.6e-10  Score=119.10  Aligned_cols=75  Identities=13%  Similarity=0.319  Sum_probs=67.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ..++|||+|||.++++++|+++|++||+|..|++    ++.++|||||+|.+.++|++|++.+ +..+.|++|.|.++..
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            4589999999999999999999999999999976    4678999999999999999999754 5689999999987653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.05  E-value=9.4e-11  Score=113.69  Aligned_cols=72  Identities=18%  Similarity=0.291  Sum_probs=64.4

Q ss_pred             cEEEEecC----CCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCC----HHH----HHHHHH--HccCcc
Q 001991          276 RTLFVRNI----NSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYD----IRA----ARNAMK--ALQNKP  336 (985)
Q Consensus       276 rtLfVgNL----P~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d----~es----A~kAi~--~Lng~~  336 (985)
                      ++|||+||    |+.+++++|+++|+.||+|.+|.+     ++.++|||||+|.+    +++    |.+|++  .++|..
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    999999999999999999999975     78999999999996    333    889988  789999


Q ss_pred             ccccccccccc
Q 001991          337 LRRRKLDIHYS  347 (985)
Q Consensus       337 I~Gr~L~V~~a  347 (985)
                      |.|++|+|.+.
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            99999999865

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.05  E-value=2.8e-10  Score=105.87  Aligned_cols=66  Identities=20%  Similarity=0.281  Sum_probs=60.0

Q ss_pred             CCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          370 SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       370 ~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ..+++++|+++|++||+|.+|++++.++|||||+|.+.++|++|++.+++  +.|++|+|.|++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            57899999999999999999999988899999999999999999997544  6899999999987653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.03  E-value=1.6e-10  Score=112.14  Aligned_cols=80  Identities=16%  Similarity=0.254  Sum_probs=68.2

Q ss_pred             cceeeecC----CCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcC----HHH----HHHHHH--HhCCce
Q 001991          361 GTLVVFNL----DSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYD----IRA----AETALR--TLNRSD  421 (985)
Q Consensus       361 ~tLfV~NL----p~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d----~ed----A~kAI~--~LNG~~  421 (985)
                      ..|||+||    |+.+++++|+++|+.||+|.+|+++.+     ++|||||+|.|    +++    |.+|+.  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    999999999999999999999988644     58999999996    433    889988  789999


Q ss_pred             eCCceEEEEeccCcchhhh
Q 001991          422 VAGKQIKLEASRPGGARRF  440 (985)
Q Consensus       422 I~Gr~IkV~~A~~k~~Rrl  440 (985)
                      |+|++|+|.+-+.....++
T Consensus        83 I~Gr~irV~ln~~g~~~~~  101 (136)
T 2j8a_A           83 IMGFKFEVILNKHSILNNI  101 (136)
T ss_dssp             ETTEEEEEEECCTTHHHHH
T ss_pred             ecCcEEEEEECcccHHHHH
Confidence            9999999999876654443

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.03  E-value=1.2e-10  Score=108.73  Aligned_cols=68  Identities=28%  Similarity=0.376  Sum_probs=58.7

Q ss_pred             eecCCCCCCHHHHHHHh------------hccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEE
Q 001991          365 VFNLDSSVSTEELHQIF------------GIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  428 (985)
Q Consensus       365 V~NLp~svTeedLrelF------------s~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~Ik  428 (985)
                      +.+|+..+++++|++.|            ++||.|.+|++..+    ++|||||+|.+.++|++|++.|||+.+.||+|+
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            45666667777666555            99999999999865    489999999999999999999999999999999


Q ss_pred             EEec
Q 001991          429 LEAS  432 (985)
Q Consensus       429 V~~A  432 (985)
                      |.|+
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=99.01  E-value=5.4e-10  Score=106.85  Aligned_cols=76  Identities=20%  Similarity=0.270  Sum_probs=65.8

Q ss_pred             cccceeeecCC--CCC---CHHHHHHHhhccCCEEEEEEcCC---------CCcEEEEEEcCHHHHHHHHHHhCCceeCC
Q 001991          359 NQGTLVVFNLD--SSV---STEELHQIFGIYGEIREIRDTQH---------KHNHKFIEFYDIRAAETALRTLNRSDVAG  424 (985)
Q Consensus       359 ~~~tLfV~NLp--~sv---TeedLrelFs~fG~I~~Vri~~~---------skGfaFVeF~d~edA~kAI~~LNG~~I~G  424 (985)
                      +.++|+|.|+-  .++   -+++|++.|++||+|.+|+|+.+         .+|++||+|.+.++|.+|++.|||+.++|
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            56789999983  222   36899999999999999988643         24899999999999999999999999999


Q ss_pred             ceEEEEeccC
Q 001991          425 KQIKLEASRP  434 (985)
Q Consensus       425 r~IkV~~A~~  434 (985)
                      |+|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>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=98.99  E-value=6.2e-10  Score=104.04  Aligned_cols=76  Identities=16%  Similarity=0.347  Sum_probs=66.6

Q ss_pred             CCCcEEEEecC--CCCCC--------HHHHHHhhcccCcEEEEEec-------cccceEEEEEeCCHHHHHHHHHHccCc
Q 001991          273 HPSRTLFVRNI--NSNVE--------DSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAMKALQNK  335 (985)
Q Consensus       273 ~~srtLfVgNL--P~~vT--------EedLrelFs~fG~I~sVkit-------gksrGfAFV~F~d~esA~kAi~~Lng~  335 (985)
                      .|++.|.|.|+  |.++.        +++|++.|++||+|.+|++.       ++++|+|||+|.+.++|.+|++.|||+
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        36899999999999999872       246899999999999999999999999


Q ss_pred             ccccccccccccC
Q 001991          336 PLRRRKLDIHYSI  348 (985)
Q Consensus       336 ~I~Gr~L~V~~a~  348 (985)
                      .+.||+|.|.|+.
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            9999999999875

>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=7.1e-10  Score=124.14  Aligned_cols=76  Identities=22%  Similarity=0.304  Sum_probs=67.0

Q ss_pred             cccccceeeec--CCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeC---Cc--eEEE
Q 001991          357 DANQGTLVVFN--LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA---GK--QIKL  429 (985)
Q Consensus       357 ~~~~~tLfV~N--Lp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~---Gr--~IkV  429 (985)
                      ..+..+|||+|  |+..+|+++|+++|++||+|.+|.+.+ .||||||+|.+.++|++|++.|||+++-   |+  .|+|
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~   93 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEE
Confidence            34567999999  578999999999999999999998765 6899999999999999999999999882   44  6888


Q ss_pred             Eecc
Q 001991          430 EASR  433 (985)
Q Consensus       430 ~~A~  433 (985)
                      .|+.
T Consensus        94 ~~~~   97 (345)
T 3tht_A           94 NFVE   97 (345)
T ss_dssp             EECS
T ss_pred             EEee
Confidence            8874

>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=98.98  E-value=9.8e-10  Score=104.49  Aligned_cols=79  Identities=15%  Similarity=0.118  Sum_probs=67.1

Q ss_pred             ccccceeeecCCC--CC--------CHHHHHHHhhccCCEEEEEEcCC-CCcEEEEEEcCHHHHHHHHHHhCCceeCCce
Q 001991          358 ANQGTLVVFNLDS--SV--------STEELHQIFGIYGEIREIRDTQH-KHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  426 (985)
Q Consensus       358 ~~~~tLfV~NLp~--sv--------TeedLrelFs~fG~I~~Vri~~~-skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~  426 (985)
                      .+.++|.|.|+=.  +.        -+++|+++|++||.|.+|.+..+ .+|++||+|.+.++|.+|++.|||+.++||+
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            3466888998832  21        24689999999999999999766 4899999999999999999999999999999


Q ss_pred             EEEEeccCcc
Q 001991          427 IKLEASRPGG  436 (985)
Q Consensus       427 IkV~~A~~k~  436 (985)
                      |+|.++....
T Consensus        85 i~v~~~~~~~   94 (114)
T 3s6e_A           85 ITAAYVPLPT   94 (114)
T ss_dssp             CEEEEECHHH
T ss_pred             EEEEEEcHHH
Confidence            9999997543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.95  E-value=3.1e-09  Score=98.73  Aligned_cols=66  Identities=17%  Similarity=0.306  Sum_probs=59.5

Q ss_pred             CCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          285 SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       285 ~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      .++++++|+++|++||+|..|++.++++|||||+|.+.++|++|++.+++  +.+++|.|.|+.++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            56999999999999999999998788999999999999999999987554  6799999999977653

>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=98.95  E-value=8e-10  Score=123.72  Aligned_cols=76  Identities=16%  Similarity=0.312  Sum_probs=66.6

Q ss_pred             CCCCCcEEEEec--CCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc---cc--ccc
Q 001991          271 GEHPSRTLFVRN--INSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR---RR--KLD  343 (985)
Q Consensus       271 ~e~~srtLfVgN--LP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~---Gr--~L~  343 (985)
                      ...++++|||+|  |+..+||++|+++|++||+|.+|.+ ...||||||+|.+.++|++|++.|||+.+.   |+  .|+
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 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEEC-CTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEE-eCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            456899999999  5789999999999999999999988 347899999999999999999999999873   34  577


Q ss_pred             cccc
Q 001991          344 IHYS  347 (985)
Q Consensus       344 V~~a  347 (985)
                      |.|.
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=98.91  E-value=4.3e-10  Score=104.92  Aligned_cols=68  Identities=19%  Similarity=0.347  Sum_probs=59.8

Q ss_pred             EecCCCCCCHHHHHHhh------------cccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          280 VRNINSNVEDSELKALF------------EQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       280 VgNLP~~vTEedLrelF------------s~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      +.+|+..+++++|++.|            ++||+|.+|++    .++++|||||+|.+.++|++|++.|||+.+.|++|.
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            56777778888877766            99999999987    345799999999999999999999999999999999


Q ss_pred             cccc
Q 001991          344 IHYS  347 (985)
Q Consensus       344 V~~a  347 (985)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9886

>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=98.83  E-value=7.8e-09  Score=94.60  Aligned_cols=85  Identities=20%  Similarity=0.335  Sum_probs=73.8

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcceEE-Eecccccccc-eeEEEEEecCCchhhHHHHHHhcCCcccCCCCcc-E
Q 001991          811 TTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFI-YLPIDFKNKC-NVGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEK-V  887 (985)
Q Consensus       811 TTvMirNIPnk~t~~~L~~~id~~~~g~yDF~-YlpiDf~~~~-N~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~K-~  887 (985)
                      |.|+||++|..+|++.++++|...  .++||+ |.|-+...+- -.+.|||||++++++..|.+.|+|+.|..-+... .
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~--~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~   79 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC--CCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCc--ccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEee
Confidence            789999999999999999999875  478988 5788877664 4689999999999999999999999999765444 8


Q ss_pred             EEEEeecccC
Q 001991          888 ASLAYARIQG  897 (985)
Q Consensus       888 ~~v~yA~iQG  897 (985)
                      +.|.||-.|-
T Consensus        80 a~VE~AP~qk   89 (91)
T 1uw4_A           80 AIVEFAPFQK   89 (91)
T ss_dssp             CEEEECSSCC
T ss_pred             eEEEEcCCCc
Confidence            8999998873

>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=98.82  E-value=6.4e-09  Score=99.44  Aligned_cols=76  Identities=14%  Similarity=0.228  Sum_probs=65.7

Q ss_pred             CCCcEEEEecCCC--CC---CHHHHHHhhcccCcEEEEEec---------cccceEEEEEeCCHHHHHHHHHHccCcccc
Q 001991          273 HPSRTLFVRNINS--NV---EDSELKALFEQFGDIRTIYTA---------CKHRGFVMISYYDIRAARNAMKALQNKPLR  338 (985)
Q Consensus       273 ~~srtLfVgNLP~--~v---TEedLrelFs~fG~I~sVkit---------gksrGfAFV~F~d~esA~kAi~~Lng~~I~  338 (985)
                      .++++|+|+|+-.  ++   -+++|++.|++||+|.+|++.         ++.+|+|||+|.+.++|.+|++.|||+.+.
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            3789999999942  22   368999999999999999761         245799999999999999999999999999


Q ss_pred             cccccccccC
Q 001991          339 RRKLDIHYSI  348 (985)
Q Consensus       339 Gr~L~V~~a~  348 (985)
                      ||.|.|.|+.
T Consensus        98 GR~i~v~~~~  107 (118)
T 3ue2_A           98 GRKVVAEVYD  107 (118)
T ss_dssp             TEECEEEEEC
T ss_pred             CcEEEEEEcC
Confidence            9999999874

>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=98.78  E-value=1e-08  Score=97.54  Aligned_cols=77  Identities=17%  Similarity=0.218  Sum_probs=65.5

Q ss_pred             CCCCcEEEEecCCCCC----------CHHHHHHhhcccCcEEEEEec-cccceEEEEEeCCHHHHHHHHHHccCcccccc
Q 001991          272 EHPSRTLFVRNINSNV----------EDSELKALFEQFGDIRTIYTA-CKHRGFVMISYYDIRAARNAMKALQNKPLRRR  340 (985)
Q Consensus       272 e~~srtLfVgNLP~~v----------TEedLrelFs~fG~I~sVkit-gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr  340 (985)
                      ..+++.|.++|+=..-          -+++|++.|++||.|.+|.+. ...+|+|||+|.+.++|++|++.|||+.+.||
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            3578899999984322          135789999999999999883 33589999999999999999999999999999


Q ss_pred             cccccccC
Q 001991          341 KLDIHYSI  348 (985)
Q Consensus       341 ~L~V~~a~  348 (985)
                      .|.|.|+.
T Consensus        84 ~i~v~~~~   91 (114)
T 3s6e_A           84 MITAAYVP   91 (114)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEEc
Confidence            99999874

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=2e-08  Score=91.70  Aligned_cols=75  Identities=27%  Similarity=0.402  Sum_probs=64.4

Q ss_pred             cccccceeeecCCC----CCCH----HHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEE
Q 001991          357 DANQGTLVVFNLDS----SVST----EELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  428 (985)
Q Consensus       357 ~~~~~tLfV~NLp~----svTe----edLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~Ik  428 (985)
                      .++..||+|.-.+.    .+-+    .+|.+.|.+||+|..+++..+.   +||+|.+.++|.+|++ |||..++||.|+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~---~fVtF~d~~sAlaAi~-mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK---MWVTFLEGSSALNVLS-LNGKELLNRTIT   79 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS---EEEEESSHHHHHHGGG-GTTCEETTEEEE
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC---EEEEECChHHHHHHHh-cCCeEeCCeEEE
Confidence            34567898888762    3333    6799999999999999998754   9999999999999999 999999999999


Q ss_pred             EEeccCc
Q 001991          429 LEASRPG  435 (985)
Q Consensus       429 V~~A~~k  435 (985)
                      |.++++.
T Consensus        80 V~lkt~d   86 (91)
T 2dnr_A           80 IALKSPS   86 (91)
T ss_dssp             EEECCCS
T ss_pred             EEeCCCC
Confidence            9998864

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.65  E-value=4.9e-08  Score=93.87  Aligned_cols=81  Identities=19%  Similarity=0.158  Sum_probs=71.8

Q ss_pred             ccccceeeecCCCC-CCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcC-HHHHHHHHHHhC--CceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYD-IRAAETALRTLN--RSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~s-vTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d-~edA~kAI~~LN--G~~I~Gr~IkV~~A~  433 (985)
                      .....|+|.||+.. ++.++|+++|++||+|..|.+..+. ..|||+|.+ .++|.+|++.||  +..|.|..++++...
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            45678999999999 9999999999999999999998764 479999999 899999999995  678999999999887


Q ss_pred             Ccchhh
Q 001991          434 PGGARR  439 (985)
Q Consensus       434 ~k~~Rr  439 (985)
                      -.+++.
T Consensus        95 GeeE~~  100 (121)
T 1owx_A           95 GEVEKE  100 (121)
T ss_dssp             HHHHHH
T ss_pred             CHHHHH
Confidence            666665

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=98.62  E-value=1.5e-08  Score=93.52  Aligned_cols=84  Identities=20%  Similarity=0.356  Sum_probs=72.6

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcceEE-Eecccccccce-eEEEEEecCCchhhHHHHHHhcCCcccCCCCcc-E
Q 001991          811 TTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFI-YLPIDFKNKCN-VGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEK-V  887 (985)
Q Consensus       811 TTvMirNIPnk~t~~~L~~~id~~~~g~yDF~-YlpiDf~~~~N-~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~K-~  887 (985)
                      -.|+||++|+.+|++.+++.|+....  .||+ |.|-|...+-+ ...|||||++++++..|.+.|+|+.|..-+... .
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            46999999999999999999987544  5777 68888877655 588999999999999999999999999776555 8


Q ss_pred             EEEEeeccc
Q 001991          888 ASLAYARIQ  896 (985)
Q Consensus       888 ~~v~yA~iQ  896 (985)
                      +.|.||..|
T Consensus        88 a~VE~APyq   96 (97)
T 2l08_A           88 AVVEFAPFQ   96 (97)
T ss_dssp             EEEEECCCC
T ss_pred             eEEEecCCC
Confidence            999999887

>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=98.46  E-value=1.6e-07  Score=86.26  Aligned_cols=74  Identities=26%  Similarity=0.355  Sum_probs=63.4

Q ss_pred             cccccceeeecCCCC-----CCH----HHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          357 DANQGTLVVFNLDSS-----VST----EELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       357 ~~~~~tLfV~NLp~s-----vTe----edLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                      .++..||+|.-++.+     +-+    .+|.+.|.+||+|..+++..+.   +||+|.+.++|.+||+ |||.+++||.|
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---~fVtF~d~~sAl~AI~-ldG~~v~Gr~L   87 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---MLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---EEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---EEEEEcChHHHHHHHh-cCCeeeCCeEE
Confidence            456789999988743     222    6699999999999999998764   9999999999999999 99999999999


Q ss_pred             EEEeccC
Q 001991          428 KLEASRP  434 (985)
Q Consensus       428 kV~~A~~  434 (985)
                      +|.+..+
T Consensus        88 ~V~~k~~   94 (95)
T 1ufw_A           88 KISGPSS   94 (95)
T ss_dssp             EEECCCC
T ss_pred             EEeccCC
Confidence            9987654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.38  E-value=1.1e-06  Score=84.56  Aligned_cols=75  Identities=19%  Similarity=0.186  Sum_probs=63.8

Q ss_pred             CCCCCcEEEEecCCCC-CCHHHHHHhhcccCcEEEEEeccccceEEEEEeCC-HHHHHHHHHHcc--Ccccccccccccc
Q 001991          271 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYD-IRAARNAMKALQ--NKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~-vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d-~esA~kAi~~Ln--g~~I~Gr~L~V~~  346 (985)
                      .-.+.+.|||+||+.+ +++++|+++|++||+|..|.+ ......|||.|.+ .++|.+|++.++  +..|.|..+.+..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~-~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC-CTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEE-ecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            4557899999999999 999999999999999999988 2333479999999 899999999985  6778887766654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.34  E-value=4.9e-07  Score=82.51  Aligned_cols=74  Identities=26%  Similarity=0.344  Sum_probs=61.8

Q ss_pred             CCCcEEEEecCCC----CCCH----HHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          273 HPSRTLFVRNINS----NVED----SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       273 ~~srtLfVgNLP~----~vTE----edLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      .+..||+|.-.+.    ++-+    .+|.+.|.+||+|..+++-.   +.+||+|.+.++|.+|++ |+|..+.||.|+|
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            3667899988772    3434    67889999999999999832   339999999999999997 9999999999999


Q ss_pred             cccCCC
Q 001991          345 HYSIPK  350 (985)
Q Consensus       345 ~~a~pk  350 (985)
                      +++.|.
T Consensus        81 ~lkt~d   86 (91)
T 2dnr_A           81 ALKSPS   86 (91)
T ss_dssp             EECCCS
T ss_pred             EeCCCC
Confidence            988753

>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=98.34  E-value=5.6e-07  Score=93.65  Aligned_cols=64  Identities=19%  Similarity=0.225  Sum_probs=57.5

Q ss_pred             CCCHHHHHHHhhccCCEEEEEEc----C-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          371 SVSTEELHQIFGIYGEIREIRDT----Q-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       371 svTeedLrelFs~fG~I~~Vri~----~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .-.+++|++.|++||.|.+|.+.    .     ..+|++||+|.+.++|.+|++.|||+.++||.|.|.++..
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            34678999999999999999885    2     3578999999999999999999999999999999999864

>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=98.08  E-value=4.2e-06  Score=87.04  Aligned_cols=62  Identities=13%  Similarity=0.155  Sum_probs=56.2

Q ss_pred             CCHHHHHHhhcccCcEEEEEe---------ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          287 VEDSELKALFEQFGDIRTIYT---------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       287 vTEedLrelFs~fG~I~sVki---------tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      -.+++|++.|++||+|.++.+         ++..+|++||+|.+.++|++|++.|||+.+.||.|.+.|..
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            356899999999999999976         22788999999999999999999999999999999999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.03  E-value=1.2e-05  Score=75.39  Aligned_cols=72  Identities=28%  Similarity=0.301  Sum_probs=66.6

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhcc-----CCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIY-----GEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~f-----G~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ..++|-+.|||+.+++..|+.+.++|     |.|+.|.+.++ -+-|+|+|.|...|.+|.-+|+|.+|.|++|+|.-
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-CCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            36799999999999999999999999     99999998887 44599999999999999999999999999999964

>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=98.01  E-value=5.3e-06  Score=76.19  Aligned_cols=72  Identities=14%  Similarity=0.204  Sum_probs=60.2

Q ss_pred             CCCcEEEEecCCCC-----CCH----HHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          273 HPSRTLFVRNINSN-----VED----SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       273 ~~srtLfVgNLP~~-----vTE----edLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      .|..||+|.-++..     +-+    .+|.+.|.+||+|..+++....   +||+|.+.++|.+||+ |+|..+.||.|+
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            47789999988753     323    5688999999999999872222   9999999999999997 999999999999


Q ss_pred             ccccC
Q 001991          344 IHYSI  348 (985)
Q Consensus       344 V~~a~  348 (985)
                      |++..
T Consensus        89 V~~k~   93 (95)
T 1ufw_A           89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EeccC
Confidence            98754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.30  E-value=0.0016  Score=60.61  Aligned_cols=89  Identities=17%  Similarity=0.206  Sum_probs=73.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcc-----cCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQ-----FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~-----fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ...++|.|.|||+.++++.|.-+|+.     =|+|..+....   +-|+|+|.+.+.|++.++ .....|.+.+|.|...
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~P~   81 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLA-QADHELHGAQLSLRPA   81 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEEEC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhc-CCcceecCeEEEEEcC
Confidence            34589999999999999999999987     26899998744   789999999999999994 4467888888988665


Q ss_pred             CCCCCCCcccccccceeeecCCCCCC
Q 001991          348 IPKDNPSEKDANQGTLVVFNLDSSVS  373 (985)
Q Consensus       348 ~pk~~~~~~~~~~~tLfV~NLp~svT  373 (985)
                      .++        ...+|++.+|++.++
T Consensus        82 ~~~--------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           82 PPR--------APARLLLQGLPPGTS   99 (104)
T ss_dssp             CCC--------CCCCCCCCSCCCCCC
T ss_pred             CCC--------CcceEeeecCCCCCC
Confidence            443        345899999998775

