Citrus Sinensis ID: 002974

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-
Protein Sequence
MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFHF
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccEEEEEEccccccccccEEEccccHHHHHHHccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEcccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEcccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccccccccHHHHcccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEHHHHHccccccEEEEEEccccHHHHHHHHHHHHHcccccccEEEEccccccccEEEcccc
Secondary Structure Prediction (SSPRO)
cccHHHccccccccccccHHccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccHHHHHHHHHccccccHHHHHccccccccccccccccHHHHHHHHHHcccccEEcccHHHHHHHHccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccccEEEEccccccEEEEEEccHHHHHHHHHHHcccEccccEEEEEEcccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEcccccccEEEEEEccHHHHHHHHHHHccccEcccEEEEEEcccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcHHHHHcccccccEEEEEcccccHHHHHHHHHHHHHccccEEEEEEcccccccEEEEEEcc
Coil and Loop (DISEMBL)
mpfeimdhrsgsapthfseeirfpaerqigfwkpntmsdqqgsdgtvpmlggkfvasspmenfspvgipsvdwLELQQSTLARDKMKRLGivgeegaanlsenswnsvnhhpkswsnlavqpginslsgnrsgingiqsesslfsssLSDIFTRKMklsgneilsrqplnavashhqpeepfesLKEIEAQTIgnllpdeddlfsgvtddmghnfqantvddledfdlfssgggmelegddrlfavqknsdfvggvsnqgvsagsvvgehpygehpsrtLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALqnkplrrrkldihysipkdnpsekdanqgtLVVFNldssvsteELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLnrsdvagkqikleasrpggarrFMVQSEqeqddlnlcqipfddlssgqmvsSGVITstcmdngsiqvlhsatrspaialteshqtssvpnglpslarvgsigkqfghyepnlsldemkfgnqhpsfhphslpeyhdslanglpynspstiADIASSVgtkikdgldsrhirgvssnghlmeptggvfgsprngsyslhgnpyvwnnsnshqqhpsspmvwpnspsflnglhanrvahmpgfprvpplmlnatspahhhigsapavnpslwdrqhayagespetsnfhlgslgsggflgrspshhvdiasqnilshvggncmdmtknvgmrspqqichlfpgrnpmmsmqtsfdssnerMRNLsyrrnesnsnhadkkqyELDIDrilrgddsrttLMIKNIPNKYTSKMLLAAIDEHcrgtydfiylpidfkaslfgfffhf
Flexible Loop (DISEMBL)
mpfeimdhrsgsapthfseeIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKalqnkplrrrkLDIHysipkdnpsekdanqgTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTlnrsdvagkqikleasrpggaRRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTeshqtssvpngLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRgvssnghlmeptggVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSyrrnesnsnhadkkqyeldidrilrgddsrttlmiknipnkytSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFHF
Low Complexity Region (SEG)
MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQsesslfssslsDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWnnsnshqqhpsspMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHlgslgsggflgrsPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFHF
Disordered region (IsUnstruct)
****************************IGFW********************************PVGIPSVDWLELQQSTLA*****RLGIV*******************************************************************************************************LL****DLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSN*GV**GSVVG***Y****SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL**********DIH****************TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN*********************************NLCQIPFDDLS**QMVSSGVITSTCMDNGSIQVL************************************************************************************************************************************PYVW*********************FLNGLHANRVAHMPGF******************************************************F*******HVDIASQNILSHVGGNCMDMTKNVG*****QICHLF*****************************************LDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFH*
Disordered Region (DISOPRED)
****************FSEEIRFPAERQIGFWKPNT***********************************************************************************************************************************************************TIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDR************************************TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI******************LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL***********************************************************************************************************************************************************************************************************************************************************A*****W*************************************************************************************************************ELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFHF
Disordered Region (DISEMBL)
***************HFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIAL*********PNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNS***********VWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFHF
Disordered Region (DISPRO)
********************IRFPAERQIGFWKPNT***************************SPVGI****WLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSV***************************************L*DIFTRKMKLSGNEILSRQPLNAV****QPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFV**********************PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK*******ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP********************************VSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSN*R***LS*R*****SN*ADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFHF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASLFGFFFHF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	861	2.2.26 [Sep-21-2011]
Q64M78	1001	Protein MEI2-like 4 OS=Or	yes	no	0.958	0.824	0.489	0.0
Q8W4I9	915	Protein MEI2-like 1 OS=Ar	yes	no	0.902	0.849	0.483	0.0
Q9LYN7	907	Protein MEI2-like 4 OS=Ar	no	no	0.897	0.852	0.483	0.0
Q6ZI17	848	Protein MEI2-like 2 OS=Or	yes	no	0.687	0.698	0.441	1e-127
Q75M35	955	Protein MEI2-like 3 OS=Or	no	no	0.881	0.794	0.374	1e-120
Q6EQX3	811	Protein MEI2-like 5 OS=Or	no	no	0.737	0.782	0.404	1e-117
Q8VWF5	800	Protein MEI2-like 5 OS=Ar	no	no	0.361	0.388	0.581	1e-100
Q9SVV9	759	Protein MEI2-like 3 OS=Ar	no	no	0.334	0.379	0.574	3e-94
Q9SJG8	843	Protein MEI2-like 2 OS=Ar	no	no	0.067	0.068	0.637	8e-15
O65001	656	Protein terminal ear1 OS=	N/A	no	0.188	0.246	0.235	2e-12