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.16  E-value=0.00054  Score=64.43  Aligned_cols=72  Identities=14%  Similarity=0.171  Sum_probs=64.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhccc-----CcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQF-----GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~f-----G~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...++|-+-|||..++++.|+.+.+++     |.|+.+.+. ...+=|+|+|.|...|-+|.-.|+|.+|.|++|++.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~-pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLV-SDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEE-TTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEe-cCCCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            346899999999999999999999999     999999883 344569999999999999998999999999999884

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.81  E-value=0.004  Score=58.01  Aligned_cols=77  Identities=21%  Similarity=0.233  Sum_probs=66.1

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhc-----cCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGI-----YGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~-----fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...+|.|.|||+.++++.|.-.|+.     =|+|..|...+   +-|+|+|.+.+.|++.++ -....|.+.+|.|....
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---CGGVLTFREPADAERVLA-QADHELHGAQLSLRPAP   82 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEEECC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhc-CCcceecCeEEEEEcCC
Confidence            3568999999999999999999987     26899998765   789999999999999987 33678899999999988


Q ss_pred             Ccchhh
Q 001991          434 PGGARR  439 (985)
Q Consensus       434 ~k~~Rr  439 (985)
                      ++..++
T Consensus        83 ~~~~~r   88 (104)
T 2dhx_A           83 PRAPAR   88 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCcce
Confidence            877666

>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=96.76  E-value=0.0013  Score=61.46  Aligned_cols=76  Identities=18%  Similarity=0.233  Sum_probs=63.8

Q ss_pred             ccceeeecCCCCC-C----HHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSV-S----TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~sv-T----eedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .++|+|.||+.++ .    .+.++++|..|+++......+.-+ -..|.|.++++|.+|-..|++..+.|++|+|-++++
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-EEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            3589999998866 2    367899999999988876655433 468999999999999999999999999999999985


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      -.
T Consensus        84 ~~   85 (104)
T 1wey_A           84 LH   85 (104)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.46  E-value=0.0097  Score=56.89  Aligned_cols=76  Identities=16%  Similarity=0.145  Sum_probs=63.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCC-ceEEEEeccCcc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG-KQIKLEASRPGG  436 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~G-r~IkV~~A~~k~  436 (985)
                      .....|.|.+.|+.. ...+.+.|++||+|.+... .....+-.|+|.+..+|++||. .||..|+| -.|-|.+...+.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~d~~   98 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   98 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECCCHH
Confidence            456789999999985 5678889999999999876 4457899999999999999999 79999984 778888765443

>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=96.17  E-value=0.0051  Score=57.41  Aligned_cols=76  Identities=16%  Similarity=0.202  Sum_probs=62.8

Q ss_pred             CcEEEEecCCCCC-CH----HHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNV-ED----SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~v-TE----edLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .++|+|.||+.+| ..    +.++++|..|+++.....-. +=.-..|.|.+.++|.+|-..|++..+.|++|+|-|+++
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lk-SFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecC-cceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            4789999999876 32    56789999999988876523 333568999999999999999999999999999999985


Q ss_pred             CC
Q 001991          350 KD  351 (985)
Q Consensus       350 k~  351 (985)
                      ..
T Consensus        84 ~~   85 (104)
T 1wey_A           84 LH   85 (104)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=95.15  E-value=0.049  Score=49.72  Aligned_cols=65  Identities=5%  Similarity=0.051  Sum_probs=53.4

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-ccc------cceEEEEEeCCHHHHHHHHHHccCcccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACK------HRGFVMISYYDIRAARNAMKALQNKPLRRR  340 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-tgk------srGfAFV~F~d~esA~kAi~~Lng~~I~Gr  340 (985)
                      ++|.|++||+.+||+++.+.++.+.++..... .|+      .-.-|||.|.+.+++....+.++|..+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            57999999999999999999999987765532 222      234799999999999999999999887643

>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=94.34  E-value=0.092  Score=48.49  Aligned_cols=56  Identities=20%  Similarity=0.306  Sum_probs=46.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHcc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ  333 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Ln  333 (985)
                      ..+.++| ++|+.+...||.++|+.||.|.--.+   ....|||.|.+++.|..|+..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            3456667 99999999999999999996554444   34589999999999999998764

>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=94.18  E-value=0.099  Score=49.96  Aligned_cols=71  Identities=15%  Similarity=0.169  Sum_probs=57.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccc-ccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR-RKLDIHY  346 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~G-r~L~V~~  346 (985)
                      ...+-|.|-+.|+.. ...|.+.|++||+|..... .....+..|.|.+..+|++||. .||+.|.| -.|-|..
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            346889999999974 6778889999999999887 3456799999999999999995 79998875 4444443

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.98  E-value=0.04  Score=53.47  Aligned_cols=73  Identities=16%  Similarity=0.190  Sum_probs=57.4

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEE-EEEc----------------CC--CCcEEEEEEcCHHHHHHHHHHhCCc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRDT----------------QH--KHNHKFIEFYDIRAAETALRTLNRS  420 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~-Vri~----------------~~--skGfaFVeF~d~edA~kAI~~LNG~  420 (985)
                      ...|.|.+.|++.+ ..+.+.|++||.|.+ +...                +.  ..++..|+|++..+|.+||. .||.
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            34688889977765 456678999999977 2111                11  35688999999999999999 8999


Q ss_pred             eeCCceEEEEeccC
Q 001991          421 DVAGKQIKLEASRP  434 (985)
Q Consensus       421 ~I~Gr~IkV~~A~~  434 (985)
                      .|+|..|-|.+..+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999999999863

>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=93.09  E-value=0.081  Score=48.96  Aligned_cols=54  Identities=20%  Similarity=0.327  Sum_probs=44.7

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHcc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ  333 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Ln  333 (985)
                      +.++| ++|+.+.-.||.++|+.||.|.--.+   .-..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEE---ETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            45566 99999999999999999995554444   34589999999999999998765

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.39  E-value=0.058  Score=62.57  Aligned_cols=56  Identities=11%  Similarity=0.282  Sum_probs=43.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHH
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK  330 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~  330 (985)
                      ..|+|||. .|..+++.+|.++|++||+|.++.......-||.|+|.+.+++..++.
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            45899998 799999999999999999999998855555699999999999997764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.12  E-value=0.053  Score=62.91  Aligned_cols=57  Identities=12%  Similarity=0.142  Sum_probs=45.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHH
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR  415 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~  415 (985)
                      ...++|+|. .+..+++.+|.+.|++||.|.++....+...|+.|||.+.+++.+++.
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            456789997 799999999999999999999998888777899999999999997765

>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=91.50  E-value=0.12  Score=47.91  Aligned_cols=53  Identities=23%  Similarity=0.360  Sum_probs=44.1

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhC
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN  418 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LN  418 (985)
                      .++| ++|+.+...||.++|+.||.| .|+.+.  ...|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~Wid--DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWID--DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEE--TTEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEc--CCeEEEEecCHHHHHHHHHhcc
Confidence            4566 999999999999999999943 344443  5789999999999999999775

>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=91.43  E-value=0.18  Score=46.49  Aligned_cols=54  Identities=22%  Similarity=0.347  Sum_probs=43.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhC
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN  418 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LN  418 (985)
                      ..++| ++|+.+...||.++|+.||.|. |+.+.  ...|||.|.+++.|..|+..++
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~Wid--DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWID--DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEE--TTEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEc--CCeEEEEecCHHHHHHHHHhcc
Confidence            35556 9999999999999999999543 33332  5689999999999999999763

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=90.69  E-value=0.37  Score=44.44  Aligned_cols=68  Identities=9%  Similarity=0.067  Sum_probs=52.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE-eccc------cceEEEEEeCCHHHHHHHHHHccCcccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-TACK------HRGFVMISYYDIRAARNAMKALQNKPLRRR  340 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk-itgk------srGfAFV~F~d~esA~kAi~~Lng~~I~Gr  340 (985)
                      ..+-+|.|+.||+.+||+++.+.++.+=++...+ +.|+      .-.-|||.|.+.++.....+..+|..+.+.
T Consensus         7 ~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A            7 HHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             ccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            3567899999999999999998888765543322 1111      123699999999999999999999887643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=87.66  E-value=0.41  Score=46.41  Aligned_cols=71  Identities=15%  Similarity=0.191  Sum_probs=52.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEE-ecc------------------ccceEEEEEeCCHHHHHHHHHHccCc
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIY-TAC------------------KHRGFVMISYYDIRAARNAMKALQNK  335 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVk-itg------------------ksrGfAFV~F~d~esA~kAi~~Lng~  335 (985)
                      ...|.|-+.|++ ....+.+.|++||.|..-. ...                  ....+..|+|.+..+|++|+. .||+
T Consensus         7 e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            456888888764 4556778899999998732 110                  134588999999999999994 8999


Q ss_pred             cccccccccccc
Q 001991          336 PLRRRKLDIHYS  347 (985)
Q Consensus       336 ~I~Gr~L~V~~a  347 (985)
                      .|.|.-|-|...
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999876666544

---

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	985
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-06
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	2e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	5e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	9e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	8e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-11
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	6e-06
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	0.004
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	7e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	6e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	4e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	6e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	9e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	7e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.003
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-04
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:) 4e-06
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:) 4e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	8e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-05
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.002
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.002
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.001
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	0.001
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003

>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 = 73.5 bits (180), Expect = 3e-16
 Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--HRGFVMISYYDIRAARNAMKA 331
            +R L++RN+   +   E+  +F ++G IR I        RG   + Y DI  A+NA   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 332 LQNKPLRRRKLDIHYSIPKDNPSEKDANQ 360
           L    +  R L + Y        + D  +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKK 94

>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 = 62.7 bits (152), Expect = 2e-12
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHN--HKFIEFYDIRAAETALRTLNR 419
            L + NL   ++ EE++ IFG YG IR+IR           ++ + DI  A+ A   L+ 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 420 SDVAGKQIKLEASRPGGARRFMVQSEQEQD 449
            +V  + + +       A + M   ++E+ 
Sbjct: 69  FNVCNRYLVVLYYNANRAFQKMDTKKKEEQ 98

>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 = 75.0 bits (183), Expect = 5e-16
 Identities = 31/171 (18%), Positives = 55/171 (32%), Gaps = 12/171 (7%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAM 329
            R LF+  ++    D  L++ FEQ+G +            + RGF  ++Y  +     AM
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 330 KAL-QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIR 388
            A       R  +     S               + V  +        L   F  YG+I 
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125

Query: 389 EIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
            I     + + K     F+ F D  + +  +       V G   ++  +  
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS 175

>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 = 65.4 bits (159), Expect = 1e-13
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI--------RTIYTACKHRGFVMISYYDIRAARNAM 329
           LF++N+N +  +  LK +F + G I        +         GF  + Y     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 330 KALQNKPLRRRKLDIHYSIPKDNPS 354
           K 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 = 54.3 bits (130), Expect = 7e-10
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK--------FIEFYDIRAAETAL 414
           L + NL+ S + E L  +F   G I+    ++ K+           F+E+     A+ AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 415 RTLNRSDVAGKQIKLEASRPG 435
           + L    V G ++++  S   
Sbjct: 61  KQLQGHTVDGHKLEVRISERA 81

>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 = 65.1 bits (158), Expect = 1e-13
 Identities = 20/81 (24%), Positives = 38/81 (46%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
            +RTL  +N++ N+ + ELK +FE   +IR +    K +G   I +     A   ++  Q
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74

Query: 334 NKPLRRRKLDIHYSIPKDNPS 354
              +  R + ++Y+  K    
Sbjct: 75  GAEIDGRSVSLYYTGEKGGTR 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 = 62.4 bits (151), Expect = 1e-12
 Identities = 22/87 (25%), Positives = 38/87 (43%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 412
            S+K     TL+  NL  +++ +EL ++F    EIR +          +IEF     AE 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 413 ALRTLNRSDVAGKQIKLEASRPGGARR 439
            L     +++ G+ + L  +   G  R
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 64.2 bits (156), Expect = 3e-13
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNA 328
            S TL+V N++    + ++  LF + GDI+ I            GF  + YY    A NA
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 329 MKALQNKPLRRRKLDIHYSIPK 350
           M+ +    L  R +   +    
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGF 87

>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 = 62.3 bits (151), Expect = 1e-12
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
           TL V NL    + E+++++F   G+I++I     K         F+E+Y    AE A+R 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           +N + +  + I+ +        R
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEGR 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 = 63.9 bits (155), Expect = 4e-13
 Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 9/93 (9%)

Query: 277 TLFVRNINSNVEDSELKALFEQFG-------DIRTIYTACKHRGFVMISYYDIRAARNAM 329
            LF+  I    +  E+     +            +     K+RGF  + Y   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 330 KALQNKPLRR--RKLDIHYSIPKDNPSEKDANQ 360
           + L    ++    ++ + ++ P+ +  E     
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 16/82 (19%), Positives = 26/82 (31%), Gaps = 9/82 (10%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYG-------EIREIRDTQHKHNHKFIEFYDIRAAETAL 414
            L +  +      EE+ +                   D        F+E+   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 415 RTLNRSDV--AGKQIKLEASRP 434
           R L    +   G QI ++ + P
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEP 84

>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 = 62.4 bits (151), Expect = 1e-12
 Identities = 23/89 (25%), Positives = 47/89 (52%), Gaps = 6/89 (6%)

Query: 274 PSRTLFVRNINSNVEDSELK----ALFEQFGDIR--TIYTACKHRGFVMISYYDIRAARN 327
           P+ T+++ N+N  ++  ELK    A+F +FG I    +  + K RG   + + ++ +A N
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPSEK 356
           A++++Q  P   + + I Y+    +   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 = 47.7 bits (113), Expect = 2e-07
 Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 362 TLVVFNLDSSVSTEELHQ----IFGIYGEIREIRDTQHKHN--HKFIEFYDIRAAETALR 415
           T+ + NL+  +  +EL +    IF  +G+I +I  ++        F+ F ++ +A  ALR
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 416 TLNRSDVAGKQIKLEASRP 434
           ++       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 = 61.2 bits (148), Expect = 3e-12
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 334
            + L+VRN+  +  +  ++  F             K R +  + + +   A  AMKAL  
Sbjct: 8   VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 335 KPLRRRKLDIHYSIPKDNPS 354
           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 = 50.4 bits (120), Expect = 2e-08
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            L V NL  S S E + + F         R  +   ++ F+ F +   A  A++ LN   
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 422 VAGKQIKLEASRP 434
           + G  I++  ++P
Sbjct: 69  LDGSPIEVTLAKP 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 = 61.5 bits (149), Expect = 3e-12
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC------KHRGFVMISYYDIRAA 325
           +  +  + VRNI       E++ LF  FG+++T+           HRGF  + +   + A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 326 RNAMKALQN-KPLRRRKLDIHYSIPKD 351
           + A  AL +   L  R+L + ++  + 
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 56.1 bits (135), Expect = 2e-10
 Identities = 18/94 (19%), Positives = 42/94 (44%), Gaps = 13/94 (13%)

Query: 348 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE------IREIRDTQHKHNHKF 401
           +PK   + K      ++V N+    +  E+ ++F  +GE       +++  T       F
Sbjct: 2   VPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 55

Query: 402 IEFYDIRAAETALRTL-NRSDVAGKQIKLEASRP 434
           ++F   + A+ A   L + + + G+++ LE +  
Sbjct: 56  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>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 = 61.2 bits (148), Expect = 3e-12
 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 328
             R L+V  +   V+D  L A F  FGDI  I         KHRGF  + +     A  A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 329 MKALQNKPLRRRKLDIHYSIPK 350
           +  +    L  R + ++ + P 
Sbjct: 64  IDNMNESELFGRTIRVNLAKPM 85

>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 = 55.1 bits (132), Expect = 4e-10
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L V  L   V  + LH  F  +G+I +I      +T+      F+EF     A  A+  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 417 LNRSDVAGKQIKLEASRP 434
           +N S++ G+ I++  ++P
Sbjct: 67  MNESELFGRTIRVNLAKP 84

>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 = 61.2 bits (148), Expect = 3e-12
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHKFIEFYDIRAAE 411
           E D    TL V NL   V+   + Q+F   G  +  +   +      + F+EFY+ R A 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 412 TALRTLNRSDVAGKQIKLEASRPGGARR 439
            AL  +N   + 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 = 59.7 bits (144), Expect = 1e-11
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYY---DIRAARNA 328
           +   RTL+V N++ +V +  +  LF Q G  ++     +H       +    + R A  A
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 64

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           + A+  + +  +++ ++++    +
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSS 88

>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 = 60.7 bits (147), Expect = 4e-12
 Identities = 13/76 (17%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKA 331
           +L+V +++ +V ++ L   F   G I +I         +  G+  +++     A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 332 LQNKPLRRRKLDIHYS 347
           +    ++ + + I +S
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>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 = 59.5 bits (144), Expect = 8e-12
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 416
           +L V +L   V+   L++ F   G I  IR      T+    + ++ F     AE AL T
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 417 LNRSDVAGKQIKLEASR 433
           +N   + GK +++  S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 61.0 bits (148), Expect = 4e-12
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 274 PSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
            +  +F+ N+N+  V+ S+++A+F ++G I        H+GF  + Y + R AR A+   
Sbjct: 14  MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNARAAVAGE 70

Query: 333 QNKPLRRRKLDIHYSIPKDNP 353
             + +  + LDI+ +      
Sbjct: 71  DGRMIAGQVLDINLAAEPKVN 91

>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 = 56.4 bits (136), Expect = 2e-10
 Identities = 15/89 (16%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTE-ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 410
             ++  +    + + NL++ V  + ++  IF  YG+I             F+++ + R A
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNA 63

Query: 411 ETALRTLNRSDVAGKQIKLEASRPGGARR 439
             A+   +   +AG+ + +  +      R
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>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 = 60.4 bits (146), Expect = 4e-12
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 416
            L+V  L   ++  EL+ +F   G I   R      T + + + F++F     ++ A++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 417 LNRSDVAGKQIKLEASRPG 435
           LN   V  K++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 = 58.1 bits (140), Expect = 3e-11
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-----FVMISYYDIRAARNAM 329
           +  L V  +  ++ D EL ALF   G I T      ++      +  + +     ++ A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 330 KALQNKPLRRRKLDIHYSIP 349
           K L    +R ++L + Y+ 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 = 59.9 bits (145), Expect = 7e-12
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRT 416
           G L+V NLD  VS  ++ ++F  +G +++       +        + F     A  A++ 
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 417 LNRSDVAGKQIKLE 430
            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 = 54.6 bits (131), Expect = 5e-10
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARNAMKALQ 333
           L V N++  V D++++ LF +FG ++        + +  G   + +     A  AMK   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 334 NKPLRRRKLDIHYS 347
             PL  R ++I   
Sbjct: 63  GVPLDGRPMNIQLV 76

>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 = 60.4 bits (146), Expect = 7e-12
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
            + T++   I S + D  ++  F  FG I  I      +G+  + +    +A +A+ ++ 
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVN 75

Query: 334 NKPLRRRKLDIHYSIPKDNPS 354
              +    +  ++     + +
Sbjct: 76  GTTIEGHVVKCYWGKESPDMT 96

>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 = 59.6 bits (144), Expect = 1e-11
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 351 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 410
           D  ++      T+    + S ++ + + Q F  +G+I EIR    +  + F+ F    +A
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESA 67

Query: 411 ETALRTLNRSDVAGKQIKLEASRP 434
             A+ ++N + + G  +K    + 
Sbjct: 68  AHAIVSVNGTTIEGHVVKCYWGKE 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 = 60.1 bits (145), Expect = 8e-12
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIF---GIYGEIREIRDTQHKHNHKFIEFYDIRA 409
           PS + +  G + + NLD S+  + L+  F   G     + + D      + F+ F    A
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 410 AETALRTLNRSDVAGKQIKLEASRP 434
           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 = 57.0 bits (137), Expect = 8e-11
 Identities = 13/79 (16%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFG---DIRTIYTACKHRGFVMISYYDIRAARNAMKA 331
              +F++N++ ++++  L   F  FG     + +      +G+  + +    AA  A++ 
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 332 LQNKPLRRRKLDIHYSIPK 350
           +    L  RK+ +     +
Sbjct: 68  MNGMLLNDRKVFVGRFKSR 86

>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 = 59.8 bits (144), Expect = 9e-12
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIR------TIYTACKHRGFVMISYYDIRAARNAMKA 331
           +F+ N++  +++  L   F  FG I               +G+  I++    A+  A++A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 332 LQNKPLRRRKLDIHYSIPKDN 352
           +  + L  R + + Y+  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 = 50.5 bits (120), Expect = 1e-08
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIRE------IRDTQHKHNHKFIEFYDIRAAETALRT 416
           + + NLD  +  + L+  F  +G I +        DT +   + FI F    A++ A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 417 LNRSDVAGKQIKLEASRPGGAR 438
           +N   +  + I +  +    ++
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 59.7 bits (144), Expect = 1e-11
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           G   S  +FV     ++ + EL+  F Q+GD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 331 ALQNKPLRRRKLDIHYSIPKDNPS 354
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>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 = 52.3 bits (125), Expect = 4e-09
 Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            + V      ++ +EL + F  YG++ ++   +      F+ F D + A++         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLI 64

Query: 422 VAGKQIKLEASRPGGARR 439
           + G  + +  + P     
Sbjct: 65  IKGISVHISNAEPKHNSN 82

>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 = 1e-11
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 266 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 325
           GE  + +     LFV N+  ++ + E++ LFE++G    ++   K +GF  I       A
Sbjct: 1   GEKTFTQR--SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLA 57

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
             A   L N PLR ++L + ++    + +
Sbjct: 58  EIAKVELDNMPLRGKQLRVRFACHSASLT 86

>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 = 54.6 bits (131), Expect = 6e-10
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL 414
           +    +  L V NL   ++ EE+ ++F  YG+  E+          FI       AE A 
Sbjct: 3   KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAK 61

Query: 415 RTLNRSDVAGKQIKLEASRPGGA 437
             L+   + GKQ+++  +    +
Sbjct: 62  VELDNMPLRGKQLRVRFACHSAS 84

>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 = 59.6 bits (144), Expect = 1e-11
 Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 9/102 (8%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI-RTIYTACKHRGFVMISYYDIRAARNAM 329
           G+ P   + V N+   V    L  +F +FG + + I     ++   ++ Y D  +A++A 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 62

Query: 330 KALQNKPL--RRRKLDIHYS------IPKDNPSEKDANQGTL 363
            +L  + +      L I +S      +  +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 = 48.9 bits (116), Expect = 9e-08
 Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKH-NHKFIEFYDIRAAETALRTLNRSD 421
           ++V NL   V+ + LHQIF  +G + +I      +     +++ D  +A+ A  +L+  +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 422 V--AGKQIKLEASRP 434
           +  A   ++++ S+ 
Sbjct: 70  IYNACCTLRIDFSKL 84

>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 = 59.3 bits (143), Expect = 2e-11
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGD-----IRTIYTACKHRGFVMISYYDIRAARNA 328
              T++V  ++  V +  L  LF Q G      +       +H+G+  + +     A  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           +K +    L  + + ++ +   + 
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 57.3 bits (138), Expect = 8e-11
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDI 407
           P  +     T+ V  LD  VS   L ++F   G +          T     + F+EF   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 408 RAAETALRTLNRSDVAGKQIKLEASRP 434
             A+ A++ ++   + GK I++  +  
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASA 88

>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 = 58.9 bits (142), Expect = 2e-11
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDI 407
           P+ +  +  T+ V NL       +L ++F  +G I        + T       FI F+  
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 408 RAAETALRTLNRSDVAGKQIKLEASRP 434
             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 = 58.1 bits (140), Expect = 4e-11
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAARNA 328
            + T+ V N++ +  +++L+ LF  FG I  IY A      + +GF  IS++    A  A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 329 MKALQNKPLRRRKLDIHYSIPKDN 352
           +  +         L++ ++ P  N
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 33/79 (41%), Gaps = 2/79 (2%)

Query: 277 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK- 335
            L++ N++  V   +L+ LF                G+  + Y D   A  A++ L  K 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 336 PLRRRKLDIHYSIPKDNPS 354
            L  + +++ YS+ 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 = 43.1 bits (101), Expect = 6e-06
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN-RS 420
            L + NL  +V+ ++L Q+FG        +       + F+++ D   A  A+ TL+ + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG-YAFVDYPDQNWAIRAIETLSGKV 61

Query: 421 DVAGKQIKLEASRPGGAR 438
           ++ GK ++++ S     R
Sbjct: 62  ELHGKIMEVDYSVSKKLR 79

>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 = 56.6 bits (136), Expect = 1e-10
 Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK---HRGFVMISYYDIRAARN 327
            +   + L V NI     D +L+ +F QFG I  +         +GF  +++ +   A  
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 328 AMKALQNKPLRRRKLDIHYSIPKDNPS 354
           A + L    +  RK++++ +  +   +
Sbjct: 67  AREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 54.3 bits (130), Expect = 9e-10
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAA 410
           SE  +    L V N+       +L Q+FG +G+I +   I + +      F+ F +   A
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 411 ETALRTLNRSDVAGKQIKLEASRP 434
           + A   L+ + V G++I++  +  
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNATA 88

>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 = 56.1 bits (135), Expect = 2e-10
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAM 329
              L+V N+   + D +L  +F ++G I            + RG   + Y     A+ A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 330 KALQNKPL--RRRKLDIHY 346
            AL N       + L +  
Sbjct: 66  SALNNVIPEGGSQPLSVRL 84

>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 = 53.8 bits (129), Expect = 1e-09
 Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIR-----EIRDTQHKHNHKFIEFYDIRAAETALRT 416
            L V NL  +++ ++L  IFG YG I        + T       F+ +     A+ A+  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 417 LNRSDVAGKQIKLE 430
           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 = 35.3 bits (81), Expect = 0.004
 Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 3/76 (3%)

Query: 806 GDDSR-TTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDP 864
           G+  + T L + N+P   T   L     ++  G+     +  D       G AF+     
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGRPRGVAFVRYNKR 58

Query: 865 RQIIPFHQAFNGKKWE 880
            +      A N    E
Sbjct: 59  EEAQEAISALNNVIPE 74

>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 = 55.9 bits (134), Expect = 2e-10
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNA 328
               LFV +I+   ++ E++  F  +G+I+ I+          +G+ ++ Y   + A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 329 MKALQNKPLRRRKLDIHYSIPK 350
            +AL    +  + + + +   K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>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 = 52.4 bits (125), Expect = 4e-09
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIR-----EIRDTQHKHNHKFIEFYDIRAAETALRT 416
            L V ++      +E+ + F  YGEI+       R T     +  +E+   + A  A   
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 417 LNRSDVAGKQIKLEASRPGG 436
           LN +++ G+ I+++     G
Sbjct: 69  LNGAEIMGQTIQVDWCFVKG 88

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 5/85 (5%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAM 329
           +  LF+  + + + D ++K L   FG ++             +G+    Y DI     A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 330 KALQNKPLRRRKLDIHYSIPKDNPS 354
             L    L  +KL +  +      +
Sbjct: 61  AGLNGMQLGDKKLLVQRASVGAKNA 85

>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 = 53.9 bits (129), Expect = 1e-09
 Identities = 12/79 (15%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 417
           L +  L + ++ +++ ++   +G ++     +           F E+ DI   + A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 418 NRSDVAGKQIKLEASRPGG 436
           N   +  K++ ++ +  G 
Sbjct: 64  NGMQLGDKKLLVQRASVGA 82

>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 = 55.8 bits (134), Expect = 3e-10
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 349 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIE 403
           P DN S ++ +  T+    L + +   +L   F   G++R++R     +++      ++E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 404 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           F +I++       L    + G  I ++AS+ 
Sbjct: 67  FCEIQSVP-LAIGLTGQRLLGVPIIVQASQA 96

>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 = 54.3 bits (130), Expect = 1e-09
 Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAAR 326
           E  +RT+F   + + +   +L+  F   G +R +         + +G   + + +I++  
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 327 NAMKALQNKPLRRRKLDIHYSIPKDN 352
            A+  L  + L    + +  S  + N
Sbjct: 75  LAIG-LTGQRLLGVPIIVQASQAEKN 99

>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 = 55.1 bits (132), Expect = 3e-10
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 416
            L+V  L  +++ EE   +FG  GEI   +      T     + F+ + D + AE A+ T
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 417 LNRSDVAGKQIKLEASRP 434
           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 = 53.2 bits (127), Expect = 2e-09
 Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 275 SRT-LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNA 328
           S+T L V  +  N+   E ++LF   G+I +             G+  ++Y D + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 329 MKALQNKPLRRRKLDIHYSIP 349
           +  L    L+ + + + Y+ P
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 3e-10
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-----FVMISYYDIRAARNA 328
           P+  L V  ++    + +L+ +F ++G I  +      +      F  + + ++  A+ A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 329 MKALQNKPLRRRKLDI 344
            +      L  R++ +
Sbjct: 68  KERANGMELDGRRIRV 83

>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 = 54.3 bits (130), Expect = 6e-10
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L VF L    +  +L ++F  YG I ++     + ++      F+ F ++  A+ A   
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 417 LNRSDVAGKQIK 428
            N  ++ G++I+
Sbjct: 71  ANGMELDGRRIR 82

>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 = 55.5 bits (133), Expect = 4e-10
 Identities = 25/103 (24%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI-----RTIYTACKHRGFVMISYYDIR 323
           P  +   R++FV NI     + +LK +F + G +            K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 324 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSE-KDANQGTLVV 365
            A +AM+ L  +    R L +  +  + N  E K    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 = 46.7 bits (110), Expect = 7e-07
 Identities = 19/93 (20%), Positives = 41/93 (44%), Gaps = 6/93 (6%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNH-----KFIEFYD 406
           +P+  D +  ++ V N+    + E+L  IF   G +   R    +         F E+ D
Sbjct: 1   DPA-VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
              A +A+R LN  + +G+ ++++ +     + 
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>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 = 55.5 bits (133), Expect = 4e-10
 Identities = 13/83 (15%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNA 328
             R LF+  ++    +  L+  +EQ+G +              RGF  +++  +     A
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 329 MKALQNKPLRRRKLDIHYSIPKD 351
           M   +   +  R ++   ++ ++
Sbjct: 79  MA-ARPHSIDGRVVEPKRAVARE 100

>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 = 51.6 bits (123), Expect = 1e-08
 Identities = 10/93 (10%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI-----REIRDTQHKHNHKF 401
           ++P +    +      L +  L    + E L   +  +G++          ++      F
Sbjct: 7   TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           + F  +   + A+       + G+ ++ + +  
Sbjct: 67  VTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA 98

>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 = 55.5 bits (133), Expect = 4e-10
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 5/96 (5%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAA 325
           G   S  LFVRN++    + +L+ LF  +G +  ++          +GF  +++     A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 361
             A   +  +  + R L +  S  K   S+   + G
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 50.9 bits (121), Expect = 2e-08
 Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIR 408
           S   +  G L V NL  + S E+L ++F  YG + E+               F+ F    
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 409 AAETALRTLNRSDVAGKQIKLEASRP 434
            A  A   ++     G+ + +  S  
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTI 87

>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 = 55.1 bits (132), Expect = 5e-10
 Identities = 30/96 (31%), Positives = 44/96 (45%), Gaps = 3/96 (3%)

Query: 260 SAGSVVGEHPYGEH-PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMIS 318
           S+GS  G+  YG+  P+  L+V  +  N   + L   F++FG IRTI    K   F  I 
Sbjct: 2   SSGSS-GKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQ 59

Query: 319 YYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
           Y  + AA+ A   ++  PL      +     K  PS
Sbjct: 60  YESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 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 = 39.7 bits (92), Expect = 2e-04
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            L V  L  + S   L + F  +G IR I       +  +I++  + AA+ A   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 422 VAG--KQIKLEASRPG 435
           + G  ++++++ ++ G
Sbjct: 78  LGGPDRRLRVDFAKSG 93

>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 = 55.1 bits (132), Expect = 5e-10
 Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 4/93 (4%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA--CKHRGFVMI 317
           S G V+   P G      ++V N+  ++   +++ +F ++G IR I          F  +
Sbjct: 1   SGGGVI-RGPAGN-NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFV 58

Query: 318 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 350
            + D R A +A+           +L + +    
Sbjct: 59  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 51.2 bits (122), Expect = 1e-08
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALRT 416
           N   + V NL   + T+++  +F  YG IR+I  ++ +      F+EF D R AE A+  
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 417 LNRSDVAGKQIKLEASRPGGAR 438
            +  D  G ++++E  R G   
Sbjct: 73  RDGYDYDGYRLRVEFPRSGRGT 94

>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 = 54.4 bits (130), Expect = 7e-10
 Identities = 13/79 (16%), Positives = 23/79 (29%), Gaps = 5/79 (6%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAMK 330
            TL++ N   +     ++ L +    +              R F  I       AR  ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 331 ALQNKPLRRRKLDIHYSIP 349
            L    +    L    S P
Sbjct: 62  KLNGLKIEGYTLVTKVSNP 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 = 50.6 bits (120), Expect = 1e-08
 Identities = 11/78 (14%), Positives = 23/78 (29%), Gaps = 5/78 (6%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 416
           TL + N   S +   +  +      +           +      +I+      A   +  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 417 LNRSDVAGKQIKLEASRP 434
           LN   + G  +  + S P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 80

>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 = 54.0 bits (129), Expect = 1e-09
 Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 6/90 (6%)

Query: 271 GEHPSRTLFVRNINSNVEDS-----ELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 325
           G   S  L     N +V        + ++LF  +    T     K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTF-QYFKSFKRVRINFSNPLSA 59

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNPSE 355
            +A   L       +++ ++++      S 
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLHIGSS 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 = 53.5 bits (128), Expect = 1e-09
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMK 330
             L+V  +   +   EL+ LF Q+G I T            RG   I +     A  A+K
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 331 ALQNKPL--RRRKLDIHYS 347
            L  +        + + ++
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 52.4 bits (125), Expect = 3e-09
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 8/82 (9%)

Query: 354 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDIR 408
           S +DAN   L V  L  +++ +EL Q+F  YG I        + T       FI F    
Sbjct: 3   SIRDAN---LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 59

Query: 409 AAETALRTLNRSDVAGKQIKLE 430
            AE A++ LN    +G    + 
Sbjct: 60  EAEEAIKGLNGQKPSGATEPIT 81

>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 = 53.4 bits (128), Expect = 2e-09
 Identities = 13/88 (14%), Positives = 26/88 (29%), Gaps = 7/88 (7%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAA 325
               +  L V  +     + +LK  F  FG++  +           +GF  + + +    
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKDNP 353
              M       +  R  D      K + 
Sbjct: 64  VKVMSQRHM--IDGRWCDCKLPNSKQSQ 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 = 47.3 bits (112), Expect = 2e-07
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            L+V  L    + ++L + F  +GE+  +       T H     F+ F +       +  
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 417 LNRSDVAGKQIKLEASRPGGAR 438
            +  D  G+    +      ++
Sbjct: 70  RHMID--GRWCDCKLPNSKQSQ 89

>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 = 52.5 bits (125), Expect = 4e-09
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAAR-----NA 328
           P++ L+++N++  V + +L +LF +F + +      +     M     I          A
Sbjct: 17  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 76

Query: 329 MKALQNKPLRRRKLDIHYSIPKDNPS 354
           +  +    L  + L I +   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 = 44.4 bits (104), Expect = 4e-06
 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 5/93 (5%)

Query: 347 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKF 401
            IP  +          L + NL   V+  +L  +F  + E +         T       F
Sbjct: 5   KIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF 64

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           I F +   A  AL  +N   + GK + +E  + 
Sbjct: 65  ITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 97

>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 = 52.4 bits (125), Expect = 5e-09
 Identities = 18/104 (17%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 254 VSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---- 309
           ++ Q + A     E P        LF+ ++     D +L  +F  FG++ +         
Sbjct: 1   LTQQSIGAAGSQKEGP----EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 56

Query: 310 -KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
              + F  +SY +  +A+ A++++    +  ++L +     K++
Sbjct: 57  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 50.5 bits (120), Expect = 3e-08
 Identities = 17/93 (18%), Positives = 45/93 (48%), Gaps = 6/93 (6%)

Query: 353 PSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYD 406
            S+K+  +G  L +++L      ++L Q+F  +G +   +    K  +      F+ + +
Sbjct: 10  GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 69

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
             +A+ A++++N   +  K++K++  R     +
Sbjct: 70  PVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 52.1 bits (124), Expect = 6e-09
 Identities = 19/95 (20%), Positives = 38/95 (40%), Gaps = 13/95 (13%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-------------CKHRGFV 315
           P  +  +  ++V+ +N +V   +L   F+Q G ++                   K +G  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 350
            +SY D   A+ A++    K  +  KL +  +  K
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 51.3 bits (122), Expect = 1e-08
 Identities = 16/93 (17%), Positives = 38/93 (40%), Gaps = 13/93 (13%)

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-------------RDTQHKHNHKF 401
           ++D++   + V  L+ SV+ ++L   F   G ++               ++T        
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 402 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 434
           + + D   A+ A+   +  D  G ++K+  +R 
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 51.0 bits (121), Expect = 2e-08
 Identities = 19/102 (18%), Positives = 43/102 (42%), Gaps = 5/102 (4%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISY 319
           S+GS    H      S  + VR +  +V +++L    E+FG I  +      +   ++ +
Sbjct: 2   SSGSSGSHHKVS--VSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEF 58

Query: 320 YDIRAARNAMKALQNKP--LRRRKLDIHYSIPKDNPSEKDAN 359
            +I +A+  +    + P  +  ++   +YS  K      ++ 
Sbjct: 59  ENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSG 100

>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 = 38.6 bits (89), Expect = 4e-04
 Identities = 17/90 (18%), Positives = 30/90 (33%), Gaps = 3/90 (3%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 411
               K +    + V  L  SV   +L +    +G I  +           +EF +I +A+
Sbjct: 7   GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAK 65

Query: 412 TALRTLNRSD--VAGKQIKLEASRPGGARR 439
             +         +AG+Q     S      R
Sbjct: 66  ECVTFAADVPVYIAGQQAFFNYSTSKRITR 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 = 50.1 bits (119), Expect = 2e-08
 Identities = 11/80 (13%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           G   S  + V+N+  +    E+  L + +          +++    ++  +   A+NA++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV--DRNKRTAFVTLLNGEQAQNAIQ 58

Query: 331 ALQNKPLRRRKLDIHYSIPK 350
                  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 = 42.0 bits (98), Expect = 1e-05
 Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            ++V NL    + +E+H +   Y    +           F+   +   A+ A++  ++  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYD--LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 422 VAGKQIKLEASRP 434
             GK + ++    
Sbjct: 65  FRGKDLIVQLQPT 77

>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 = 50.2 bits (119), Expect = 3e-08
 Identities = 19/97 (19%), Positives = 41/97 (42%), Gaps = 11/97 (11%)

Query: 269 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIR 323
           P      +T+F+RN++ + E+  L  + +QFGD++ +           +G     +    
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 324 AARNAMKALQ------NKPLRRRKLDIHYSIPKDNPS 354
           AA+  + A           L  R+L +  ++ +D  +
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>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 = 43.6 bits (102), Expect = 6e-06
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 12/91 (13%)

Query: 356 KDANQG-TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRA 409
            D  +G T+ + NL      E L ++   +G+++ +      DT+H     F +F    A
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 410 AETALRTLNRS------DVAGKQIKLEASRP 434
           A+  L   +         + G+Q+K++ +  
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>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 = 48.8 bits (116), Expect = 4e-08
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMKAL 332
           +F+  ++       L+  F QFG+++             RGF  +++ D       +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 333 QNKPLRRRKLDI 344
               L  + +D 
Sbjct: 62  SRHELDSKTIDP 73

>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 = 48.8 bits (116), Expect = 5e-08
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHN-----HKFIEFYDIRAAETALRTL 417
           + +  L    + E L + FG +GE++E    +           F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 418 NRSDVAGKQIK 428
           +R ++  K I 
Sbjct: 62  SRHELDSKTID 72

>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 = 48.9 bits (116), Expect = 5e-08
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
              TL+V   +  +  + L+  F  FG+I  +           ++Y  + +A  A+  L 
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQAVAELN 60

Query: 334 NKPLRRRKLDIHYSIPK 350
              +   +L ++ +  +
Sbjct: 61  GTQVESVQLKVNIARKQ 77

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
           TL V+  D  ++   L   F  +G I ++       N  F+ +  + +A+ A+  LN + 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 422 VAGKQIKLEASRP 434
           V   Q+K+  +R 
Sbjct: 64  VESVQLKVNIARK 76

>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 = 50.3 bits (119), Expect = 8e-08
 Identities = 27/128 (21%), Positives = 55/128 (42%), Gaps = 13/128 (10%)

Query: 316 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTE 375
           ++S YD       ++ LQ +  +          P     E D  +  L+V  + ++V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQHIP-------PTQMNPEPDVLR-NLMVNYIPTTVDEV 57

Query: 376 ELHQIFGIYGEIREIRDTQHKHN-----HKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 430
           +L Q+F  YG I  ++    +       + F++F    +A+ A+  LN  ++  K++K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 431 ASRPGGAR 438
            +  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 = 48.4 bits (114), Expect = 3e-07
 Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-----FVMISYYDIRAARNA 328
             R L V  I + V++ +L+ LFE++G I ++   C         +  + +    +A+ A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 329 MKALQNKPLRRRKLDIHYSIPKD 351
           +  L    +  ++L +  +    
Sbjct: 101 IAGLNGFNILNKRLKVALAASGH 123

>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 = 8e-08
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 274 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 332
             R + + +         +L  L E FG I              I       A+ A+   
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYY 65

Query: 333 QNKP--LRRRKLDIHYS 347
              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 = 37.4 bits (86), Expect = 8e-04
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 362 TLVVFNLDSSVSTE-ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLN 418
            + + +     +   +L Q+   +G I       +K N  FIE      A+ A+   T  
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL-ILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 419 RSDVAGKQIKLEASRP 434
            + V 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 = 49.0 bits (116), Expect = 8e-08
 Identities = 18/100 (18%), Positives = 39/100 (39%), Gaps = 8/100 (8%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD-----IRTIYTACKHRGF 314
           S+GS     P  + P  T F+ N+  +V +  +K  F           R      + +GF
Sbjct: 2   SSGSSGSRLP--KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGF 59

Query: 315 VMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 354
               + D+ +  +A+  L  + L  +++ +  +    +  
Sbjct: 60  GYAEFEDLDSLLSALS-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 = 38.9 bits (90), Expect = 3e-04
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGE-----IREIRDTQHKHNHKFIEFYDIRAAETALRT 416
           T  + NL   V+ E + + F           RE  + +      + EF D+ +  +AL +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 417 LNRSDVAGKQIKLEASRPGGARR 439
           LN   +  K+I+++ +     + 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 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 = 47.5 bits (112), Expect = 2e-07
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 1/75 (1%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           P++ LF+ N+     +  L  LF QF   + +           + +     +  A +ALQ
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQ 66

Query: 334 NKPL-RRRKLDIHYS 347
              +     + I ++
Sbjct: 67  GFKITPTHAMKITFA 81

>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 = 47.8 bits (113), Expect = 2e-07
 Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 275 SRTLFVRNINSNVEDSELKALFEQFGDI-----RTIYTACKHRGFVMISYYDIRAARNAM 329
              LFV  ++ +  +  L+ +F ++G I            + RGF  +++ +I  A++AM
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 330 KALQNKPLRRRKLDIHYSIPKDN 352
            A+  K +  R++ +  +    +
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSD 87

>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 = 43.6 bits (102), Expect = 5e-06
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 5/87 (5%)

Query: 358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAET 412
           +++G L V  L    + + L Q+F  YG+I E+   + +   +     F+ F +I  A+ 
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 413 ALRTLNRSDVAGKQIKLEASRPGGARR 439
           A+  +N   V G+QI+++ +      R
Sbjct: 63  AMMAMNGKSVDGRQIRVDQAGKSSDNR 89

>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 = 47.0 bits (111), Expect = 3e-07
 Identities = 15/83 (18%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 275 SRTLFVRNINSNV-EDSELKALFEQFGDIRTIYTA------CKHRGFVMISYYDIRAARN 327
            R + +RN+++ + +++ L+  FE FG I  I           +     + + +  +A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 328 AMKALQNKPLRRRKLDIHYSIPK 350
           A++ +    L  R++ +  +  K
Sbjct: 64  ALQ-MNRSLLGNREISVSLADKK 85

>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 = 47.1 bits (111), Expect = 3e-07
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDI-RTIYTACKHRGFVMISYYDIRAARNAMKAL 332
           PS TL + NI  +V + +LK LF   G + +      K R   +I    +  A  A+  L
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 333 QNKPLRR-RKLDIHYS 347
            N  L     L + +S
Sbjct: 69  HNHDLGENHHLRVSFS 84

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.3 bits (109), Expect = 4e-07
 Identities = 10/71 (14%), Positives = 26/71 (36%), Gaps = 6/71 (8%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRTL 417
           + V  L  + + E++   F  +G++ +        T       F+ F      E     +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 418 NRSDVAGKQIK 428
           +  ++  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 = 7e-06
 Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAMKAL 332
           +FV  ++ N    ++K  FEQFG +         T  +HRGF  +++          + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 333 QNKPLRRRKLDI 344
               +  + ++ 
Sbjct: 61  HFHEINNKMVEC 72

>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 = 46.4 bits (109), Expect = 4e-07
 Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           PSR L +R +   V ++E+ AL   FG +  I    K +    +      AA   +    
Sbjct: 7   PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYS 65

Query: 334 NKP--LRRRKLDIHYSIPK 350
                LR + + I YS  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 = 46.6 bits (110), Expect = 6e-07
 Identities = 11/80 (13%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 273 HPSRTLFVR--NINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 330
           + +++L V    + + V  ++L  + E+ G +  +     ++ +    Y     ++ A  
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYV 74

Query: 331 ALQNKPL---RRRKLDIHYS 347
            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 = 42.8 bits (100), Expect = 1e-05
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 8/75 (10%)

Query: 362 TLVVF--NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 419
           +LVV    L + VS  +L  +    G +  +        + F  +     ++ A  TLN 
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLN- 77

Query: 420 SDVAGKQIKLEASRP 434
               GK++  +  + 
Sbjct: 78  ----GKEVVDDLGQK 88

>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 = 46.7 bits (110), Expect = 6e-07
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 275 SRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
           +  L V N+N   V    L  LF  +GD++ +      +   ++   D   A+ AM  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 334 NKPLRRRKLDIHYSIPKDNPSEKDANQGT 362
              L  + + I  S  ++    ++  +  
Sbjct: 62  GHKLHGKPIRITLSKHQNVQLPREGQEDQ 90

>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 = 44.4 bits (104), Expect = 4e-06
 Identities = 20/79 (25%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 362 TLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 420
            L+V NL+   V+ + L  +FG+YG+++ ++   +K  +  ++  D   A+ A+  LN  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 63