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

 Score =  692 bits (1785), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/911 (48%), Positives = 567/911 (62%), Gaps = 86/911 (9%)

Query: 1   MPFEIMDHR----SGSAPT----HFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGG 52
           MP ++MD R      S PT     FSEE+R P ERQ+GFWK  ++    GS         
Sbjct: 1   MPSQVMDQRHHMSQYSHPTLAASSFSEELRLPTERQVGFWKQESLPHHMGS--------- 51

Query: 53  KFVASSPMENFSPVGIPSVDWLELQQSTLARDKMKRLGI----VGEEGAANLSENSWNSV 108
           K VASSP+E   P+G      LEL Q    RD+     +     G+E  ANL  + W   
Sbjct: 52  KSVASSPIEKPQPIGTRMAGRLELLQPYKLRDQGAAFSLEHKLFGQERHANLPPSPW--- 108

Query: 109 NHHPKSWSNLAVQPGINS---LSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILS 165
              P   +       + S    S  R   NG  +E+ LFSSS+SDIF +K++L+    L 
Sbjct: 109 --RPDQETGRQTDSSLKSAALFSDGRINPNGAYNENGLFSSSVSDIFDKKLRLTSKNGLV 166

Query: 166 RQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLED 225
            Q +  V  +H  +EPFE  +EIEAQ IGNLLPD+DDL SGV D++G+        D  D
Sbjct: 167 GQSIEKVDLNHVDDEPFELTEEIEAQIIGNLLPDDDDLLSGVVDEVGYP-TNANNRDDAD 225

Query: 226 FDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQ-GVSAGSVVGEHPYGEHPSRTLFVRN 284
            D+F +GGGMELE D+     +K  +F G  ++  G+  G + GEH Y E PSRTLFVRN
Sbjct: 226 DDIFYTGGGMELETDEN----KKLQEFNGSANDGIGLLNGVLNGEHLYREQPSRTLFVRN 281

Query: 285 INSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL 344
           INSNVEDSELK LFE FGDIR +YTACKHRGFVMISYYDIR+A NA   LQNK LRRRKL
Sbjct: 282 INSNVEDSELKLLFEHFGDIRALYTACKHRGFVMISYYDIRSALNAKMELQNKALRRRKL 341

Query: 345 DIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFI 404
           DIHYSIPKDNPSEKD NQGT+V+FN+D S++ ++LH+IFG YGEI+EIRDT  K +HK I
Sbjct: 342 DIHYSIPKDNPSEKDINQGTIVLFNVDLSLTNDDLHKIFGDYGEIKEIRDTPQKGHHKII 401

Query: 405 EFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFM--VQSEQEQDDLNLCQIPFDD 462
           EFYD+RAAE ALR LNR+D+AGK+IKLE SR G ARR    + SE  Q++  +C++    
Sbjct: 402 EFYDVRAAEAALRALNRNDIAGKKIKLETSRLGAARRLSQHMSSELCQEEFGVCKLGSPS 461

Query: 463 LSSGQMVSSG-----VITSTCMDNGSIQVLHSATRSPAIALTESH---------QTSSVP 508
            SS  + S G      ITST  +NGSIQ +HS  ++      E+          Q+ S P
Sbjct: 462 TSSPPIASFGSTNLATITSTGHENGSIQGMHSGLQTSISQFRETSFPGLSSTIPQSLSTP 521

Query: 509 NGLPS------LARVG----SIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLA 558
            G+ S       A +G    S+G+  GH   N S   M       + HPHSLPE H+ + 
Sbjct: 522 IGISSGATHSNQAALGEISQSLGRMNGHM--NYSFQGMS------ALHPHSLPEVHNGVN 573

Query: 559 NGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSS---NGHLMEPTGGVFGSPRNGSYS 615
           NG+PYN  +++A + +   ++  + +D+RH+  V S   NGH  +   G  G  R+GS S
Sbjct: 574 NGVPYNL-NSMAQVVNGTNSRTAEAVDNRHLHKVGSGNLNGHSFDRAEGALGFSRSGSSS 632

Query: 616 LHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPL-MLNATSPA 674
           + G+  +WNNS++   HP+SP++WP+  SF+N + +   A M G PR P   M++   P 
Sbjct: 633 VRGHQLMWNNSSNFHHHPNSPVLWPSPGSFVNNVPSRSPAQMHGVPRAPSSHMIDNVLPM 692

Query: 675 HH-HIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILS 733
           HH H+GSAPA+NPSLWDR+H YAGE  E  NFH GS+GS GF G    H +++   NI  
Sbjct: 693 HHLHVGSAPAINPSLWDRRHGYAGELTEAPNFHPGSVGSMGFPGSPQLHSMEL--NNIYP 750

Query: 734 HVGGNCMDMT---KNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNS 790
             GGNCMD T     +G  SPQQ   +F GRNPM+ +  SFDS  ERMR+   RRN+SN 
Sbjct: 751 QTGGNCMDPTVSPAQIGGPSPQQRGSMFHGRNPMVPL-PSFDSPGERMRS---RRNDSNG 806

Query: 791 NHAD-KKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPID 849
           N +D KKQYELD+DRI+RGDDSRTTLMIKNIPNKYTSKMLLAAIDE+ +GTYDFIYLPID
Sbjct: 807 NQSDNKKQYELDVDRIVRGDDSRTTLMIKNIPNKYTSKMLLAAIDENHKGTYDFIYLPID 866

Query: 850 FKASL-FGFFF 859
           FK     G+ F
Sbjct: 867 FKNKCNVGYAF 877

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 =  651 bits (1680), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/856 (48%), Positives = 546/856 (63%), Gaps = 79/856 (9%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPM 60
           MP +IM+ R  S P+HF E+I   +ERQ GF K + M + QG                  
Sbjct: 1   MPSDIMEQRGVSTPSHFHEDIHITSERQFGFMKTDMMPENQG------------------ 42

Query: 61  ENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAV 120
                                 RD++           +++ ++SW S ++  K  S+ + 
Sbjct: 43  ---------------------GRDRL-----------SSMPKSSWTSESYQLKPQSSFSG 70

Query: 121 QPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEE 180
                S +  R+  NG Q ESSLFSSS+SD+F+RK++L G+++LS    N V +H + EE
Sbjct: 71  SHPSGSPNA-RNTTNGSQWESSLFSSSMSDLFSRKLRLQGSDMLSTMSANTVVTH-REEE 128

Query: 181 PFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD 240
           P ESL+EIEAQTIGNLLPDEDDLF+ VT ++G   +ANT D+L++FDLFSS GGMEL+GD
Sbjct: 129 PSESLEEIEAQTIGNLLPDEDDLFAEVTGEVGRKSRANTGDELDEFDLFSSVGGMELDGD 188

Query: 241 DRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQ 300
                  +N +  G  S         VGE   GE PSRTL V NI+SNVED ELK LFEQ
Sbjct: 189 IFSSVSHRNGERGGNNS---------VGELNRGEIPSRTLLVGNISSNVEDYELKVLFEQ 239

Query: 301 FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDA 360
           FGDI+ ++TACK+RGF+M+SY DIRAA+NA +ALQNK LR  KLDI YSI K+NPS+KD 
Sbjct: 240 FGDIQALHTACKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRYSISKENPSQKDT 299

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           ++G L+V NLDSS+S +EL+++   YGE++EIR T H ++  +IEF+D+RAA  AL  LN
Sbjct: 300 SKGALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFDVRAAAAALGGLN 359

Query: 421 RSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVS--SGVITSTC 478
             +VAGK+++L  + P G R +  Q      +  L +  + + SSG +     G+I+ST 
Sbjct: 360 GLEVAGKKLQLVPTYPEGTR-YTSQCAANDTEGCLPKTSYSNTSSGHIGRHFPGMISSTS 418