Query: 421 DVAGKQIKLEASRPGGARR 439
            + GK I++  S+    + 
Sbjct: 64  KLHGKPIRITLSKHQNVQL 82

>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 = 46.3 bits (109), Expect = 6e-07
 Identities = 11/82 (13%), Positives = 27/82 (32%), Gaps = 4/82 (4%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGD----IRTIYTACKHRGFVMISYYDIRAARN 327
           E     L++ N+  ++++ EL+ + + FG          ++   RG              
Sbjct: 15  EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 328 AMKALQNKPLRRRKLDIHYSIP 349
            +     K ++        + P
Sbjct: 75  VIGHFNGKFIKTPPGVSAPTEP 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 = 42.1 bits (98), Expect = 2e-05
 Identities = 12/84 (14%), Positives = 27/84 (32%), Gaps = 4/84 (4%)

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK----HNHKFIEFYDIRAA 410
           +++ +   L + NL  S+  +EL  +   +G++   R  +          F         
Sbjct: 13  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 72

Query: 411 ETALRTLNRSDVAGKQIKLEASRP 434
           E  +   N   +         + P
Sbjct: 73  EAVIGHFNGKFIKTPPGVSAPTEP 96

>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 = 7e-07
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMK 330
           R LF+  ++    D  L++ FEQ+G +              RGF  ++Y  +     AM 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 331 ALQNKPLRRRKLDI 344
           A +   +  R ++ 
Sbjct: 67  A-RPHKVDGRVVEP 79

>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 = 40.4 bits (94), Expect = 6e-05
 Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDIRAAETALRT 416
            L +  L    + E L   F  +G + +       +T+      F+ +  +   + A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 417 LNRSDVAGKQIK 428
                V G+ ++
Sbjct: 67  ARPHKVDGRVVE 78

>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 = 45.1 bits (106), Expect = 9e-07
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 5/71 (7%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDIRAAETALRTL 417
           L +  L    + ++L ++   YG+I        + T     + F++F    AA+ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 418 NRSDVAGKQIK 428
             S V  +  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 = 42.4 bits (99), Expect = 7e-06
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDI-----RTIYTACKHRGFVMISYYDIRAARNAMKAL 332
           L++R +     D +L  L + +G I         T  K +G+  + +    AA+ A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 333 QNKPLRRRKL 342
           +   ++ +  
Sbjct: 61  KASGVQAQMA 70

>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 = 45.5 bits (107), Expect = 1e-06
 Identities = 16/91 (17%), Positives = 28/91 (30%), Gaps = 4/91 (4%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISY 319
           S+GS  G  P        + V  +  +    +LK    + GD+          G V    
Sbjct: 2   SSGSSGG--PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYL- 58

Query: 320 YDIRAARNAMKALQNKPLRRRKLDIHYSIPK 350
                   A++ L +   R  + +  Y    
Sbjct: 59  -RKEDMEYALRKLDDTKFRSHEGETSYIRVY 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 = 35.9 bits (82), Expect = 0.003
 Identities = 15/78 (19%), Positives = 27/78 (34%), Gaps = 2/78 (2%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
            ++V  L  S S ++L       G++        K     +E+      E ALR L+ + 
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVC--YADVQKDGMGMVEYLRKEDMEYALRKLDDTK 74

Query: 422 VAGKQIKLEASRPGGARR 439
               + +    R    R 
Sbjct: 75  FRSHEGETSYIRVYPERS 92

>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 = 45.0 bits (106), Expect = 1e-06
 Identities = 13/72 (18%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMKAL 332
           +FV  ++ +  + +++  F  FG++ +I           RGF  I++ +    +  M+  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 333 QNKPLRRRKLDI 344
           +   +   K +I
Sbjct: 61  KYHNVGLSKCEI 72

>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 = 43.8 bits (103), Expect = 2e-06
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 6/71 (8%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 417
           + V  L      E++ + FG +GE+  I        +K     FI F +    +  +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 418 NRSDVAGKQIK 428
              +V   + +
Sbjct: 61  KYHNVGLSKCE 71

>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 = 1e-06
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 6/93 (6%)

Query: 352 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYD 406
           + S+KD     + V  L    +   L + F  +G+I E      +   K     F+   D
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 407 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 439
             AAE A +  N   + G++  +  +  G   R
Sbjct: 62  RAAAERACKDPN-PIIDGRKANVNLAYLGAKPR 93

>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 = 45.5 bits (107), Expect = 2e-06
 Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 6/93 (6%)

Query: 268 HPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDI 322
               +     +FV  +  +  D+ L+  FE FGDI            K RG+  ++  D 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 323 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE 355
            AA  A K   N  +  RK +++ +     P  
Sbjct: 63  AAAERACKDP-NPIIDGRKANVNLAYLGAKPRS 94

>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 = 44.6 bits (105), Expect = 2e-06
 Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 363 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 417
           + +  L    + ++L   F  +GE+ +        T       F+ F +  + +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 418 NRSDVAGKQIK 428
               + 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 = 12/72 (16%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAARNAMKAL 332
           +F+  ++ +    +LK  F +FG++            + RGF  + + +  +    M   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 333 QNKPLRRRKLDI 344
           +   L  + +D 
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 13/77 (16%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYD-IRAARNAMKALQN 334
              F  +++      +L  LF   G+I+ I          +I + +  + A    K   N
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANN 70

Query: 335 KPLRRRKLDIHYSIPKD 351
             L+ R  ++ + + + 
Sbjct: 71  GNLQLRNKEVTWEVLEG 87

>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 = 39.0 bits (90), Expect = 3e-04
 Identities = 14/88 (15%), Positives = 30/88 (34%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 421
                +LD     E+LH +F  +GEI+ I   +       +     + A    +  N  +
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 422 VAGKQIKLEASRPGGARRFMVQSEQEQD 449
           +  +  ++      G        +  +D
Sbjct: 73  LQLRNKEVTWEVLEGEVEKEALKKIIED 100

>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 = 44.3 bits (104), Expect = 4e-06
 Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 346 YSIPKDNPSEKDANQGT---LVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHN 398
           Y  P+++    D  +     + +         E   ++   YGE+ E+        H   
Sbjct: 10  YRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG 69

Query: 399 HKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS 432
           + +++F     AE A+  LN     G+ I  E S
Sbjct: 70  NVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 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 = 41.2 bits (96), Expect = 4e-05
 Identities = 8/74 (10%), Positives = 24/74 (32%), Gaps = 4/74 (5%)

Query: 278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMKALQ 333
           + ++       +     + E++G++  +             V + +     A  A+  L 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 334 NKPLRRRKLDIHYS 347
           N+    + +    S
Sbjct: 90  NRWFNGQPIHAELS 103

>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 = 43.6 bits (102), Expect = 6e-06
 Identities = 13/86 (15%), Positives = 26/86 (30%), Gaps = 13/86 (15%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTI----------YTACKHRGFVMISYYDIRAA 325
           R L+V NI   + +  +   F     +  +              + + F  + +  +   
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 326 RNAMKALQNKPLRRRKLDIHYSIPKD 351
             AM        + + L I    P D
Sbjct: 62  TQAMA-FDGIIFQGQSLKI--RRPHD 84

>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 = 37.8 bits (87), Expect = 6e-04
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 13/87 (14%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREIR----------DTQHKHNHKFIEFYDIRAAE 411
            L V N+   ++ E +   F     +  +                 N  F+EF  +    
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 412 TALRTLNRSDVAGKQIKLEASRPGGAR 438
            A+   +     G+ +K+   RP   +
Sbjct: 63  QAMA-FDGIIFQGQSLKI--RRPHDYQ 86

>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 = 43.8 bits (103), Expect = 6e-06
 Identities = 10/91 (10%), Positives = 29/91 (31%), Gaps = 12/91 (13%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFG-DIRTIYTAC-----------KHRGFVMISYYD 321
             R + ++N+   ++  +   +  +   D+R   +                G   +S+ D
Sbjct: 7   HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRD 66

Query: 322 IRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
              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 = 42.8 bits (100), Expect = 8e-06
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 4/77 (5%)

Query: 276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISY----YDIRAARNAMKA 331
           + +FV  I  + E+  L+  FEQ+G I  I             +    +D   + + +  
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 332 LQNKPLRRRKLDIHYSI 348
            +   +     ++  ++
Sbjct: 63  QKYHTVNGHNCEVRKAL 79

>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 = 37.8 bits (87), Expect = 5e-04
 Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 6/72 (8%)

Query: 362 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 416
            + V  +        L   F  YG+I  I     R +  K    F+ F D  + +  +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 417 LNRSDVAGKQIK 428
                V G   +
Sbjct: 63  QKYHTVNGHNCE 74

>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 = 43.4 bits (102), Expect = 8e-06
 Identities = 14/101 (13%), Positives = 34/101 (33%), Gaps = 18/101 (17%)

Query: 274 PSRTLFVRNI------NSNVEDSELK-ALFEQFGDIRTIYTACKHR----------GFVM 316
           P+  L + N+        + E  E+   + ++      + +    R          G + 
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 317 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKD 357
           + +  +   + AM+ L  +    R +   Y    D+   +D
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYC-DPDSYHRRD 102

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 9/80 (11%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARN 327
           +  +R+++++   ++    ++K   E  G +  I             + + +  I +A+ 
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 62

Query: 328 AMKALQNKPLRRRKLDIHYS 347
            ++    +  +   L I + 
Sbjct: 63  FVE-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 = 36.3 bits (83), Expect = 0.002
 Identities = 7/80 (8%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 355 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAA 410
           + D    ++ +    +  + +++ +     G++  I+      +      F+ F  I +A
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 411 ETALRTLNRSDVAGKQIKLE 430
           +  +            + + 
Sbjct: 61  KKFVE-TPGQKYKETDLLIL 79

>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 = 41.9 bits (97), Expect = 2e-05
 Identities = 12/81 (14%), Positives = 26/81 (32%), Gaps = 5/81 (6%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAM 329
               LF+ N+N N   +ELK    +      +       G    F  + +        A+
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71

Query: 330 KALQNKPLRRRKLDIHYSIPK 350
           + L    +   ++ +     +
Sbjct: 72  E-LTGLKVFGNEIKLEKPKGR 91

>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 = 40.3 bits (93), Expect = 1e-04
 Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 4/90 (4%)

Query: 274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 333
               +  +N+ +    +E++  F +FG +  +          ++ + +   AR A + L 
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLA 67

Query: 334 NKPLRRRKLDIHYS---IPKDNPSEKDANQ 360
                   L + ++   +    P +KD+  
Sbjct: 68  YSKFHHVPLYLEWAPIGVFGAAPQKKDSQH 97

>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 = 38.9 bits (90), Expect = 2e-04
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVMISYYDIRAA 325
           G+     + V+N+   V   E+   F  +  I        +      G  M+++     A
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 64

Query: 326 RNAMKALQNKPLRRRKLDI 344
             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 = 37.3 bits (86), Expect = 7e-04
 Identities = 8/74 (10%), Positives = 19/74 (25%), Gaps = 2/74 (2%)

Query: 806 GDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPR 865
           G    T + ++N+P   +   +L     +              +     G A +      
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVC--LKYNEKGMPTGEAMVAFESRD 62

Query: 866 QIIPFHQAFNGKKW 879
           +        N +  
Sbjct: 63  EATAAVIDLNDRPI 76

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 5/83 (6%)

Query: 353 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDI 407
            S        + V N+  +VS +E+   F  Y  I         +         + F   
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 408 RAAETALRTLNRSDVAGKQIKLE 430
             A  A+  LN   +  +++KL 
Sbjct: 62  DEATAAVIDLNDRPIGSRKVKLV 84

>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 = 36.7 bits (84), Expect = 0.001
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 11/78 (14%)

Query: 276 RTLFVRNINSNVEDSELKALFE---QFGDIRTIYTA--------CKHRGFVMISYYDIRA 324
             +FV  ++  + D E+    E   +FG I  +                   ++Y     
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 325 ARNAMKALQNKPLRRRKL 342
           A  A++ + N  +  R L
Sbjct: 69  ALRAIQCVNNVVVDGRTL 86

>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 = 36.9 bits (84), Expect = 0.001
 Identities = 8/83 (9%), Positives = 20/83 (24%), Gaps = 2/83 (2%)

Query: 272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA 331
           +   R + + N+  +           +       Y   + +    I       A   +  
Sbjct: 15  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDH 74

Query: 332 LQNKP--LRRRKLDIHYSIPKDN 352
              K    + R + +  S     
Sbjct: 75  CLKKALWFQGRCVKVDLSEKYKK 97

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 0.003
 Identities = 11/96 (11%), Positives = 30/96 (31%), Gaps = 6/96 (6%)

Query: 260 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVM 316
           S+GS      +       + +R +     ++++   F     +R         +  G   
Sbjct: 2   SSGS--SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEAD 59

Query: 317 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 352
           + +     A  AM       ++ R +++  +     
Sbjct: 60  VEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGT 94

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	985
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.93
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.61
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.6
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.6
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.6
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.6
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.59
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.59
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.59
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.59
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.59
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.59
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.58
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.58
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.57
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.57
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.57
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.57
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.56
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.56
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.56
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.56
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.56
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.55
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.55
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.55
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.54
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.54
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.54
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.54
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.54
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.54
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.54
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.54
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.53
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.53
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.53
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.53
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.53
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.53
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.53
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.53
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.53
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.53
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.53
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.52
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.52
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.52
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.52
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.52
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.52
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.51
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.51
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.51
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.51
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.51
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.51
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.51
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.51
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.51
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.5
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.5
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.5
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.5
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.5
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.5
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.5
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.5
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.5
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.5
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.5
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.5
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.5
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.5
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.5
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.49
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.49
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.49
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.49
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.49
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.49
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.49
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.48
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.47
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.47
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.47
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.47
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.47
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.47
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.47
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.47
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.47
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.46
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.46
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.46
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.46
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.46
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.46
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.45
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.45
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.45
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.45
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.45
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.45
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.45
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.45
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.45
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.44
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.44
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.44
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.44
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.44
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.43
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.43
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.43
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.43
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.42
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.42
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.42
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.42
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.42
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.42
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.41
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.41
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.41
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.4
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.39
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.39
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.39
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.38
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.37
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.37
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.36
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.36
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.35
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.35
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.35
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.34
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.33
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.33
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.31
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.29
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.29
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.27
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.23
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.22
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	99.18
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.17
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.16
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.16
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.14
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.13
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.13
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.1
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.07
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	99.06
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.06
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.96
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.94
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.91
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.8
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.99
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.54
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	95.06
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	94.73
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.62
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	80.38

>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=1.2e-25  Score=224.93  Aligned_cols=164  Identities=18%  Similarity=0.336  Sum_probs=141.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..|+|||+|||+++|+++|+++|++||+|..+++     ++.++|||||+|.+.++|++|+. +.+..+.++.+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            3489999999999999999999999999999875     57889999999999999999996 66677777777777665


Q ss_pred             CCCCCC--cccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCce
Q 001991          349 PKDNPS--EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSD  421 (985)
Q Consensus       349 pk~~~~--~~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~  421 (985)
                      ++....  ......++|||+|||..+|+++|+++|+.||.|..+.+..     .++|||||+|.+.++|.+|++ +++..
T Consensus        84 ~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~  162 (183)
T d1u1qa_          84 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHT  162 (183)
T ss_dssp             CTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEE
T ss_pred             hcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCe
Confidence            544322  2334567999999999999999999999999999998864     356899999999999999997 89999


Q ss_pred             eCCceEEEEeccCcchhh
Q 001991          422 VAGKQIKLEASRPGGARR  439 (985)
Q Consensus       422 I~Gr~IkV~~A~~k~~Rr  439 (985)
                      |.|++|+|.+|.+|+++.
T Consensus       163 ~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         163 VNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             ETTEEEEEEECCCHHHHH
T ss_pred             ECCEEEEEEecCCccccc
Confidence            999999999999887654

>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=99.69  E-value=1.8e-17  Score=164.92  Aligned_cols=163  Identities=18%  Similarity=0.326  Sum_probs=119.5

Q ss_pred             cccccccCCC-CCcccccccCcccccCCCCCCCCCcccccceeeEecCcCCCh--hhhhccCCCCeeeeecCCChhhhhh
Q 001991          147 SDIFTRKMKL-SGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDE--DDLFSGVTDDMGHNFQANTVDDLED  223 (985)
Q Consensus       147 ~~lFv~nL~~-~dn~~L~~~~~d~~~~~~~~~E~F~s~EEie~~~iGnILpde--dDL~sG~SkGfGFV~ff~t~Edaee  223 (985)
                      ..|||+||+. ++.++|.+.              |+..        |+|+...  .+..++.++||+||. |.+.++++ 
T Consensus         7 r~lfV~nLp~~~te~~L~~~--------------F~~~--------G~v~~~~~~~~~~~~~~~g~afv~-f~~~~~a~-   62 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSH--------------FEQW--------GTLTDCVVMRDPNTKRSRGFGFVT-YATVEEVD-   62 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHH--------------HGGG--------SCEEEEEEEECTTTCCEEEEEEEE-ESSHHHHH-
T ss_pred             CEEEEECCCCCCCHHHHHHH--------------HHHc--------CCEEEEEeeecccCCCccCceecc-cCCHHHHH-
Confidence            4699999998 888889988              8444        4333311  223478899999999 55777777 


Q ss_pred             hHHHhccCCeeEcCCcchhhhcccccccCCCCCCCCCCCCcCCCCCCCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEE
Q 001991          224 FDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIR  303 (985)
Q Consensus       224 ~~ai~~~nG~eLegd~~~~vg~~ls~l~k~~~n~~~~~~~~~~e~~~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~  303 (985)
                       .|+...++. +. ...+.+.....              .............++|||+|||..+|+++|+++|+.||.|.
T Consensus        63 -~a~~~~~~~-~~-~~~~~~~~~~~--------------~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~  125 (183)
T d1u1qa_          63 -AAMNARPHK-VD-GRVVEPKRAVS--------------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE  125 (183)
T ss_dssp             -HHHHTCSCE-ET-TEECEEEECCC--------------TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEE
T ss_pred             -HHHHhcCCc-cc-ccchhhhhhhh--------------cccccccccccccceeEEccCCCcCCHHHHhhhhccCCcee
Confidence             677655443 33 22111111100              00111123455678999999999999999999999999999


Q ss_pred             EEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          304 TIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       304 sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      .+.+     +++++|||||+|.+.++|++|++ +++..+.|++|.|.++.++.
T Consensus       126 ~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             EEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHH
T ss_pred             eeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCcc
Confidence            9875     47889999999999999999996 89999999999999987753

>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=99.61  E-value=6.2e-16  Score=135.59  Aligned_cols=76  Identities=26%  Similarity=0.423  Sum_probs=70.7

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .++|||+|||.++|+++|+++|++||.|.+|++..+     .+|||||+|.+.++|++|++.|||..+.|++|+|+||+|
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            457999999999999999999999999999998643     478999999999999999999999999999999999987


Q ss_pred             c
Q 001991          435 G  435 (985)
Q Consensus       435 k  435 (985)
                      +
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.60  E-value=6e-16  Score=135.66  Aligned_cols=75  Identities=25%  Similarity=0.474  Sum_probs=71.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .++|||+|||+++|+++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|||..+.|++|+|+|++|
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            578999999999999999999999999999975     577899999999999999999999999999999999999976

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.4e-15  Score=136.07  Aligned_cols=81  Identities=26%  Similarity=0.392  Sum_probs=73.9

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ...++|||+|||.++|+++|+++|++||.|.+|++..+   .++||||+|.+.++|.+|++.|||..|.|+.|+|.||++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            44579999999999999999999999999999998654   578999999999999999999999999999999999987


Q ss_pred             cchh
Q 001991          435 GGAR  438 (985)
Q Consensus       435 k~~R  438 (985)
                      +..+
T Consensus        86 ~~~~   89 (90)
T d2cqia1          86 PSSQ   89 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            6543

>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=99.60  E-value=4.3e-16  Score=139.18  Aligned_cols=80  Identities=21%  Similarity=0.347  Sum_probs=73.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ...+|||+|||.++++++|+++|++||.|.++++..+   ++|||||+|.+.++|++|++.|||..|+|++|+|.+++++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3458999999999999999999999999999998764   5789999999999999999999999999999999999987


Q ss_pred             chh
Q 001991          436 GAR  438 (985)
Q Consensus       436 ~~R  438 (985)
                      .+|
T Consensus        87 ~~R   89 (89)
T d1cvja2          87 KER   89 (89)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>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=99.60  E-value=1.1e-15  Score=133.92  Aligned_cols=75  Identities=31%  Similarity=0.492  Sum_probs=69.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .++|||+|||.++++++|+++|++||.|.+|++..+     .+|||||+|.+.++|++|++.|||..+.|++|+|.||+|
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            357999999999999999999999999999998643     467999999999999999999999999999999999987

>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=99.59  E-value=1e-15  Score=136.50  Aligned_cols=80  Identities=20%  Similarity=0.415  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ...+.++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|||..|.|++|.|+
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3446789999999999999999999999999999875     47789999999999999999999999999999999999


Q ss_pred             ccCCC
Q 001991          346 YSIPK  350 (985)
Q Consensus       346 ~a~pk  350 (985)
                      |+.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99865

>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=99.59  E-value=1.4e-15  Score=136.12  Aligned_cols=80  Identities=24%  Similarity=0.471  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     ++.++|||||+|.+.++|++|++.|+|..|.|++|.|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            346689999999999999999999999999999975     577899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 001991          347 SIPKD  351 (985)
Q Consensus       347 a~pk~  351 (985)
                      +.|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98874

>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=99.59  E-value=1.1e-15  Score=136.39  Aligned_cols=80  Identities=21%  Similarity=0.343  Sum_probs=72.6

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      .....+|||+|||..+|+++|+++|++||+|.+|++..+     ++|||||+|.+.++|++|++.|||..+.|++|+|+|
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            345679999999999999999999999999999988653     468999999999999999999999999999999999


Q ss_pred             ccCcc
Q 001991          432 SRPGG  436 (985)
Q Consensus       432 A~~k~  436 (985)
                      |.+++
T Consensus        84 a~~kG   88 (88)
T d1rk8a_          84 CFVKG   88 (88)
T ss_dssp             SEECC
T ss_pred             ecCCC
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=8.8e-16  Score=137.10  Aligned_cols=80  Identities=25%  Similarity=0.422  Sum_probs=73.4

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||.++++++|+++|++||+|.+|+++.     .++|||||+|.+.++|++|++.|||..|+|++|+|.+|+
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            356999999999999999999999999999999864     367899999999999999999999999999999999999


Q ss_pred             Ccchh
Q 001991          434 PGGAR  438 (985)
Q Consensus       434 ~k~~R  438 (985)
                      ++..|
T Consensus        84 p~~~k   88 (89)
T d2cqba1          84 PMRIK   88 (89)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.59  E-value=1.1e-15  Score=136.75  Aligned_cols=79  Identities=20%  Similarity=0.325  Sum_probs=73.0

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||.++++++|+++|++||+|.+|+++.+     ++|||||+|.+.++|++|++.|||..|+|++|+|+||
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            34678999999999999999999999999999998653     4779999999999999999999999999999999999


Q ss_pred             cCcc
Q 001991          433 RPGG  436 (985)
Q Consensus       433 ~~k~  436 (985)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            9864

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.8e-15  Score=136.32  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=74.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....++|||+|||.++|+++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++.|+|..|.|++|+|++
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999975     578999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 001991          347 SIPKD  351 (985)
Q Consensus       347 a~pk~  351 (985)
                      +.++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98765