Query: 479 MDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKF 538
            D GS++V+H++  SP  +  E H++ S+P G P  A   S  K  G  E     D    
Sbjct: 419 SDGGSMRVIHNSIGSPVNSFIERHRSLSIPIGFPPSANGISASKPVGLQEHGHHFDNSNM 478

Query: 539 GNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGH 597
           G Q  P+ HPHS  EY D+ ANG PY S S  +++ S  G+K  +G    ++RGV     
Sbjct: 479 GIQSMPNLHPHSFSEYVDNFANGSPYTS-SAFSEMVSD-GSKANEGFMIHNVRGVEGF-- 534

Query: 598 LMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHM 657
               +GG  GSP + S     N  +W+NSN+ QQ+PSS M+WPNSPS +N +   R   +
Sbjct: 535 ----SGGGIGSPMHQSSRRPIN--LWSNSNTQQQNPSSGMMWPNSPSHINSIPTQRPP-V 587

Query: 658 PGFPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFL 716
             F R PP+M+N A+SP HHHIGSAP +N   WDR+ AY  ES E+S FH+GS GS G  
Sbjct: 588 TVFSRAPPIMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAESLESSGFHIGSHGSMGIP 647

Query: 717 GRSPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSN 775
           G SPSH +DI S    S VGGN MD+ ++N  +RSPQQ+ HLFPGR+PM SM  SFDS N
Sbjct: 648 GSSPSHPMDIGSHKTFS-VGGNRMDVNSQNAVLRSPQQLSHLFPGRSPMGSMPGSFDSPN 706

Query: 776 ERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDE 835
           ER RNLS+RR+ES+S++ADKK YELD+DRILRG+D RTTLMIKNIPNKYTSKMLL+AIDE
Sbjct: 707 ERYRNLSHRRSESSSSNADKKLYELDVDRILRGEDRRTTLMIKNIPNKYTSKMLLSAIDE 766

Query: 836 HCRGTYDFIYLPIDFK 851
           HC+GTYDF+YLPIDFK
Sbjct: 767 HCKGTYDFLYLPIDFK 782

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 =  649 bits (1674), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/858 (48%), Positives = 543/858 (63%), Gaps = 85/858 (9%)

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

Query: 61  ENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLA- 119
               P G                         G + ++NL  +SW S ++     S+L+ 
Sbjct: 38  ----PEG-------------------------GVDRSSNLPTSSWTSDSYQLSQQSSLSG 68

Query: 120 VQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPE 179
             P    +   R+  N    ESSLFSSSLSD+F+RK++L  ++ L      A  S ++ E
Sbjct: 69  ALPSF--IPNGRTTTNDTHWESSLFSSSLSDLFSRKLRLPRSDKL------AFMSANREE 120

Query: 180 EPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEG 239
           EP ESL+E+EAQTIGNLLPDEDDLF+ V  +  H  +AN  DDL+D DLFSS GGMEL+G
Sbjct: 121 EPSESLEEMEAQTIGNLLPDEDDLFAEVVGEGVHKSRANGGDDLDDCDLFSSVGGMELDG 180

Query: 240 DDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFE 299
           D  +F+     D   G      S  S V EHP GE  SR LFVRN++S++ED EL  LF+
Sbjct: 181 D--VFSSVSQRDGKRG------SNVSTVAEHPQGEILSRILFVRNVDSSIEDCELGVLFK 232

Query: 300 QFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKD 359
           QFGD+R ++TA K+RGF+M+SYYDIRAA+ A +AL  + LR RKLDI YSIPK+NP E +
Sbjct: 233 QFGDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRKLDIRYSIPKENPKE-N 291

Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL 419
           +++G L V NLDSS+S EELH IF  YGEIRE+R T H+++  +IEF+D+R A+ AL+ L
Sbjct: 292 SSEGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVYIEFFDVRKAKVALQGL 351

Query: 420 NRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVS--SGVITST 477
           N  +VAG+Q+KL  + P G   F  Q   +  +  L ++ F++LSS  M     G++ ST
Sbjct: 352 NGLEVAGRQLKLAPTCPEGTS-FWPQFASDDGEGGLPKMAFNNLSSAHMGRHFPGILAST 410

Query: 478 CMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMK 537
            +D GSI+ +H++  SP  +  E HQ+  VP GLP  ARV S  K  G  E     D  K
Sbjct: 411 SIDGGSIRGMHNSVGSPMNSFIERHQSLDVPIGLPPSARVISASKPVGLQEFGNPFDNSK 470