>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=99.58  E-value=1.4e-15  Score=133.15  Aligned_cols=75  Identities=23%  Similarity=0.496  Sum_probs=70.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .++|||+|||+++++++|+++|++||+|..|++     .++++|||||+|.+.++|++|++.|+|..|.|++|+|.|++|
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            367999999999999999999999999999876     468899999999999999999999999999999999999976

>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=2.8e-15  Score=132.14  Aligned_cols=78  Identities=18%  Similarity=0.312  Sum_probs=72.6

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCcee-CCceEEEEeccC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV-AGKQIKLEASRP  434 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I-~Gr~IkV~~A~~  434 (985)
                      .++.++|||+|||..+++++|+++|++||.|.+|++.++++|||||+|.+.++|.+|++.|||..| +|++|+|.||+.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~akk   83 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK   83 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEecC
Confidence            345679999999999999999999999999999999988899999999999999999999999988 579999999973

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=4e-15  Score=133.97  Aligned_cols=80  Identities=21%  Similarity=0.358  Sum_probs=73.7

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ....++|||+|||..+++++|+++|++||+|.+|++..+   ++|||||+|.+.++|.+|++.|||..|+|++|+|++|+
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            345668999999999999999999999999999998754   57899999999999999999999999999999999999


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            864

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=3.5e-15  Score=135.65  Aligned_cols=83  Identities=24%  Similarity=0.393  Sum_probs=76.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ...+++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
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            345788999999999999999999999999999976     578899999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 001991          347 SIPKDNPS  354 (985)
Q Consensus       347 a~pk~~~~  354 (985)
                      +.++....
T Consensus        85 a~~~~~~~   92 (99)
T d1whwa_          85 STIKKEAS   92 (99)
T ss_dssp             CCCCSTTC
T ss_pred             CCCCCccC
Confidence            98876543

>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=1.6e-15  Score=138.97  Aligned_cols=82  Identities=16%  Similarity=0.351  Sum_probs=74.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .+.++|||+|||.++++++|+++|++||.|.+++++.+     .+|||||+|.+.++|++||+.|||..|+|++|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999887643     4689999999999999999999999999999999999


Q ss_pred             cCcchhh
Q 001991          433 RPGGARR  439 (985)
Q Consensus       433 ~~k~~Rr  439 (985)
                      +++.+++
T Consensus        96 ~~k~~~k  102 (102)
T d2cpza1          96 RSKNDSK  102 (102)
T ss_dssp             CCSCCCC
T ss_pred             CCCCCCC
Confidence            9987653

>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=3.2e-15  Score=136.87  Aligned_cols=81  Identities=17%  Similarity=0.373  Sum_probs=74.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .+.++|||+|||+++++++|+++|++||.|.++++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            35678999999999999999999999999998865     5788999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 001991          348 IPKDNP  353 (985)
Q Consensus       348 ~pk~~~  353 (985)
                      .++.+.
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            887653

>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=99.57  E-value=3.3e-15  Score=135.54  Aligned_cols=76  Identities=21%  Similarity=0.333  Sum_probs=72.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ..++|||+|||..+++++|+++|++||.|.+|++.++ +|||||+|.+.++|++|+..|||..|.|++|+|.|++++
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 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            3568999999999999999999999999999999876 899999999999999999999999999999999999864

>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=99.57  E-value=1.3e-15  Score=136.00  Aligned_cols=78  Identities=29%  Similarity=0.504  Sum_probs=73.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..++|||+|||+++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.||+..|.|++|.|.++.
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            4689999999999999999999999999999976     57899999999999999999999999999999999999998


Q ss_pred             CCC
Q 001991          349 PKD  351 (985)
Q Consensus       349 pk~  351 (985)
                      |+.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.56  E-value=3.2e-15  Score=134.65  Aligned_cols=78  Identities=22%  Similarity=0.330  Sum_probs=72.4

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+|+++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++|++.|||..|.|++|+|.+|+
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            3568999999999999999999999999999998643     57899999999999999999999999999999999998


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            865

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.6e-15  Score=140.95  Aligned_cols=102  Identities=26%  Similarity=0.407  Sum_probs=85.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ..+++|||+|||.++++++|+++|++||+|..|++  ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.++
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            45789999999999999999999999999999987  5778999999999999999999999999999999999998643


Q ss_pred             CCCCcccccccceeeecCCCCCCHHHHHHHhhccCC
Q 001991          351 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE  386 (985)
Q Consensus       351 ~~~~~~~~~~~tLfV~NLp~svTeedLrelFs~fG~  386 (985)
                      ....            .......+++++.+.++||.
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            11222346778888888874

>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=99.56  E-value=4.5e-15  Score=133.96  Aligned_cols=79  Identities=19%  Similarity=0.433  Sum_probs=72.5

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHh-CCceeCCceEEEE
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTL-NRSDVAGKQIKLE  430 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~L-NG~~I~Gr~IkV~  430 (985)
                      ....+|||+|||..+++++|+++|++||.|.+|+++.+      ++|||||+|.+.++|.+|++.| ||..|.|++|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            34678999999999999999999999999999998643      5789999999999999999998 8999999999999


Q ss_pred             eccCcc
Q 001991          431 ASRPGG  436 (985)
Q Consensus       431 ~A~~k~  436 (985)
                      ||.++.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998765

>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=99.56  E-value=4e-15  Score=134.04  Aligned_cols=79  Identities=27%  Similarity=0.436  Sum_probs=73.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.+     ++.++|||||+|.+.++|++|++.|||..|.|++|.|.|+
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            46789999999999999999999999999999976     5778999999999999999999999999999999999998


Q ss_pred             CCCC
Q 001991          348 IPKD  351 (985)
Q Consensus       348 ~pk~  351 (985)
                      ....
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>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=99.56  E-value=3.7e-15  Score=134.30  Aligned_cols=78  Identities=24%  Similarity=0.321  Sum_probs=71.9

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+|+++|+++|++||+|.+|+++.+     .+|||||+|.+.++|++|++.|||..+.|++|+|+|+.
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            4679999999999999999999999999999998653     46799999999999999999999999999999999997


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      ...
T Consensus        86 ~~~   88 (93)
T d1h2vz_          86 GFK   88 (93)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.56  E-value=4.4e-15  Score=133.99  Aligned_cols=80  Identities=26%  Similarity=0.530  Sum_probs=73.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe------ccccceEEEEEeCCHHHHHHHHHHc-cCcccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKLDI  344 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki------tgksrGfAFV~F~d~esA~kAi~~L-ng~~I~Gr~L~V  344 (985)
                      ...+++|||+|||.++++++|+++|++||.|..|++      +++++|||||+|.+.++|.+|++.| |+..|.|++|.|
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            346788999999999999999999999999999976      4678999999999999999999998 899999999999


Q ss_pred             cccCCCC
Q 001991          345 HYSIPKD  351 (985)
Q Consensus       345 ~~a~pk~  351 (985)
                      .|+.++.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9997654

>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=4.8e-15  Score=142.54  Aligned_cols=83  Identities=20%  Similarity=0.419  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .....++|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|.+|++.|||..|.|++|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3445689999999999999999999999999999876     57889999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++..+
T Consensus       118 ~a~~~~~~  125 (139)
T d1u6fa1         118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             EcCCCCCC
Confidence            99876654

>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=99.55  E-value=4.4e-15  Score=132.75  Aligned_cols=82  Identities=18%  Similarity=0.443  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ++.+.++|||+|||.++|+++|+++|++||+|..|++   ....+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3456789999999999999999999999999999976   3446899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 001991          348 IPKDN  352 (985)
Q Consensus       348 ~pk~~  352 (985)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            76543

>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=99.55  E-value=8.4e-15  Score=131.80  Aligned_cols=82  Identities=22%  Similarity=0.405  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .....++|||+|||+++++++|+++|++||+|..|++   .+.++|||||+|.+.++|++|++.|++..|.|++|+|.++
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3445688999999999999999999999999999976   3457899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 001991          348 IPKDN  352 (985)
Q Consensus       348 ~pk~~  352 (985)
                      .++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            87643

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=7.1e-15  Score=128.08  Aligned_cols=73  Identities=21%  Similarity=0.366  Sum_probs=68.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      +.|||+|||.++++++|+++|++||.|.+|++..+    ++|||||+|.+.++|++|++.|||..+.|++|+|+++.
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            36999999999999999999999999999998754    57799999999999999999999999999999999985

>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=99.55  E-value=3.8e-15  Score=130.31  Aligned_cols=74  Identities=15%  Similarity=0.195  Sum_probs=67.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ++|||+|||.++|+++|+++|++||.|..+.+..     .++|||||+|.+.++|++|++.|||..+.|++|+|++++|
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            6899999999999999999999999998776643     3678999999999999999999999999999999999987

>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=99.55  E-value=4.4e-15  Score=136.66  Aligned_cols=77  Identities=26%  Similarity=0.503  Sum_probs=71.9

Q ss_pred             ccceeeecCCC-CCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          360 QGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       360 ~~tLfV~NLp~-svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..+|||+||++ .+|+++|+++|++||+|.+|+++.+++|||||+|.+.++|.+|++.|||..|.|++|+|.|++.+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            46899999965 699999999999999999999999999999999999999999999999999999999999987543

>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=99.55  E-value=8.2e-15  Score=133.15  Aligned_cols=79  Identities=23%  Similarity=0.344  Sum_probs=72.9

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++|++.|||..|.|++|+|.+++
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            4568999999999999999999999999999998643     57899999999999999999999999999999999999


Q ss_pred             Ccch
Q 001991          434 PGGA  437 (985)
Q Consensus       434 ~k~~  437 (985)
                      ++..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            8653

>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=99.54  E-value=4.1e-15  Score=132.64  Aligned_cols=79  Identities=22%  Similarity=0.488  Sum_probs=73.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..++|||+|||+++++++|+++|++||.|..+.+     ++.++|||||+|.+.++|++|++.|+|..|.|++|.|.++.
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            4678999999999999999999999999999864     57789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      ++.+
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.54  E-value=3.1e-15  Score=135.30  Aligned_cols=82  Identities=23%  Similarity=0.328  Sum_probs=76.0

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ....++|||+|||.++|+++|+++|++||.|..++....+++||||+|.+.++|++|++.|||..|.|++|+|.|+.++.
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            34567999999999999999999999999999888887789999999999999999999999999999999999999876


Q ss_pred             hh
Q 001991          437 AR  438 (985)
Q Consensus       437 ~R  438 (985)
                      .+
T Consensus        93 ~~   94 (96)
T d1fjca_          93 GT   94 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=4.3e-15  Score=130.00  Aligned_cols=73  Identities=27%  Similarity=0.337  Sum_probs=68.5

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      +|||+|||..+|+++|+++|++||+|.+|+++.+     ++|||||+|.++++|.+|++.|||..+.|++|+|.|++.
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            6999999999999999999999999999998754     368999999999999999999999999999999999964

>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=99.54  E-value=4e-15  Score=132.73  Aligned_cols=80  Identities=26%  Similarity=0.491  Sum_probs=72.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+++++|+++|++||.|..+.+..     .++|||||+|.++++|++|++.|||..|+|++|+|+++.
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            356799999999999999999999999999988754     268899999999999999999999999999999999998


Q ss_pred             Ccchh
Q 001991          434 PGGAR  438 (985)
Q Consensus       434 ~k~~R  438 (985)
                      ++..+
T Consensus        84 ~~~~~   88 (90)
T d1x5sa1          84 KSSDN   88 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87644

>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=99.54  E-value=3.8e-15  Score=134.71  Aligned_cols=82  Identities=24%  Similarity=0.400  Sum_probs=77.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...+.++|||+|||.++|+++|+++|++||.|..++.+++++|||||+|.+.++|++|++.||+..|.|++|.|.|+.++
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k   91 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            34567999999999999999999999999999999888999999999999999999999999999999999999999887


Q ss_pred             CC
Q 001991          351 DN  352 (985)
Q Consensus       351 ~~  352 (985)
                      ..
T Consensus        92 ~~   93 (96)
T d1fjca_          92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=1.3e-14  Score=132.44  Aligned_cols=79  Identities=14%  Similarity=0.260  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      .+...++|||+|||+++++++|+++|++||+|..+.+    ++.++|||||+|.+.++|++|++.|||+.|.|+++.|.+
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3445689999999999999999999999999988865    567899999999999999999999999999999999987


Q ss_pred             cCC
Q 001991          347 SIP  349 (985)
Q Consensus       347 a~p  349 (985)
                      +.|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

>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=99.54  E-value=2.9e-15  Score=131.02  Aligned_cols=74  Identities=18%  Similarity=0.230  Sum_probs=66.5

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ++|||+|||+++|+++|+++|++||.|..+.+     .++++|||||+|.+.++|++|++.|||..+.|++|.|+++.|
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            69999999999999999999999999976653     578899999999999999999999999999999999999976

>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=99.54  E-value=3.3e-15  Score=133.31  Aligned_cols=78  Identities=18%  Similarity=0.380  Sum_probs=72.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      ..+|||+|||+++++++|+++|++||.|..+++   .+.++|||||+|.+.++|++|++.|||..|.|++|.|.++.++.
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            468999999999999999999999999999986   34578999999999999999999999999999999999998765


Q ss_pred             C
Q 001991          352 N  352 (985)
Q Consensus       352 ~  352 (985)
                      +
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=5.3e-15  Score=130.53  Aligned_cols=74  Identities=24%  Similarity=0.402  Sum_probs=68.2

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC--------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       363 LfV~NLp~svTeedLrelFs~fG~I~~Vri~~~--------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      |||+|||.++|+++|+++|++||.|.+|++..+        ++|||||+|.+.++|++|++.|||..++|++|+|+++++
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            799999999999999999999999999988642        368999999999999999999999999999999999975


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=5.7e-15  Score=130.86  Aligned_cols=76  Identities=21%  Similarity=0.429  Sum_probs=71.4

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      .+|||+|||.++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|.|.++.+.
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            47999999999999999999999999999976     5788999999999999999999999999999999999999765


Q ss_pred             C
Q 001991          351 D  351 (985)
Q Consensus       351 ~  351 (985)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=5.1e-15  Score=129.53  Aligned_cols=72  Identities=18%  Similarity=0.379  Sum_probs=68.7

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      +|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|+.
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            6999999999999999999999999999986     57789999999999999999999999999999999999984

>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=6.3e-15  Score=130.45  Aligned_cols=78  Identities=22%  Similarity=0.337  Sum_probs=73.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      ..++|||+|||+++++++|+++|++||.|..+++ ++++|||||+|.+.++|.+|+..|||..|.|++|.|.|+.|+..
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            4589999999999999999999999999988887 67899999999999999999999999999999999999988764

>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=2.4e-15  Score=137.77  Aligned_cols=80  Identities=24%  Similarity=0.450  Sum_probs=73.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      +...++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus         5 ~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~   84 (104)
T d1p1ta_           5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999875     577899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 001991          347 SIPKD  351 (985)
Q Consensus       347 a~pk~  351 (985)
                      +.++.
T Consensus        85 a~~~~   89 (104)
T d1p1ta_          85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCCC
Confidence            87654

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.53  E-value=9.1e-15  Score=129.21  Aligned_cols=75  Identities=23%  Similarity=0.431  Sum_probs=69.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccc--cccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIH  345 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~  345 (985)
                      ...++|||+|||.++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|||..+.|  ++|.|+
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            35678999999999999999999999999999975     57899999999999999999999999999987  889998


Q ss_pred             cc
Q 001991          346 YS  347 (985)
Q Consensus       346 ~a  347 (985)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.53  E-value=9e-15  Score=134.80  Aligned_cols=78  Identities=19%  Similarity=0.253  Sum_probs=71.9

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ...++|||+|||..+++++|+++|++||+|..|.+. ..++||||+|.+.++|++|++.|||..|.|++|+|+|+....
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            345799999999999999999999999999999875 468999999999999999999999999999999999997544

>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=99.53  E-value=7e-15  Score=129.72  Aligned_cols=74  Identities=27%  Similarity=0.466  Sum_probs=67.9

Q ss_pred             EEEecCCCCCCHHHHHHhhcccCcEEEEEe-----c---cccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          278 LFVRNINSNVEDSELKALFEQFGDIRTIYT-----A---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       278 LfVgNLP~~vTEedLrelFs~fG~I~sVki-----t---gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      |||+|||.++|+++|+++|++||+|.++++     +   +.++|||||+|.+.++|++|++.|||..+.|++|.|+++.+
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            799999999999999999999999999876     1   24689999999999999999999999999999999999865


Q ss_pred             CC
Q 001991          350 KD  351 (985)
Q Consensus       350 k~  351 (985)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.53  E-value=1.2e-14  Score=128.07  Aligned_cols=78  Identities=18%  Similarity=0.350  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc-cccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~-Gr~L~V~~a~  348 (985)
                      ...|+++|||+|||.++++++|+++|++||+|..|++....+|||||+|.+.++|.+|++.|+|..|. |++|.|.|++
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            44578999999999999999999999999999999987777899999999999999999999999884 6899999985

>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=99.53  E-value=2.4e-15  Score=131.86  Aligned_cols=77  Identities=25%  Similarity=0.299  Sum_probs=69.9

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCc-eeCCceEEEEeccCcchh
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS-DVAGKQIKLEASRPGGAR  438 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~-~I~Gr~IkV~~A~~k~~R  438 (985)
                      .+|||+|||.++|+++|+++|++||.|..+++.. ++|||||+|.+.++|++|++.|||. .+.|++|+|+|+.++..|
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            3699999999999999999999999998766554 4899999999999999999999996 699999999999987654

>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=99.53  E-value=6.6e-15  Score=130.82  Aligned_cols=77  Identities=25%  Similarity=0.364  Sum_probs=71.9

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..++|||+|||.++++++|+++|++||+|.+|++.++ ++||||+|.+.++|++|++.|||..|.|++|+|+||.++.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3457999999999999999999999999999998765 8999999999999999999999999999999999998754

>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=99.53  E-value=8.2e-15  Score=140.86  Aligned_cols=79  Identities=24%  Similarity=0.393  Sum_probs=72.5

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      .++|||+|||.++|+++|+++|++||+|.+|+++.+     ++|||||+|.+.++|++||+.|||..|+|++|+|+++++
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            458999999999999999999999999999988643     578999999999999999999999999999999999987


Q ss_pred             cchh
Q 001991          435 GGAR  438 (985)
Q Consensus       435 k~~R  438 (985)
                      +..|
T Consensus       122 ~~~~  125 (139)
T d1u6fa1         122 GHQR  125 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6644

>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=7.1e-15  Score=129.25  Aligned_cols=73  Identities=19%  Similarity=0.428  Sum_probs=68.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  344 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V  344 (985)
                      ..++++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            346789999999999999999999999999999875     4778999999999999999999999999999999986

>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=99.52  E-value=1.2e-14  Score=134.95  Aligned_cols=78  Identities=26%  Similarity=0.376  Sum_probs=71.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC--CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~--~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..++|||+|||..+++++|+++|++||.|.+|++..  ..+|||||+|.+.++|.+|++.|||..|.|++|+|.++.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   85 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANR   85 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            356899999999999999999999999999999864  368999999999999999999999999999999999987543

>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=99.52  E-value=1.1e-14  Score=128.84  Aligned_cols=74  Identities=23%  Similarity=0.391  Sum_probs=67.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHY  346 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~  346 (985)
                      ..++|||+|||+++|+++|+++|++||+|.++++     +++++|||||+|.+.++|++|++.|||..+.|  ++|.|.|
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            3578999999999999999999999999999876     47789999999999999999999999999998  4588877


Q ss_pred             c
Q 001991          347 S  347 (985)
Q Consensus       347 a  347 (985)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.52  E-value=1.9e-14  Score=129.87  Aligned_cols=78  Identities=31%  Similarity=0.461  Sum_probs=71.6

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC--CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~--~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ...++|||+|||..+|+++|+++|++||.|..+++..  ..++||||+|.+.++|++||+.|||..|.|++|+|+|+++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            3456899999999999999999999999999998864  36789999999999999999999999999999999999864

>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=99.52  E-value=7.4e-15  Score=127.97  Aligned_cols=72  Identities=25%  Similarity=0.450  Sum_probs=68.5

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      +|||+|||+++++++|+++|++||+|..+++    +++++|||||+|.+.++|++|++.|||..+.|++|+|+++.
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            6999999999999999999999999999986    67789999999999999999999999999999999999874

>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=99.52  E-value=1.4e-14  Score=130.50  Aligned_cols=82  Identities=22%  Similarity=0.472  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHcc------Cccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQ------NKPLRR  339 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Ln------g~~I~G  339 (985)
                      .....++|||+|||+++|+++|+++|++||+|..+.+     ++.++|||||+|.+.++|.+|++.|+      |..+.|
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            3445789999999999999999999999999998875     46689999999999999999999886      567899


Q ss_pred             ccccccccCCCCC
Q 001991          340 RKLDIHYSIPKDN  352 (985)
Q Consensus       340 r~L~V~~a~pk~~  352 (985)
                      ++|.|.++.++.+
T Consensus        84 r~l~v~~a~~k~~   96 (98)
T d1x4ha1          84 RQLKVDLAVTRDE   96 (98)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCCc
Confidence            9999999988754

>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=1.4e-14  Score=129.99  Aligned_cols=79  Identities=16%  Similarity=0.313  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....++|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.+  ..|.|+.|.|++
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEe
Confidence            346689999999999999999999999999999975     5889999999999999999999744  479999999999


Q ss_pred             cCCCCC
Q 001991          347 SIPKDN  352 (985)
Q Consensus       347 a~pk~~  352 (985)
                      +.++..
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            988754

>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=99.52  E-value=1.3e-14  Score=132.09  Aligned_cols=76  Identities=18%  Similarity=0.326  Sum_probs=69.1

Q ss_pred             ccccceeeecCC-CCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          358 ANQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       358 ~~~~tLfV~NLp-~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ....+|||+||+ ..+++++|+++|++||.|.+|++   .++||||+|.+.++|++|++.|||..|.|++|+|++++++.
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            345689999997 57889999999999999999998   47999999999999999999999999999999999997643

>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=99.51  E-value=2e-14  Score=129.68  Aligned_cols=79  Identities=16%  Similarity=0.338  Sum_probs=72.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ..+.++|||+|||+++|+++|+++|++||.|..+++  ....++||||+|++.++|++|++.||+..|.|++|+|.|+.+
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            345678999999999999999999999999999887  466789999999999999999999999999999999999875


Q ss_pred             C
Q 001991          350 K  350 (985)
Q Consensus       350 k  350 (985)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=7.4e-15  Score=129.01  Aligned_cols=75  Identities=19%  Similarity=0.344  Sum_probs=68.1

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCEEEE-EEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          363 LVVFNLDSSVSTEELHQIFGIYGEIREI-RDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       363 LfV~NLp~svTeedLrelFs~fG~I~~V-ri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      |||+|||.++|+++|+++|++||.|.++ +++.     .++|||||+|.+.++|++|++.|||..+.|++|+|.++.+++
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            7999999999999999999999998664 5553     357999999999999999999999999999999999999876


Q ss_pred             h
Q 001991          437 A  437 (985)
Q Consensus       437 ~  437 (985)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.51  E-value=4.6e-15  Score=135.92  Aligned_cols=82  Identities=21%  Similarity=0.357  Sum_probs=73.8

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||.++++++|+++|++||+|.+|+++.+     ++|||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999999988643     4689999999999999999999999999999999999


Q ss_pred             cCcchhh
Q 001991          433 RPGGARR  439 (985)
Q Consensus       433 ~~k~~Rr  439 (985)
                      .++..+.
T Consensus        86 ~~~~~~~   92 (104)
T d1p1ta_          86 ASEKNKE   92 (104)
T ss_dssp             TCTTHHH
T ss_pred             CCCCCcc
Confidence            8766444

>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=99.51  E-value=8.1e-15  Score=134.26  Aligned_cols=78  Identities=21%  Similarity=0.425  Sum_probs=70.9

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...++|||+|||..+++++|+++|+.||+|.+|+++.+     ++|||||+|.+.++|.+|++ |||..|.|++|+|.++
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            34568999999999999999999999999999999753     68899999999999999996 9999999999999998


Q ss_pred             cCcc
Q 001991          433 RPGG  436 (985)
Q Consensus       433 ~~k~  436 (985)
                      .++.
T Consensus        95 ~~~~   98 (101)
T d2cq4a1          95 QAEK   98 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
Confidence            7543

>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=99.51  E-value=1.9e-14  Score=131.97  Aligned_cols=81  Identities=25%  Similarity=0.380  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      .+...++|||+|||..+++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++ .|.|++|.|+
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            3445678999999999999999999999999999986     478999999999999999999988765 7999999999


Q ss_pred             ccCCCCC
Q 001991          346 YSIPKDN  352 (985)
Q Consensus       346 ~a~pk~~  352 (985)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (103)
T d2cqda1          85 LAYLGAK   91 (103)
T ss_dssp             ESTTTCC
T ss_pred             EcCCCCC
Confidence            9876544

>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=99.51  E-value=1.5e-14  Score=128.08  Aligned_cols=74  Identities=28%  Similarity=0.405  Sum_probs=67.3

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCC--ceEEEEe
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLEA  431 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~G--r~IkV~~  431 (985)
                      ..++|||+|||..+|+++|+++|++||+|.+|+++.+     ++|||||+|.+.++|++|++.|||..+.|  ++|+|.|
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            3568999999999999999999999999999998643     56799999999999999999999999987  5699998


Q ss_pred             c
Q 001991          432 S  432 (985)
Q Consensus       432 A  432 (985)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.51  E-value=1e-14  Score=129.13  Aligned_cols=76  Identities=16%  Similarity=0.368  Sum_probs=70.7

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      .+|||+|||..+|+++|+++|++||+|.+|+++.+     ++|||||+|.++++|++|++.|||..|+|++|+|++|.++
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            36999999999999999999999999999998643     5799999999999999999999999999999999999865


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.51  E-value=1.6e-14  Score=132.34  Aligned_cols=80  Identities=23%  Similarity=0.294  Sum_probs=71.7

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ++...++|||+|||..+++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++||+.+|+ .|.|++|+|.
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            3445568999999999999999999999999999998754     679999999999999999998876 7999999999


Q ss_pred             eccCcc
Q 001991          431 ASRPGG  436 (985)
Q Consensus       431 ~A~~k~  436 (985)
                      ++..+.
T Consensus        85 ~a~~~~   90 (103)
T d2cqda1          85 LAYLGA   90 (103)
T ss_dssp             ESTTTC
T ss_pred             EcCCCC
Confidence            998654

>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=99.51  E-value=1.3e-14  Score=131.51  Aligned_cols=77  Identities=16%  Similarity=0.339  Sum_probs=71.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      ..++|||+|||.++++++|+++|++||+|.+|++ ...+|||||+|.+.++|++|+..|+|..|.|++|+|.|+.++.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i-~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEE-EecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            4578999999999999999999999999999998 4569999999999999999999999999999999999997643

>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=99.50  E-value=2e-14  Score=127.15  Aligned_cols=76  Identities=24%  Similarity=0.239  Sum_probs=70.3

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      .++|||+|||..+++++|+++|++||.|..+++. ..+|||||+|.+.++|.+|+..|||..|.|++|+|.|++|+.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~-~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE-ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc-cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            4689999999999999999999999998777664 468999999999999999999999999999999999999875

>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=99.50  E-value=1.5e-14  Score=133.26  Aligned_cols=77  Identities=13%  Similarity=0.279  Sum_probs=72.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...++|||+|||+++++++|+++|++||+|..|.+ .+.+|||||+|.+.++|++|++.|||..|.|++|.|.|+...
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            35589999999999999999999999999999998 678999999999999999999999999999999999998654

>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=133.86  Aligned_cols=79  Identities=11%  Similarity=0.259  Sum_probs=72.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||.++++++|+++|++||.|..+.+..     .++|||||+|.+.++|++|++ +++..|.|++|.|.+|.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            346899999999999999999999999999999854     368999999999999999997 89999999999999999


Q ss_pred             Ccchh
Q 001991          434 PGGAR  438 (985)
Q Consensus       434 ~k~~R  438 (985)
                      +++++
T Consensus        98 ~ke~~  102 (103)
T d1x4ba1          98 AREES  102 (103)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            87643

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=6.8e-15  Score=131.08  Aligned_cols=79  Identities=22%  Similarity=0.449  Sum_probs=73.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      ..+++|||+|||.++|+++|+++|++||+|..|++...++|||||+|++.++|++|+.  ++..|.|++|.|.++.++..
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            4678999999999999999999999999999999988899999999999999999984  78899999999999988765


Q ss_pred             C
Q 001991          353 P  353 (985)
Q Consensus       353 ~  353 (985)
                      .
T Consensus        81 ~   81 (88)
T d1wf0a_          81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.50  E-value=2.2e-14  Score=131.93  Aligned_cols=77  Identities=23%  Similarity=0.359  Sum_probs=71.1

Q ss_pred             CcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          275 SRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       275 srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      +++|||+|||+ .+|+++|+++|++||+|..|++....+|||||+|++.++|++|++.|+|..|.|+.|+|.|+....
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            57999999965 599999999999999999999866778999999999999999999999999999999999986543

>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=99.50  E-value=1.2e-14  Score=130.13  Aligned_cols=80  Identities=28%  Similarity=0.627  Sum_probs=72.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHH----hhcccCcEEEEEe--ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKA----LFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLre----lFs~fG~I~sVki--tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      +|+++|||+|||+++++++|++    +|++||+|.+|++  +++++|||||+|.+.++|.+|++.+||..+.|+.|.|.|
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            3689999999999999999864    6899999999987  466899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 001991          347 SIPKDN  352 (985)
Q Consensus       347 a~pk~~  352 (985)
                      +.++.+
T Consensus        81 ak~~~~   86 (91)
T d1nu4a_          81 AKTDSD   86 (91)
T ss_dssp             CSSCCT
T ss_pred             eCCCch
Confidence            987653

>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=99.50  E-value=4.1e-15  Score=130.31  Aligned_cols=77  Identities=22%  Similarity=0.361  Sum_probs=70.3

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCc-ccccccccccccCCCCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK-PLRRRKLDIHYSIPKDNP  353 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~-~I~Gr~L~V~~a~pk~~~  353 (985)
                      .+|||+|||.++|+++|+++|++||.|..+++ .+.+|||||+|.+.++|++|++.|||. .+.|++|+|.|+.|+..+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~-~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCE-EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEE-ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            47999999999999999999999999987766 567899999999999999999999996 599999999999987653

>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=99.50  E-value=9.5e-15  Score=129.57  Aligned_cols=76  Identities=21%  Similarity=0.401  Sum_probs=67.9

Q ss_pred             CCcEEEEecCCCCCCH-HHHHHhhcccCcEEEEEe------ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          274 PSRTLFVRNINSNVED-SELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       274 ~srtLfVgNLP~~vTE-edLrelFs~fG~I~sVki------tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ..++|||+|||+++++ ++|+++|++||+|..|++      +++++|||||+|.+.++|++|++ ||+..|.|++|.|.+
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            4689999999999865 569999999999999975      46789999999999999999995 999999999999999


Q ss_pred             cCCC
Q 001991          347 SIPK  350 (985)
Q Consensus       347 a~pk  350 (985)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=99.50  E-value=1.8e-14  Score=127.81  Aligned_cols=76  Identities=22%  Similarity=0.354  Sum_probs=68.1

Q ss_pred             cccceeeecCCCCCC-HHHHHHHhhccCCEEEEEEcC------CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEe
Q 001991          359 NQGTLVVFNLDSSVS-TEELHQIFGIYGEIREIRDTQ------HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  431 (985)
Q Consensus       359 ~~~tLfV~NLp~svT-eedLrelFs~fG~I~~Vri~~------~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~  431 (985)
                      ..++|||+|||.+++ +++|+++|++||.|.+|++..      .++|||||+|.+.++|++|++ |||..++|++|+|.+
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            357999999999986 566999999999999999853      257899999999999999996 999999999999999


Q ss_pred             ccCc
Q 001991          432 SRPG  435 (985)
Q Consensus       432 A~~k  435 (985)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=99.50  E-value=1.4e-14  Score=126.51  Aligned_cols=74  Identities=24%  Similarity=0.426  Sum_probs=68.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      ..++|||+||+  +|+++|+++|++||.|.+|++.+ .++||||+|.+.++|.+|++.|||..+.|++|+|.|++++
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--MTPTLLRGAFSPFGNIIDLSMDP-PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET-TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeecc-CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            35699999996  89999999999999999999875 4789999999999999999999999999999999999875

>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=99.50  E-value=2.2e-14  Score=126.11  Aligned_cols=72  Identities=22%  Similarity=0.421  Sum_probs=66.4

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEE
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL  429 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV  429 (985)
                      .+.++|||+|||..+|+++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++|++.|||..|+|++|+|
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            34679999999999999999999999999999988643     4679999999999999999999999999999987

>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=99.50  E-value=1.9e-14  Score=127.15  Aligned_cols=74  Identities=23%  Similarity=0.409  Sum_probs=67.8

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCC--ceEEEEe
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLEA  431 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~G--r~IkV~~  431 (985)
                      ..++|||+|||.++++++|+++|++||.|.+|+++.+     ++|||||+|.+.++|.+|++.|||..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            4567999999999999999999999999999998643     46899999999999999999999999976  8999998


Q ss_pred             c
Q 001991          432 S  432 (985)
Q Consensus       432 A  432 (985)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.50  E-value=2e-14  Score=127.70  Aligned_cols=77  Identities=29%  Similarity=0.432  Sum_probs=70.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCccc-ccccccccccCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPL-RRRKLDIHYSIP  349 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I-~Gr~L~V~~a~p  349 (985)
                      .|+++|||+|||.++++++|+++|++||.|..+.. .++.+|||||+|.+.++|.+|+..|+|..| .|++|+|.|+++
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            46899999999999999999999999999987654 677899999999999999999999999988 589999999865

>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=99.50  E-value=1.7e-14  Score=128.11  Aligned_cols=76  Identities=28%  Similarity=0.532  Sum_probs=71.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      .++|||+|||.++++++|+++|++||+|.+|++ .+.+|||||+|.+.++|++|++.|||..|.|++|+|+|+.++.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~-~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE-ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeee-ecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            467999999999999999999999999999998 5678999999999999999999999999999999999997654

>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=99.50  E-value=3.6e-14  Score=127.81  Aligned_cols=79  Identities=20%  Similarity=0.367  Sum_probs=71.3

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhC------CceeCCceE
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLN------RSDVAGKQI  427 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LN------G~~I~Gr~I  427 (985)
                      ..++|||+|||..+|+++|+++|++||.|.++.+..+     ++|||||+|.+.++|.+|++.||      |..+.|++|
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            4568999999999999999999999999999988643     57899999999999999999987      668899999


Q ss_pred             EEEeccCcch
Q 001991          428 KLEASRPGGA  437 (985)
Q Consensus       428 kV~~A~~k~~  437 (985)
                      +|.++.++.+
T Consensus        87 ~v~~a~~k~~   96 (98)
T d1x4ha1          87 KVDLAVTRDE   96 (98)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCc
Confidence            9999998753

>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=99.49  E-value=1.6e-14  Score=126.10  Aligned_cols=75  Identities=19%  Similarity=0.356  Sum_probs=70.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ...++|||+||+  +|+++|+++|++||+|.+|++ .+.+|||||+|.+.++|.+|++.|||..+.|++|+|.|+.++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~-~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeee-ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            456899999996  999999999999999999998 677899999999999999999999999999999999999765

>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=99.49  E-value=8.3e-15  Score=128.68  Aligned_cols=75  Identities=23%  Similarity=0.500  Sum_probs=68.6

Q ss_pred             EEEecCCCCCCHHHHHHhhcccCcEEEE-Ee-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          278 LFVRNINSNVEDSELKALFEQFGDIRTI-YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       278 LfVgNLP~~vTEedLrelFs~fG~I~sV-ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      |||+|||+++|+++|+++|++||.|..+ ++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.++.++.
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     57789999999999999999999999999999999999998765


Q ss_pred             C
Q 001991          352 N  352 (985)
Q Consensus       352 ~  352 (985)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.49  E-value=6.9e-15  Score=131.03  Aligned_cols=77  Identities=16%  Similarity=0.301  Sum_probs=72.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ..++|||+|||..+|+++|+++|++||.|.+|+++.++++||||+|.+.++|++|+.  ++..|.|++|+|.+++++..
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            457999999999999999999999999999999998899999999999999999985  88899999999999988664

>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=99.49  E-value=1.8e-14  Score=130.70  Aligned_cols=83  Identities=22%  Similarity=0.338  Sum_probs=73.1

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE--------Ee-----ccccceEEEEEeCCHHHHHHHHHHccCcc
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI--------YT-----ACKHRGFVMISYYDIRAARNAMKALQNKP  336 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV--------ki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~  336 (985)
                      ..+...++|||+|||.++|+++|+++|++||+|..+        .+     +++++|||||+|.+.++|++|++.|+|..
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            345567899999999999999999999999998643        21     46788999999999999999999999999


Q ss_pred             cccccccccccCCCCC
Q 001991          337 LRRRKLDIHYSIPKDN  352 (985)
Q Consensus       337 I~Gr~L~V~~a~pk~~  352 (985)
                      |.|++|+|.++.++..
T Consensus        83 ~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          83 FQGSKLKVSLARKKPP   98 (101)
T ss_dssp             ETTEECEEECSSCCCC
T ss_pred             ECCEEEEEEEcCCCCC
Confidence            9999999999987643

>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=7.7e-15  Score=133.53  Aligned_cols=81  Identities=21%  Similarity=0.400  Sum_probs=74.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .++++|||+|||.++++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|||..|.|++|.|.|+
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            46899999999999999999999999999887643     5789999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 001991          348 IPKDNP  353 (985)
Q Consensus       348 ~pk~~~  353 (985)
                      .++.++
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            887654

>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=99.49  E-value=3.1e-14  Score=126.42  Aligned_cols=77  Identities=23%  Similarity=0.318  Sum_probs=69.5

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEE-cCCCCcEEEEEEcCHHHHHHHHHHhCCcee-CCceEEEEeccCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDV-AGKQIKLEASRPG  435 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri-~~~skGfaFVeF~d~edA~kAI~~LNG~~I-~Gr~IkV~~A~~k  435 (985)
                      +.++|||+|||.++++++|+++|++||.|..+.+ .++.++||||+|.+.++|.+|+..|||..| .|++|+|+|+++.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            4679999999999999999999999999987654 455789999999999999999999999988 5899999999863

>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=2.7e-14  Score=126.24  Aligned_cols=74  Identities=22%  Similarity=0.443  Sum_probs=68.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      ..++|||+|||.++|+++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ +++..|.|+.|+|..|.
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            4589999999999999999999999999999875     58899999999999999999996 79999999999998774

>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=99.48  E-value=1.1e-14  Score=129.37  Aligned_cols=74  Identities=18%  Similarity=0.141  Sum_probs=68.8

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ++|||+|||.++++++|+++|++||.|.++++..  +|||||+|.+.++|++||+.|||..|.|+.|+|.+++++.
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 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT--TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc--cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            3699999999999999999999999999999875  5999999999999999999999999999999999886544

>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=2.5e-14  Score=131.44  Aligned_cols=78  Identities=17%  Similarity=0.426  Sum_probs=72.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      .++|||+|||+++++++|+++|++||+|..+.+     ++.++|||||+|.+.++|++|++ +++..|.|+.|.|.++.+
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            489999999999999999999999999999976     46789999999999999999995 899999999999999998


Q ss_pred             CCCC
Q 001991          350 KDNP  353 (985)
Q Consensus       350 k~~~  353 (985)
                      +.+.
T Consensus        99 ke~~  102 (103)
T d1x4ba1          99 REES  102 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7653

>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=3.6e-14  Score=122.73  Aligned_cols=70  Identities=17%  Similarity=0.413  Sum_probs=65.2

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +|||+|||+++|+++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ +++..|.|+.|.|+.|
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            5899999999999999999999999999975     57899999999999999999996 8999999999998754

>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=99.47  E-value=1.1e-14  Score=132.48  Aligned_cols=81  Identities=22%  Similarity=0.271  Sum_probs=73.1

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .+.++|||+|||.++++++|+++|++||.|..+.+.     +..++||||+|.+.++|.+|++.|||..|.|++|+|+|+
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            356799999999999999999999999998776543     457899999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++.+|
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            987754

>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=6.2e-14  Score=126.96  Aligned_cols=77  Identities=21%  Similarity=0.390  Sum_probs=71.2

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCC--ceEEEEeccCc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPG  435 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~G--r~IkV~~A~~k  435 (985)
                      .+.++|||+|||.++++++|+++|++||.|..|++.++ ++||||+|.+.++|++|++.||+..|.|  ++|+|+|++++
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 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            45679999999999999999999999999999998864 7899999999999999999999999976  58999999864

>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=99.47  E-value=5.6e-14  Score=127.83  Aligned_cols=77  Identities=26%  Similarity=0.512  Sum_probs=69.9

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          272 EHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       272 e~~srtLfVgNLP~-~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ....++|||+|||+ .+++++|+++|++||+|..|++   ++|||||+|++.++|++|++.|||+.|.|++|+|.++.++
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            34557899999975 6788999999999999999998   6899999999999999999999999999999999999765


Q ss_pred             C
Q 001991          351 D  351 (985)
Q Consensus       351 ~  351 (985)
                      .
T Consensus        89 ~   89 (98)
T d1wf2a_          89 K   89 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.47  E-value=3.9e-14  Score=126.79  Aligned_cols=80  Identities=21%  Similarity=0.423  Sum_probs=71.8

Q ss_pred             cccceeeecCCCCCCHHHHHH----HhhccCCEEEEEEcCC--CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          359 NQGTLVVFNLDSSVSTEELHQ----IFGIYGEIREIRDTQH--KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLre----lFs~fG~I~~Vri~~~--skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      +.++|||+|||..+++++|++    +|++||+|.+|++...  .+|||||+|.+.++|.+|++.|||..+.|++|+|.||
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            357999999999999999864    6899999999988643  5899999999999999999999999999999999999


Q ss_pred             cCcchh
Q 001991          433 RPGGAR  438 (985)
Q Consensus       433 ~~k~~R  438 (985)
                      +++.+.
T Consensus        82 k~~~~~   87 (91)
T d1nu4a_          82 KTDSDI   87 (91)
T ss_dssp             SSCCTH
T ss_pred             CCCchh
Confidence            987644

>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=99.47  E-value=2.1e-14  Score=127.99  Aligned_cols=76  Identities=14%  Similarity=0.334  Sum_probs=68.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  351 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~  351 (985)
                      .+++|||+|||+++++++|+++|++|| +..+.+ .+.+|||||+|.+.++|++|++.||+..|.|++|.|+++.++.
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-LKYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            468999999999999999999999999 333444 6789999999999999999999999999999999999996554

>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=99.47  E-value=4.2e-14  Score=128.25  Aligned_cols=83  Identities=18%  Similarity=0.305  Sum_probs=71.5

Q ss_pred             ccccccceeeecCCCCCCHHHHHHHhhccCCEEEE--------EEc-----CCCCcEEEEEEcCHHHHHHHHHHhCCcee
Q 001991          356 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--------RDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDV  422 (985)
Q Consensus       356 ~~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~V--------ri~-----~~skGfaFVeF~d~edA~kAI~~LNG~~I  422 (985)
                      .+....+|||+|||..+|+++|+++|+.||.|..+        .+.     +..++||||+|.+.++|.+|++.|||..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            34456799999999999999999999999998543        332     23568999999999999999999999999


Q ss_pred             CCceEEEEeccCcchh
Q 001991          423 AGKQIKLEASRPGGAR  438 (985)
Q Consensus       423 ~Gr~IkV~~A~~k~~R  438 (985)
                      .|++|+|++++++..+
T Consensus        84 ~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          84 QGSKLKVSLARKKPPM   99 (101)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCEEEEEEEcCCCCCC
Confidence            9999999999986543

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.7e-14  Score=122.54  Aligned_cols=72  Identities=22%  Similarity=0.478  Sum_probs=66.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      .++|||+|||+++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++ ++|+.|.|++|.|+.|
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            479999999999999999999999999999875     57789999999999999999995 8999999999999876

>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=99.46  E-value=1.1e-14  Score=133.45  Aligned_cols=77  Identities=17%  Similarity=0.390  Sum_probs=70.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ...++|||+|||.++++++|+++|+.||+|.+|++     +++++|||||+|.+.++|++|++ |+|..|.|++|.|+++
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            34589999999999999999999999999999976     57899999999999999999995 9999999999999987


Q ss_pred             CCC
Q 001991          348 IPK  350 (985)
Q Consensus       348 ~pk  350 (985)
                      .++
T Consensus        95 ~~~   97 (101)
T d2cq4a1          95 QAE   97 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>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=99.46  E-value=7.1e-14  Score=125.29  Aligned_cols=77  Identities=14%  Similarity=0.341  Sum_probs=69.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...+|||+|||.++|+++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++||+.  +..|+|+.|.|.++.
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            4568999999999999999999999999999998643     578999999999999999984  458999999999998


Q ss_pred             Ccch
Q 001991          434 PGGA  437 (985)
Q Consensus       434 ~k~~  437 (985)
                      +++.
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8653

>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=99.46  E-value=3.4e-14  Score=126.25  Aligned_cols=75  Identities=16%  Similarity=0.198  Sum_probs=68.6

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCCCC
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  352 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk~~  352 (985)
                      .+|||+|||+++++++|+++|++||+|..+++  ..+|||||+|.+.++|++||+.|+|..|.|+.|.|.++.++..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~   75 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV--YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   75 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEE--CTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccc--cccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcC
Confidence            36999999999999999999999999999987  3459999999999999999999999999999999998865543

>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=99.46  E-value=1.7e-14  Score=125.65  Aligned_cols=71  Identities=17%  Similarity=0.428  Sum_probs=66.3

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ++|||+|||+++|+++|+++|++||+|..+++     ++++||||||+|.+.++|++|++ +++..|.|++|.|+.|
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            57999999999999999999999999998875     58899999999999999999996 7999999999999875

>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=99.46  E-value=4e-14  Score=126.22  Aligned_cols=75  Identities=15%  Similarity=0.287  Sum_probs=65.9

Q ss_pred             ccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcc
Q 001991          360 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  436 (985)
Q Consensus       360 ~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~  436 (985)
                      ..+|||+|||.++++++|+++|++||. ..+.+ ...++||||+|.+.++|++|++.|||..|.|++|+|++++.+.
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 SSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV-DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE-EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-eeeee-eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            468999999999999999999999992 22333 2458999999999999999999999999999999999997654

>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=99.46  E-value=7.8e-14  Score=126.33  Aligned_cols=79  Identities=29%  Similarity=0.502  Sum_probs=71.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccc--ccccccccCC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIP  349 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~G--r~L~V~~a~p  349 (985)
                      ..|+++|||+|||+++++++|+++|++||+|..+++ .+.++||||+|.+.++|++|++.||+..|.|  ++|+|.|+++
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~-~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEE-CSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEee-eccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCC
Confidence            357899999999999999999999999999999998 5678999999999999999999999999987  5799999875


Q ss_pred             CC
Q 001991          350 KD  351 (985)
Q Consensus       350 k~  351 (985)
                      ..
T Consensus        93 ~~   94 (97)
T d1whya_          93 GP   94 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=9.5e-14  Score=126.86  Aligned_cols=80  Identities=18%  Similarity=0.396  Sum_probs=70.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe------ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki------tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ..+.++|||+|||.++|+++|+++|++|| |..+++      +++++|||||+|.+.++|++|+ .|++..|.|++|+|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEE
Confidence            45679999999999999999999999999 555543      4678899999999999998777 599999999999999


Q ss_pred             ccCCCCCC
Q 001991          346 YSIPKDNP  353 (985)
Q Consensus       346 ~a~pk~~~  353 (985)
                      ++.++...
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99877554

>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=99.45  E-value=5.9e-14  Score=129.45  Aligned_cols=82  Identities=22%  Similarity=0.290  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCccc--ccccccccccC
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPL--RRRKLDIHYSI  348 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I--~Gr~L~V~~a~  348 (985)
                      ..+..+|||+|||.++|+++|+++|++||.|..|.+ ..+.+|||||+|.+.++|++|++.|||..|  .+++|+|.|+.
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            456789999999999999999999999999999876 456789999999999999999999999998  57889999987


Q ss_pred             CCCCC
Q 001991          349 PKDNP  353 (985)
Q Consensus       349 pk~~~  353 (985)
                      ++...
T Consensus        84 ~~~~~   88 (108)
T d2adba1          84 LTSLN   88 (108)
T ss_dssp             SCSCC
T ss_pred             Ccccc
Confidence            76543

>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=99.45  E-value=8e-14  Score=126.79  Aligned_cols=82  Identities=15%  Similarity=0.204  Sum_probs=73.8

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCC
Q 001991          270 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  349 (985)
Q Consensus       270 ~~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~p  349 (985)
                      ......++|||+|||+++++++|+++|++||+|..+++  ..+|||||+|.+.++|++||+.|||..|.|+.|+|.+..+
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 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV--QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEE--ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccc--cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            34456788999999999999999999999999999988  3579999999999999999999999999999999999876


Q ss_pred             CCCC
Q 001991          350 KDNP  353 (985)
Q Consensus       350 k~~~  353 (985)
                      +.++
T Consensus        88 ~~~~   91 (98)
T d1wg4a_          88 YPER   91 (98)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            5543

>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=99.45  E-value=9.8e-14  Score=123.26  Aligned_cols=80  Identities=26%  Similarity=0.361  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHc--cCcccccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL--QNKPLRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~L--ng~~I~Gr~L~V~~a~  348 (985)
                      ...|+++|||+|||.++++++|+++|++||.|..+++ .+.++||||+|.+.++|++|++.+  ++..+.|++|+|.|+.
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            4568999999999999999999999999999999988 567899999999999999999866  4678999999999997


Q ss_pred             CCC
Q 001991          349 PKD  351 (985)
Q Consensus       349 pk~  351 (985)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>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=1.3e-13  Score=119.38  Aligned_cols=71  Identities=15%  Similarity=0.339  Sum_probs=65.0

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCc
Q 001991          363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  435 (985)
Q Consensus       363 LfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k  435 (985)
                      |||+|||.++++++|+++|++|| +..+++. ..+|||||+|.+.++|++|++.|||..+.|++|+|++++.+
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-LKYCFVD-KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555543 46899999999999999999999999999999999999764

>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=1.2e-14  Score=130.62  Aligned_cols=78  Identities=15%  Similarity=0.232  Sum_probs=70.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ....++|||+|||+++++++|+++|++||.|..+++    +++++|||||+|.+.++|++||+ |+|..|.|++|.|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            445679999999999999999999999999887654    68899999999999999999995 9999999999999998


Q ss_pred             CCC
Q 001991          348 IPK  350 (985)
Q Consensus       348 ~pk  350 (985)
                      ..+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            753

>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=99.45  E-value=1e-13  Score=122.48  Aligned_cols=74  Identities=14%  Similarity=0.282  Sum_probs=67.6

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ..++|||+|||..+|+++|+++|++||.|..|++..+     ++|||||+|.+.++|++|++ +++..|.|++|+|..|.
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            3468999999999999999999999999999988643     57899999999999999998 79999999999998875

>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=99.45  E-value=5.5e-14  Score=127.88  Aligned_cols=79  Identities=18%  Similarity=0.152  Sum_probs=72.0

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ....+|||+|||..+++++|+++|++||+|+++++..  +|||||+|.+.++|++||+.|||..|.|+.|+|.+++.+..
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~--~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK--DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET--TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc--cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            3456899999999999999999999999999999864  69999999999999999999999999999999999876553


Q ss_pred             h
Q 001991          438 R  438 (985)
Q Consensus       438 R  438 (985)
                      +
T Consensus        91 ~   91 (98)
T d1wg4a_          91 R   91 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.45  E-value=1.5e-13  Score=122.03  Aligned_cols=79  Identities=19%  Similarity=0.193  Sum_probs=71.8

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh--CCceeCCceEEEEeccC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRP  434 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L--NG~~I~Gr~IkV~~A~~  434 (985)
                      ..+.++|||+|||.++++++|+++|++||.|.++++.++ ++||||+|.+.++|++|++.+  ++..+.|++|+|.|++.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            456789999999999999999999999999999998754 789999999999999999865  57799999999999987


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      ++
T Consensus        84 ~~   85 (88)
T d2cq1a1          84 KE   85 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.44  E-value=3.9e-14  Score=129.23  Aligned_cols=77  Identities=16%  Similarity=0.210  Sum_probs=69.9

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEeccC
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ..++|||+|||.++++++|+++|++||.|..+++..+    ++|||||+|.+.++|++|++.|||..|.|+++.|.+++|
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            4568999999999999999999999999999877643    467999999999999999999999999999999988876


Q ss_pred             c
Q 001991          435 G  435 (985)
Q Consensus       435 k  435 (985)
                      -
T Consensus        97 l   97 (101)
T d1x5oa1          97 L   97 (101)
T ss_dssp             B
T ss_pred             c
Confidence            3

>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=99.44  E-value=8.1e-14  Score=120.64  Aligned_cols=71  Identities=17%  Similarity=0.428  Sum_probs=65.7

Q ss_pred             EEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccccccccccccCCC
Q 001991          278 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       278 LfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      |||+|||+++++++|+++|++|| +..+++ ++.+|||||+|.+.++|++|++.|||..+.|++|.|+++...
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 566665 778999999999999999999999999999999999998643

>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=99.44  E-value=8.9e-14  Score=120.22  Aligned_cols=70  Identities=14%  Similarity=0.311  Sum_probs=64.6

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .|||+|||.++|+++|+++|++||+|..|++..+     ++|||||+|.+.++|++|++ +++..|.|++|.|..|
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            4899999999999999999999999999998653     57999999999999999998 8999999999999654

>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=99.44  E-value=5.1e-14  Score=120.86  Aligned_cols=70  Identities=19%  Similarity=0.427  Sum_probs=65.3

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +|||+|||+++|+++|+++|++||.|..+.+     ++..+|||||+|.+.++|++|++ ++|+.|.|++|.|++|
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            5999999999999999999999999999865     57789999999999999999996 9999999999999875

>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=99.44  E-value=9.2e-14  Score=125.40  Aligned_cols=80  Identities=20%  Similarity=0.329  Sum_probs=70.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCc-EEEEEe------ccccceEEEEEeCCHHHHHHHHHHccC--ccccccccccc
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGD-IRTIYT------ACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIH  345 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~-I~sVki------tgksrGfAFV~F~d~esA~kAi~~Lng--~~I~Gr~L~V~  345 (985)
                      .++|||+|||.++++++|+++|++||+ |..+++      +++++|||||+|.+.++|.+|++.|++  ..+.|+.|.|.
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 888876      367899999999999999999999875  45679999999


Q ss_pred             ccCCCCCCC
Q 001991          346 YSIPKDNPS  354 (985)
Q Consensus       346 ~a~pk~~~~  354 (985)
                      |+.|+.++.
T Consensus        81 ~A~p~~~~~   89 (96)
T d2disa1          81 WAEPEIDVD   89 (96)
T ss_dssp             ESCSSCSTT
T ss_pred             EcCCCCCCC
Confidence            999877653

>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=99.43  E-value=1.1e-13  Score=120.27  Aligned_cols=71  Identities=18%  Similarity=0.316  Sum_probs=65.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ++|||+|||.++|+++|+++|++||.|..+++..+     ++|||||+|.+.++|++|++ +||..|+|++|+|..|
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            58999999999999999999999999999888643     57899999999999999996 8999999999999876

>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=99.43  E-value=3.9e-14  Score=123.37  Aligned_cols=71  Identities=21%  Similarity=0.396  Sum_probs=65.9

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ++|||+|||.++|+++|+++|++||.|.+++++.+     ++|||||+|.+.++|++|++ +|+..|+|++|.|..|
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            57999999999999999999999999999988543     68999999999999999998 7999999999999876

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.43  E-value=2.5e-14  Score=128.36  Aligned_cols=77  Identities=22%  Similarity=0.264  Sum_probs=69.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEc----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ....+|||+|||.++++++|+++|++||.|..++++    +.++|||||+|.+.++|++|++ |||..|+|++|+|++|+
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            345689999999999999999999999998877664    3478999999999999999996 99999999999999998


Q ss_pred             Cc
Q 001991          434 PG  435 (985)
Q Consensus       434 ~k  435 (985)
                      .|
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=119.03  Aligned_cols=71  Identities=21%  Similarity=0.218  Sum_probs=65.3

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC---CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~---skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .+|||+|||.++++++|+++|+.||.|..|++..+   .++||||+|.+.++|++|+. +|+..|+|++|.|+.+
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            47999999999999999999999999999998654   45799999999999999996 9999999999999864

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=4.2e-13  Score=122.95  Aligned_cols=81  Identities=17%  Similarity=0.261  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHcc--CcccccccccccccC
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ--NKPLRRRKLDIHYSI  348 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Ln--g~~I~Gr~L~V~~a~  348 (985)
                      ...++++|||+|||+++|+++|+++|++||.|..+++ .+.+++|||+|.+.++|++|++.++  +..+.|++|+|.|+.
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            4457899999999999999999999999999999998 5789999999999999999999875  456889999999997


Q ss_pred             CCCC
Q 001991          349 PKDN  352 (985)
Q Consensus       349 pk~~  352 (985)
                      .+..
T Consensus        90 ~~~~   93 (104)
T d1wexa_          90 SKRI   93 (104)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            6543

>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=99.42  E-value=1.1e-13  Score=123.69  Aligned_cols=72  Identities=18%  Similarity=0.379  Sum_probs=65.1

Q ss_pred             cccceeeecCCCCCCHHHH---HHHhhccCCEEEEEEcCC--------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          359 NQGTLVVFNLDSSVSTEEL---HQIFGIYGEIREIRDTQH--------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedL---relFs~fG~I~~Vri~~~--------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                      ..++|||+|||+++++++|   +++|++||+|..|.+..+        .+|||||+|.+.++|.+|++.|||..+.|++|
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            3568999999999999999   678999999999998643        24799999999999999999999999999999


Q ss_pred             EEE
Q 001991          428 KLE  430 (985)
Q Consensus       428 kV~  430 (985)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.42  E-value=7.8e-14  Score=128.63  Aligned_cols=78  Identities=22%  Similarity=0.313  Sum_probs=70.7

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-CCcEEEEEEcCHHHHHHHHHHhCCcee--CCceEEEEeccCc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-KHNHKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEASRPG  435 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-skGfaFVeF~d~edA~kAI~~LNG~~I--~Gr~IkV~~A~~k  435 (985)
                      +..+|||+|||..+|+++|+++|++||.|.+|++..+ .+|||||+|.+.++|++|++.|||..|  .|++|+|.+++++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            3457999999999999999999999999999988654 578999999999999999999999998  5899999999875


Q ss_pred             c
Q 001991          436 G  436 (985)
Q Consensus       436 ~  436 (985)
                      .
T Consensus        86 ~   86 (108)
T d2adba1          86 S   86 (108)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.42  E-value=1.3e-13  Score=124.35  Aligned_cols=78  Identities=21%  Similarity=0.224  Sum_probs=69.1

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCC-EEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHhCCc--eeCCceEEEEe
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDTQH------KHNHKFIEFYDIRAAETALRTLNRS--DVAGKQIKLEA  431 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~-I~~Vri~~~------skGfaFVeF~d~edA~kAI~~LNG~--~I~Gr~IkV~~  431 (985)
                      ++|||+|||.++++++|+++|++||+ |.+|+++.+      ++|||||+|.+.++|.+|++.|++.  .++|++|+|.|
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 899998643      5789999999999999999999754  55799999999


Q ss_pred             ccCcchh
Q 001991          432 SRPGGAR  438 (985)
Q Consensus       432 A~~k~~R  438 (985)
                      |+++.+.
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9986643

>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=99.42  E-value=9.5e-14  Score=119.12  Aligned_cols=70  Identities=13%  Similarity=0.277  Sum_probs=64.5

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC-----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~-----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .|||+|||.++|+++|+++|++||.|..+.+..     ..++||||+|.+.++|++|++ |||..|+|++|+|.+|
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            489999999999999999999999999987753     357899999999999999997 9999999999999876

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=3.7e-13  Score=123.31  Aligned_cols=79  Identities=19%  Similarity=0.172  Sum_probs=71.4

Q ss_pred             cccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh--CCceeCCceEEEEeccC
Q 001991          357 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRP  434 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L--NG~~I~Gr~IkV~~A~~  434 (985)
                      ..+..+|||+|||..+|+++|+++|++||.|..|++.+ .+++|||+|.+.++|++|+..|  ++..++|++|+|.|++.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~-~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe-cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            34577999999999999999999999999999999875 4899999999999999999988  55678999999999987


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      +.
T Consensus        91 ~~   92 (104)
T d1wexa_          91 KR   92 (104)
T ss_dssp             SS
T ss_pred             Cc
Confidence            54

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=1.1e-13  Score=118.24  Aligned_cols=66  Identities=21%  Similarity=0.434  Sum_probs=62.3

Q ss_pred             EEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          278 LFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       278 LfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      |||+|||.++|+++|+++|++||+|..+++     ++.++|||||+|.+.++|++|++.|||+.|.|+.|+
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            799999999999999999999999999875     577899999999999999999999999999999875

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=7.9e-14  Score=120.90  Aligned_cols=70  Identities=20%  Similarity=0.476  Sum_probs=64.6

Q ss_pred             EEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          277 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       277 tLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++ .++..|.|+.|.|+.|
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            5999999999999999999999999999986     57899999999999999999995 6888999999998764

>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=99.41  E-value=1.7e-13  Score=121.27  Aligned_cols=73  Identities=14%  Similarity=0.349  Sum_probs=67.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..++|||+|||.++|+++|+++|+.||+|..|++    +++++|||||+|.+.++|++|++ +++..+.|+.|.|.+.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            4589999999999999999999999999999976    57789999999999999999995 8999999999999875

>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=99.40  E-value=3e-13  Score=123.54  Aligned_cols=77  Identities=22%  Similarity=0.322  Sum_probs=67.4

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC------CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~------skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      +..+|||+|||.++|+++|+++|++|| |.+++++.+      .+|||||+|.+.++|++|++ ||+..|.|++|+|.++
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            457999999999999999999999999 777776532      46899999999999987775 9999999999999999


Q ss_pred             cCcch
Q 001991          433 RPGGA  437 (985)
Q Consensus       433 ~~k~~  437 (985)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T d1wi8a_          92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.39  E-value=1.8e-13  Score=121.19  Aligned_cols=75  Identities=8%  Similarity=0.162  Sum_probs=68.0

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...++|||+|||.++|+++|+++|+.||.|..|++..+    .+|||||+|.+.++|++|++ ++|..+.|+.|.|.++.
T Consensus         4 ~~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           4 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HHTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CCcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            34679999999999999999999999999999988643    46899999999999999997 89999999999999853

>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=4.1e-13  Score=122.20  Aligned_cols=80  Identities=15%  Similarity=0.183  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEecCCCC-CCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHH--HccCccccccccccccc
Q 001991          271 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK--ALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~-vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~--~Lng~~I~Gr~L~V~~a  347 (985)
                      ...++++|||+|||.+ +|+++|+++|++||.|..+++ .+.+|||||+|.+.++|.+|++  .+++..+.|+.|+|.|+
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~-~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEE-ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEE-eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            4457799999999985 899999999999999999998 5678999999999999999998  47788999999999999


Q ss_pred             CCCC
Q 001991          348 IPKD  351 (985)
Q Consensus       348 ~pk~  351 (985)
                      ..+.
T Consensus        93 ~~~~   96 (99)
T d1x4fa1          93 EKYK   96 (99)
T ss_dssp             CSCS
T ss_pred             CCcc
Confidence            7553

>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=2.4e-13  Score=123.70  Aligned_cols=78  Identities=18%  Similarity=0.162  Sum_probs=70.0

Q ss_pred             ccccceeeecCCCC-CCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHH--HhCCceeCCceEEEEeccC
Q 001991          358 ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNRSDVAGKQIKLEASRP  434 (985)
Q Consensus       358 ~~~~tLfV~NLp~s-vTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~--~LNG~~I~Gr~IkV~~A~~  434 (985)
                      ...++|||+|||.+ +|+++|+++|++||.|.+|++.++ +++|||+|.+.++|.+|++  .+++..+.|++|+|.|++.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            45578999999975 899999999999999999998764 7999999999999999998  5788899999999999976


Q ss_pred             cc
Q 001991          435 GG  436 (985)
Q Consensus       435 k~  436 (985)
                      +.
T Consensus        95 ~~   96 (99)
T d1x4fa1          95 YK   96 (99)
T ss_dssp             CS
T ss_pred             cc
Confidence            43

>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=99.38  E-value=1.7e-13  Score=118.78  Aligned_cols=70  Identities=17%  Similarity=0.339  Sum_probs=64.4

Q ss_pred             ceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          362 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       362 tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      .|||+|||.++|+++|+++|++||.|.+|+++.+     ++|||||+|.+.++|++||+ +++..|+|+.|.|..|
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            4899999999999999999999999999998754     67999999999999999997 6888999999999865

>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=99.37  E-value=4e-13  Score=116.17  Aligned_cols=71  Identities=17%  Similarity=0.247  Sum_probs=64.5

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe---ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki---tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ++|||+|||+++++++|+++|+.||+|..+++   ....++||||+|.+.++|++|+ .++++.|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999986   3445689999999999999999 59999999999998754

>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=7.2e-13  Score=118.30  Aligned_cols=77  Identities=18%  Similarity=0.223  Sum_probs=69.6

Q ss_pred             ccccceeeecCCCC-CCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHh--CCceeCCceEEEEeccC
Q 001991          358 ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRP  434 (985)
Q Consensus       358 ~~~~tLfV~NLp~s-vTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~L--NG~~I~Gr~IkV~~A~~  434 (985)
                      ...++|||+|||.. +|++||+++|++||+|.+|++.++ +++|||+|++.++|.+|++.|  ++..+.|++|+|.||++
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            45679999999986 889999999999999999999864 789999999999999999966  67899999999999975


Q ss_pred             c
Q 001991          435 G  435 (985)
Q Consensus       435 k  435 (985)
                      .
T Consensus        85 ~   85 (89)
T d1x4da1          85 Y   85 (89)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=3.6e-13  Score=120.19  Aligned_cols=71  Identities=20%  Similarity=0.343  Sum_probs=63.7

Q ss_pred             CCcEEEEecCCCCCCHHHH---HHhhcccCcEEEEEe-----c---cccceEEEEEeCCHHHHHHHHHHccCcccccccc
Q 001991          274 PSRTLFVRNINSNVEDSEL---KALFEQFGDIRTIYT-----A---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  342 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedL---relFs~fG~I~sVki-----t---gksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L  342 (985)
                      ..++|||+|||+++++++|   +++|++||+|..|.+     +   +..+|||||+|.+.++|.+|++.|||..|.|+.|
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            3568999999999999999   778999999999976     1   2345899999999999999999999999999999


Q ss_pred             cc
Q 001991          343 DI  344 (985)
Q Consensus       343 ~V  344 (985)
                      +|
T Consensus        87 kv   88 (89)
T d2cpia1          87 KA   88 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            87

>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=99.36  E-value=1.7e-13  Score=116.92  Aligned_cols=66  Identities=23%  Similarity=0.347  Sum_probs=61.4

Q ss_pred             eeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC-----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEE
Q 001991          363 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  428 (985)
Q Consensus       363 LfV~NLp~svTeedLrelFs~fG~I~~Vri~~~-----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~Ik  428 (985)
                      |||+|||.++|+++|+++|++||.|..+++..+     .+|||||+|.+.++|++|++.|||..|.|+.|+
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            799999999999999999999999999887543     678999999999999999999999999999874

>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=8.9e-13  Score=117.73  Aligned_cols=79  Identities=15%  Similarity=0.139  Sum_probs=70.8

Q ss_pred             CCCCCcEEEEecCCCC-CCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHc--cCccccccccccccc
Q 001991          271 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL--QNKPLRRRKLDIHYS  347 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~-vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~L--ng~~I~Gr~L~V~~a  347 (985)
                      ...++++|||+|||.. +|++||+++|++||+|..|++ ...+++|||+|++.++|..|++.+  ++..+.|++|+|.|+
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i-~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s   82 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   82 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-CSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEe-eccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEEC
Confidence            4567899999999986 899999999999999999998 556789999999999999999966  567899999999999


Q ss_pred             CCC
Q 001991          348 IPK  350 (985)
Q Consensus       348 ~pk  350 (985)
                      .+.
T Consensus        83 ~~~   85 (89)
T d1x4da1          83 QKY   85 (89)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            753

>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=8.7e-13  Score=120.37  Aligned_cols=81  Identities=10%  Similarity=0.211  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEE---eccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVk---itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ......+|||+|||+++|+++|+++|+.||.+....   .+++.+|||||+|.+.++|++|++ ++++.|.||.|+|.++
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            445668999999999999999999999999553222   267789999999999999999995 9999999999999998


Q ss_pred             CCCCC
Q 001991          348 IPKDN  352 (985)
Q Consensus       348 ~pk~~  352 (985)
                      .++..
T Consensus        90 ~~~~~   94 (102)
T d1weza_          90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77653

>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=99.35  E-value=3.2e-13  Score=119.15  Aligned_cols=75  Identities=19%  Similarity=0.267  Sum_probs=66.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEE-EE----eccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRT-IY----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~s-Vk----itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ...++|||+|||.++++++|+++|+.||.|.. +.    .+++++|+|||+|.+.++|++|++.||++.|.|++|+|.++
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            34578999999999999999999999998754 22    26788999999999999999999999999999999999764

>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=99.34  E-value=1.8e-12  Score=118.54  Aligned_cols=81  Identities=14%  Similarity=0.188  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          271 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       271 ~e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVki-----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      ......+|||+|||+++|+++|+++|..||.|..+.+     +++++|||||+|.+.++|++|++ +++..|.||.|.|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            3445678999999999999999999999999887432     67789999999999999999995 99999999999999


Q ss_pred             ccCCCCC
Q 001991          346 YSIPKDN  352 (985)
Q Consensus       346 ~a~pk~~  352 (985)
                      ++.+++.
T Consensus        90 ~~~~~~~   96 (104)
T d1wg5a_          90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHh
Confidence            9877643

>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=99.33  E-value=5.1e-13  Score=117.80  Aligned_cols=74  Identities=20%  Similarity=0.240  Sum_probs=65.2

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEE-EEEc----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~-Vri~----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ...+|||+|||.++++++|+++|+.||.|.. +.+.    ..++|+|||+|.+.++|++|++.||+..|.|++|+|+++
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            4557999999999999999999999999854 3333    235789999999999999999999999999999999875

>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=99.33  E-value=1.7e-12  Score=118.66  Aligned_cols=79  Identities=22%  Similarity=0.246  Sum_probs=68.8

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEE-EEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~V-ri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ....+|||+|||.++|+++|+++|..||.|..+ .+..    ..+|||||+|.++++|++|++ +|+..|+||.|+|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            355689999999999999999999999998774 3332    257899999999999999997 9999999999999999


Q ss_pred             cCcch
Q 001991          433 RPGGA  437 (985)
Q Consensus       433 ~~k~~  437 (985)
                      .+++.
T Consensus        92 ~~~~~   96 (104)
T d1wg5a_          92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHh
Confidence            87653

>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=99.31  E-value=6.2e-13  Score=121.36  Aligned_cols=78  Identities=10%  Similarity=0.170  Sum_probs=67.3

Q ss_pred             ccccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          358 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       358 ~~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ....+|||+|||.++|+++|+++|..||.+ .|+++.    ..+|||||+|.+.++|++|++ ||+..|+||.|+|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            445689999999999999999999999854 454432    247899999999999999987 99999999999999998


Q ss_pred             Ccch
Q 001991          434 PGGA  437 (985)
Q Consensus       434 ~k~~  437 (985)
                      ++..
T Consensus        91 ~~~~   94 (102)
T d1weza_          91 TAGT   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.29  E-value=6.7e-13  Score=122.06  Aligned_cols=77  Identities=18%  Similarity=0.248  Sum_probs=69.2

Q ss_pred             cccceeeecCCCCC-C----HHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSV-S----TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~sv-T----eedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...+|||+||+.++ +    +++|+++|++||.|.++++.+ +++||||+|.+.++|.+|++.|||..|.|++|+|.|++
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 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            45689999999876 3    367999999999999999875 58899999999999999999999999999999999998


Q ss_pred             Ccc
Q 001991          434 PGG  436 (985)
Q Consensus       434 ~k~  436 (985)
                      +..
T Consensus        83 ~~~   85 (104)
T d1weya_          83 TLH   85 (104)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            754

>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=99.29  E-value=8.2e-13  Score=121.43  Aligned_cols=79  Identities=16%  Similarity=0.206  Sum_probs=71.0

Q ss_pred             CCCcEEEEecCCCCC-CH----HHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNV-ED----SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~v-TE----edLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ..+.+|||+||+.++ ++    ++|+++|++||+|.++++ .++++||||+|.+.++|.+|++.|||..|.|++|+|.|+
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            357899999999987 33    568999999999999988 578999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 001991          348 IPKDN  352 (985)
Q Consensus       348 ~pk~~  352 (985)
                      .++..
T Consensus        82 ~~~~~   86 (104)
T d1weya_          82 QTLHI   86 (104)
T ss_dssp             CCSSC
T ss_pred             ccCCC
Confidence            77654

>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=1.9e-12  Score=118.01  Aligned_cols=79  Identities=13%  Similarity=0.147  Sum_probs=68.2

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEE-EEEcC----CCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~-Vri~~----~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...+|||+|||.++|+++|+++|..||.|.. +.+..    ..+|||||+|.+.++|++|++ ||+..|+|+.|.|.++.
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            4568999999999999999999999998865 44432    368999999999999999997 99999999999999986


Q ss_pred             Ccchh
Q 001991          434 PGGAR  438 (985)
Q Consensus       434 ~k~~R  438 (985)
                      .+..+
T Consensus        86 ~~~~~   90 (103)
T d2cpya1          86 LEDMR   90 (103)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            54433

>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=99.23  E-value=2.1e-12  Score=117.72  Aligned_cols=75  Identities=15%  Similarity=0.202  Sum_probs=66.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEE-EEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRT-IYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~s-Vki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      ....+|||+|||.++|+++|+++|+.||.|.. +.+    +++++|||||+|.+.++|++|++ +++..|.|+.|.|.++
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            34578999999999999999999999998864 332    67899999999999999999995 9999999999999876


Q ss_pred             C
Q 001991          348 I  348 (985)
Q Consensus       348 ~  348 (985)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
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=99.23  E-value=3.4e-13  Score=120.06  Aligned_cols=71  Identities=17%  Similarity=0.347  Sum_probs=63.6

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----------ccccceEEEEEeCCHHHHHHHHHHccCccccccccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT----------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  345 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki----------tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~  345 (985)
                      |+|||+|||.++|+++|+++|++||.|..+.+          +++++|||||+|.+.++|++|+ +|||..+.|++|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            78999999999999999999999998765432          4678999999999999999999 499999999999997


Q ss_pred             cc
Q 001991          346 YS  347 (985)
Q Consensus       346 ~a  347 (985)
                      ..
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=4.1e-12  Score=117.82  Aligned_cols=77  Identities=9%  Similarity=0.184  Sum_probs=67.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHhhcccCcEEEE---E--eccccceEEEEEeCCHHHHHHHHHHccCcccccccccccc
Q 001991          272 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI---Y--TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  346 (985)
Q Consensus       272 e~~srtLfVgNLP~~vTEedLrelFs~fG~I~sV---k--itgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~  346 (985)
                      ....++|||+|||.++|+++|+++|+.||.|..+   .  .++..+|||||+|.+.++|++|++ ||+..|.|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3456799999999999999999999999987542   1  268899999999999999999995 999999999999987


Q ss_pred             cCC
Q 001991          347 SIP  349 (985)
Q Consensus       347 a~p  349 (985)
                      +.+
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            643

>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=99.18  E-value=3.3e-12  Score=117.32  Aligned_cols=72  Identities=21%  Similarity=0.254  Sum_probs=67.1

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCC----CCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEec
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  432 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~----skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A  432 (985)
                      ..++|.++...+++++|+++|++||+|.+|+|+.+    .+|+|||+|.+.++|.+|++.|||+.++||+|+|+|+
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            46899999999999999999999999999998743    5799999999999999999999999999999999985

>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=99.17  E-value=4.2e-12  Score=117.75  Aligned_cols=80  Identities=11%  Similarity=0.118  Sum_probs=68.0

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEE-EEc----CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~V-ri~----~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      ...+|||+|||.++|+++|+++|+.||.|..+ .+.    +..+|||||+|.+.++|++|++ |||..|+|+.|.|.++.
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            45689999999999999999999999988542 221    3357899999999999999997 99999999999999987


Q ss_pred             Ccchhh
Q 001991          434 PGGARR  439 (985)
Q Consensus       434 ~k~~Rr  439 (985)
                      +++..+
T Consensus        96 ~~~~~~  101 (112)
T d1wela1          96 KKGMLE  101 (112)
T ss_dssp             HHHHHH
T ss_pred             hHHHHH
Confidence            766433

>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=2.5e-11  Score=110.72  Aligned_cols=64  Identities=23%  Similarity=0.303  Sum_probs=58.5

Q ss_pred             ccccceeeec--CCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCcee
Q 001991          358 ANQGTLVVFN--LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV  422 (985)
Q Consensus       358 ~~~~tLfV~N--Lp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I  422 (985)
                      .+..+|+|.|  ||..+|+++|+++|++||.|+.|++.++ ++||||+|.+.++|.+|++.|||+.|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3456888866  9999999999999999999999998765 78999999999999999999999987

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=1.8e-11  Score=113.77  Aligned_cols=76  Identities=20%  Similarity=0.192  Sum_probs=67.1

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCH-HHHHHHHHHhCCceeCCceEEEEeccCcch
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDI-RAAETALRTLNRSDVAGKQIKLEASRPGGA  437 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~-edA~kAI~~LNG~~I~Gr~IkV~~A~~k~~  437 (985)
                      ..+||+|||+.+|+++|+++|++||+|.+|+++.. ++||||+|.+. ++|.+|+..||+..+.++.+.|.++..+.+
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~~   88 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGE   88 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHH
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccch
Confidence            36699999999999999999999999999999864 89999999995 789999999999999888777777765543

>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=99.14  E-value=2.4e-11  Score=110.82  Aligned_cols=67  Identities=16%  Similarity=0.305  Sum_probs=60.8

Q ss_pred             CCCCCcEEEEec--CCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCcccc
Q 001991          271 GEHPSRTLFVRN--INSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR  338 (985)
Q Consensus       271 ~e~~srtLfVgN--LP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~  338 (985)
                      ...++++|||.|  ||.++|+++|+++|++||.|..|++ .+.++||||+|.+.++|.+|++.|||+.|.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~-~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEEC-CTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEee-ccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            345788999965  9999999999999999999999988 567899999999999999999999998873

>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=99.13  E-value=3.9e-11  Score=108.98  Aligned_cols=80  Identities=19%  Similarity=0.252  Sum_probs=69.0

Q ss_pred             cccccceeeecC--CCCCC---------HHHHHHHhhccCCEEEEEEcCC-CCcEEEEEEcCHHHHHHHHHHhCCceeCC
Q 001991          357 DANQGTLVVFNL--DSSVS---------TEELHQIFGIYGEIREIRDTQH-KHNHKFIEFYDIRAAETALRTLNRSDVAG  424 (985)
Q Consensus       357 ~~~~~tLfV~NL--p~svT---------eedLrelFs~fG~I~~Vri~~~-skGfaFVeF~d~edA~kAI~~LNG~~I~G  424 (985)
                      ....++|+|+||  |.++.         +++|++.|++||.|..|++..+ .+|+|||+|.+.++|.+|+..|||+.++|
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            345679999999  54331         3789999999999999988654 67999999999999999999999999999


Q ss_pred             ceEEEEeccCcc
Q 001991          425 KQIKLEASRPGG  436 (985)
Q Consensus       425 r~IkV~~A~~k~  436 (985)
                      ++|+|+++.++.
T Consensus        85 r~i~v~~~~g~~   96 (99)
T d2dita1          85 RQITAQAWDGTT   96 (99)
T ss_dssp             EECEEEECCSCC
T ss_pred             EEEEEEEeCCcC
Confidence            999999998754

>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=99.13  E-value=8.9e-13  Score=117.31  Aligned_cols=70  Identities=17%  Similarity=0.332  Sum_probs=62.4

Q ss_pred             cceeeecCCCCCCHHHHHHHhhccCCEEEEEEc----------CCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceEEEE
Q 001991          361 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----------QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  430 (985)
Q Consensus       361 ~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~----------~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~  430 (985)
                      ++|||+|||.++|+++|+++|++||.|..+.+.          ..++|||||+|.+.++|++|++ |||..+.|++|+|.
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            579999999999999999999999988765443          2368999999999999999996 99999999999996


Q ss_pred             e
Q 001991          431 A  431 (985)
Q Consensus       431 ~  431 (985)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=5.8e-11  Score=107.82  Aligned_cols=82  Identities=17%  Similarity=0.306  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEecC--CCCCC---------HHHHHHhhcccCcEEEEEe-ccccceEEEEEeCCHHHHHHHHHHccCcccc
Q 001991          271 GEHPSRTLFVRNI--NSNVE---------DSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLR  338 (985)
Q Consensus       271 ~e~~srtLfVgNL--P~~vT---------EedLrelFs~fG~I~sVki-tgksrGfAFV~F~d~esA~kAi~~Lng~~I~  338 (985)
                      ....+++|+|+||  |.++.         +++|++.|++||.|..|++ ....+|+|||+|.+.++|.+|++.|||..+.
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            4567899999999  65432         3689999999999999987 5677899999999999999999999999999


Q ss_pred             cccccccccCCCCC
Q 001991          339 RRKLDIHYSIPKDN  352 (985)
Q Consensus       339 Gr~L~V~~a~pk~~  352 (985)
                      |++|.|.|..++.+
T Consensus        84 gr~i~v~~~~g~~~   97 (99)
T d2dita1          84 GRQITAQAWDGTTD   97 (99)
T ss_dssp             TEECEEEECCSCCC
T ss_pred             CEEEEEEEeCCcCC
Confidence            99999999877643

>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=99.07  E-value=1.2e-10  Score=108.03  Aligned_cols=76  Identities=17%  Similarity=0.257  Sum_probs=67.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCH-HHHHHHHHHccCcccccccccccccCCC
Q 001991          274 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDI-RAARNAMKALQNKPLRRRKLDIHYSIPK  350 (985)
Q Consensus       274 ~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~-esA~kAi~~Lng~~I~Gr~L~V~~a~pk  350 (985)
                      ....+||+|||..+|+++|+++|++||+|..|++ -+.+|||||.|.+. ++|..|+..+++..+.++.+.|.+...+
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i-~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC-CTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEE-ecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            3566799999999999999999999999999998 46799999999995 7899999999999999988888776543

>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=99.06  E-value=7.4e-12  Score=114.96  Aligned_cols=72  Identities=13%  Similarity=0.208  Sum_probs=67.6

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe----ccccceEEEEEeCCHHHHHHHHHHccCccccccccccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  347 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki----tgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a  347 (985)
                      +.++|++++.+++|++|+++|++||+|..|++    +++++|||||+|.+.++|.+|++.|||+.+.|++|.|.|+
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            56889999999999999999999999999987    5788999999999999999999999999999999999885

>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=99.06  E-value=1.3e-10  Score=102.00  Aligned_cols=75  Identities=17%  Similarity=0.175  Sum_probs=64.7

Q ss_pred             cccceeeecCCCCCCHHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCc-eEEEEeccCcc
Q 001991          359 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGK-QIKLEASRPGG  436 (985)
Q Consensus       359 ~~~tLfV~NLp~svTeedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr-~IkV~~A~~k~  436 (985)
                      +.+.|+|.++|++.+++.| ++|++||+|.++++.. .++||||+|.++++|++||+ +||..|+|+ .|.|.++..|.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~-~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k~   78 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN-TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   78 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS-SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC-CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCChh
Confidence            3567999999999986655 5799999999999764 58999999999999999997 999999998 46799887654

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.96  E-value=2.7e-10  Score=99.96  Aligned_cols=71  Identities=17%  Similarity=0.207  Sum_probs=61.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccc-ccccccC
Q 001991          275 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK-LDIHYSI  348 (985)
Q Consensus       275 srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~-L~V~~a~  348 (985)
                      .+.|+|.++|++++++.| ++|++||+|.++++ .+.++||||+|.+.++|++|++ +||+.|.|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999987655 57999999999998 6778999999999999999995 9999999985 5576654

>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=98.94  E-value=3.2e-10  Score=103.65  Aligned_cols=77  Identities=17%  Similarity=0.312  Sum_probs=66.3

Q ss_pred             ccccceeeecC--CCCCC--------HHHHHHHhhccCCEEEEEEcCC-------CCcEEEEEEcCHHHHHHHHHHhCCc
Q 001991          358 ANQGTLVVFNL--DSSVS--------TEELHQIFGIYGEIREIRDTQH-------KHNHKFIEFYDIRAAETALRTLNRS  420 (985)
Q Consensus       358 ~~~~tLfV~NL--p~svT--------eedLrelFs~fG~I~~Vri~~~-------skGfaFVeF~d~edA~kAI~~LNG~  420 (985)
                      .+.++|.|.|+  +..+.        .++|++.|++||.|++|.|..+       ..|++||+|.+.++|.+|+..|||+
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            35678999999  55442        3679999999999999998642       3579999999999999999999999


Q ss_pred             eeCCceEEEEeccC
Q 001991          421 DVAGKQIKLEASRP  434 (985)
Q Consensus       421 ~I~Gr~IkV~~A~~  434 (985)
                      .++||+|.|.++.+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999874

>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=98.91  E-value=1.5e-09  Score=97.00  Aligned_cols=84  Identities=20%  Similarity=0.345  Sum_probs=75.2

Q ss_pred             eeEEeecCCCCCCHHHHHHHHHhhCCCcceEE-Eecccccccce-eEEEEEecCCchhhHHHHHHhcCCcccCCCCcc-E
Q 001991          811 TTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFI-YLPIDFKNKCN-VGYAFINMIDPRQIIPFHQAFNGKKWEKFNSEK-V  887 (985)
Q Consensus       811 TTvMirNIPnk~t~~~L~~~id~~~~g~yDF~-YlpiDf~~~~N-~GYaFiNf~~~~~~~~f~~~f~g~~w~~~~s~K-~  887 (985)
                      |.|.||++|+.+|++.+++.|+  ..+++||+ |.|-|...+-+ ...|||||.+++++..|.+.|+|+.+..-+... .
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~--~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~   79 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQ--PMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYP   79 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHC--SCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhC--CcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEee
Confidence            8999999999999999999997  57899999 68888887755 589999999999999999999999998765555 8


Q ss_pred             EEEEeeccc
Q 001991          888 ASLAYARIQ  896 (985)
Q Consensus       888 ~~v~yA~iQ  896 (985)
                      +.|.||..|
T Consensus        80 a~VE~AP~q   88 (91)
T d1uw4a_          80 AIVEFAPFQ   88 (91)
T ss_dssp             CEEEECSSC
T ss_pred             eEEEEcCcc
Confidence            899999887

>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=98.80  E-value=1.9e-09  Score=98.40  Aligned_cols=76  Identities=16%  Similarity=0.347  Sum_probs=65.5

Q ss_pred             CCCcEEEEecC--CCCCC--------HHHHHHhhcccCcEEEEEec-------cccceEEEEEeCCHHHHHHHHHHccCc
Q 001991          273 HPSRTLFVRNI--NSNVE--------DSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAMKALQNK  335 (985)
Q Consensus       273 ~~srtLfVgNL--P~~vT--------EedLrelFs~fG~I~sVkit-------gksrGfAFV~F~d~esA~kAi~~Lng~  335 (985)
                      .|++.|.|+||  |..+.        .++|++.|++||.|..|++.       ....|++||+|.+.++|.+|++.|+|+
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  55443        35789999999999999872       234589999999999999999999999


Q ss_pred             ccccccccccccC
Q 001991          336 PLRRRKLDIHYSI  348 (985)
Q Consensus       336 ~I~Gr~L~V~~a~  348 (985)
                      .+.||.|.|.|..
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            9999999999875

>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=96.99  E-value=0.0012  Score=55.20  Aligned_cols=59  Identities=17%  Similarity=0.358  Sum_probs=53.0

Q ss_pred             HHHHHHhhccCCEEEEEEcCCCCc--EEEEEEcCHHHHHHHHHHhCCceeCCceEEEEecc
Q 001991          375 EELHQIFGIYGEIREIRDTQHKHN--HKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  433 (985)
Q Consensus       375 edLrelFs~fG~I~~Vri~~~skG--faFVeF~d~edA~kAI~~LNG~~I~Gr~IkV~~A~  433 (985)
                      +.|...|.++|.|.++.+.+...+  .|-|...+..+|.-|+..|+..+|++|+|.|.++.
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            446678999999999999877665  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=96.54  E-value=0.0017  Score=56.80  Aligned_cols=73  Identities=26%  Similarity=0.393  Sum_probs=58.7

Q ss_pred             cccccceeeecCCCCCC---------HHHHHHHhhccCCEEEEEEcCCCCcEEEEEEcCHHHHHHHHHHhCCceeCCceE
Q 001991          357 DANQGTLVVFNLDSSVS---------TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  427 (985)
Q Consensus       357 ~~~~~tLfV~NLp~svT---------eedLrelFs~fG~I~~Vri~~~skGfaFVeF~d~edA~kAI~~LNG~~I~Gr~I  427 (985)
                      .++..||.|.=..++..         -.+|.+.|..||+|.-||+..   +...|+|.+-+.|.+|+. ++|.++.|+.|
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~---d~mwVTF~dG~SAL~al~-l~g~~v~G~~l   87 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ---GQMLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET---TEEEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC---CeEEEEECCcHHHHHHhc-cCCeEEcceEE
Confidence            34566777754443322         257889999999999999875   489999999999999999 99999999999


Q ss_pred             EEEecc
Q 001991          428 KLEASR  433 (985)
Q Consensus       428 kV~~A~  433 (985)
                      +|....
T Consensus        88 ~It~~~   93 (95)
T d1ufwa_          88 KISGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEecCC
Confidence            997643

>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=95.06  E-value=0.025  Score=49.43  Aligned_cols=64  Identities=5%  Similarity=0.050  Sum_probs=53.8

Q ss_pred             cEEEEecCCCCCCHHHHHHhhcccCcEEEEEe-ccc------cceEEEEEeCCHHHHHHHHHHccCccccc
Q 001991          276 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACK------HRGFVMISYYDIRAARNAMKALQNKPLRR  339 (985)
Q Consensus       276 rtLfVgNLP~~vTEedLrelFs~fG~I~sVki-tgk------srGfAFV~F~d~esA~kAi~~Lng~~I~G  339 (985)
                      ++|.|+.||+.+||+++.+.+...|++...+. .++      .-.-|||.|.+.++.....+..+|..+.+
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            58999999999999999999999998877642 111      22479999999999999999999988754

>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=94.73  E-value=0.015  Score=50.72  Aligned_cols=71  Identities=17%  Similarity=0.327  Sum_probs=56.8

Q ss_pred             CCCcEEEEecCCCCCCH---------HHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHccCccccccccc
Q 001991          273 HPSRTLFVRNINSNVED---------SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  343 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTE---------edLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Lng~~I~Gr~L~  343 (985)
                      .+..||.|.=..++..+         .+|.+.|..||+|.-++.   -.+-.+|+|.+-+.|.+|+. +++.++.|+.|.
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            46678888655544333         467788999999998887   44578999999999999995 999999999999


Q ss_pred             cccc
Q 001991          344 IHYS  347 (985)
Q Consensus       344 V~~a  347 (985)
                      |...
T Consensus        89 It~~   92 (95)
T d1ufwa_          89 ISGP   92 (95)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            8643

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.62  E-value=0.021  Score=47.52  Aligned_cols=58  Identities=12%  Similarity=0.238  Sum_probs=50.9

Q ss_pred             HHHHhhcccCcEEEEEeccccce--EEEEEeCCHHHHHHHHHHccCcccccccccccccC
Q 001991          291 ELKALFEQFGDIRTIYTACKHRG--FVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  348 (985)
Q Consensus       291 dLrelFs~fG~I~sVkitgksrG--fAFV~F~d~esA~kAi~~Lng~~I~Gr~L~V~~a~  348 (985)
                      .|.+.|.++|.|.++.+...+.|  .|-|...+..+|..|+..|+-.+|++++|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            35578999999999998555554  89999999999999999999999999999998874

>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=80.38  E-value=1.5  Score=38.28  Aligned_cols=58  Identities=16%  Similarity=0.237  Sum_probs=48.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHhhcccCcEEEEEeccccceEEEEEeCCHHHHHHHHHHcc
Q 001991          273 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ  333 (985)
Q Consensus       273 ~~srtLfVgNLP~~vTEedLrelFs~fG~I~sVkitgksrGfAFV~F~d~esA~kAi~~Ln  333 (985)
                      .....||.-.+|..+...||.++|+.||.|.--.+   ..--|||...+.++|+.++..+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI---ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe---cCceEEEEecCHHHHHHHHHHhc
Confidence            34467999999999999999999999998876666   22379999999999999987543