Query: 538 FGNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNG 596
            G Q  P+ HPH  P+Y D+ A+G PY S +T +++ S  G K  +G    ++RGV  +G
Sbjct: 471 TGIQSMPNLHPH-FPDYLDNFASGSPYKSSTTFSEMVSD-GQKANEGFMMSNVRGVGVDG 528

Query: 597 HLMEPTGGVFGSPRN-GSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVA 655
                 GGV GSP N GS+   GN  +W+NSNS Q + SS M+WPNSPS +NG+ + R+ 
Sbjct: 529 F----NGGVIGSPINQGSH--RGNLNLWSNSNSQQHNQSSGMMWPNSPSRVNGVPSQRIP 582

Query: 656 HMPGFPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGG 714
            +  F R  PLM+N A+SP HHHIGSAP +N   WDR+ AY  ESPE+S FHLGS GS G
Sbjct: 583 PVTAFSRASPLMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAESPESSGFHLGSPGSMG 642

Query: 715 FLGRSPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHLFPGRNPMMSMQTSFDS 773
           F G SPSH +D  S  + SHVGGN M+  +KN  +RS +Q+ HLF GR+PM+S+  SFD 
Sbjct: 643 FPGSSPSHPMDFGSHKVFSHVGGNRMEANSKNAVLRSSRQMPHLFTGRSPMLSVSGSFDL 702

Query: 774 SNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAI 833
            NER RNLS+RR+ESNS++A+KK YELD+DRILRG+DSRTTLMIKNIPNKYTSKMLLAAI
Sbjct: 703 PNERYRNLSHRRSESNSSNAEKKLYELDVDRILRGEDSRTTLMIKNIPNKYTSKMLLAAI 762

Query: 834 DEHCRGTYDFIYLPIDFK 851
           DE+C+GTYDF+YLPIDFK
Sbjct: 763 DEYCKGTYDFLYLPIDFK 780

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 =  458 bits (1178), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 309/700 (44%), Positives = 414/700 (59%), Gaps = 108/700 (15%)

Query: 187 EIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD--DRLF 244
           + + + I +LLP+EDDLF+G+T+++    Q N++++LE+FD+F SGGGMEL+ D  + + 
Sbjct: 97  DFDLRQIDDLLPNEDDLFAGITNEIEPAGQTNSMEELEEFDVFGSGGGMELDTDPVESIT 156

Query: 245 AVQKNSDFVGGVSNQGV-------SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKAL 297
           A   N+    G+   GV       SA +V GEHPYGEHPSRTLFVRNINSNV+D+EL++L
Sbjct: 157 AGLGNTSIADGLRGNGVNHFGPSNSASTVAGEHPYGEHPSRTLFVRNINSNVDDTELRSL 216

Query: 298 FEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE 357
           FEQ+GDIRT+YTA KHRGFVMISY+DIRAAR AM+ LQNKPLRRRKLDIH+SIPK+NPS+
Sbjct: 217 FEQYGDIRTLYTATKHRGFVMISYFDIRAARGAMRGLQNKPLRRRKLDIHFSIPKENPSD 276

Query: 358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR 417
           KD NQGTLV+FNLD SVS EE+ QIFG YGE++EIR+T +K +HKFIEFYD+RAAE ALR
Sbjct: 277 KDLNQGTLVIFNLDPSVSNEEVRQIFGTYGEVKEIRETPNKKHHKFIEFYDVRAAEAALR 336

Query: 418 TLNRSDVAGKQIKLEASRPGGARRFMVQS---EQEQDDLNLCQIPFDDLSSGQMVSSG-- 472
           +LN+S++AGK+IKLE SRPGG RR ++Q    + +QD+    +IP      G  ++S   
Sbjct: 337 SLNKSEIAGKRIKLEPSRPGGTRRNLMQQLGHDIDQDEPRSYRIP----HVGSPIASSPP 392

Query: 473 ---VITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLP-----SLARVGSIGKQF 524
                 S+  DN  +Q  +++     ++          P G+P     +  ++  IGK  
Sbjct: 393 GAWAQYSSPTDNNLLQAFNASPTGNGMS----------PIGMPPSLISNAVKIAPIGK-- 440

Query: 525 GHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGL 584
              + N S  +  F N +    PH           G  +    +  D             
Sbjct: 441 ---DSNWSKYDKVFSNNN---QPH-----------GAAFQHSHSYQD------------H 471

Query: 585 DSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPS 644
            S H+   SS G L  P   ++GSP+   YS H    +W         PS      N+ S
Sbjct: 472 KSEHMS--SSPGTLTGPE-FLWGSPK--PYSEHAQSPIWRPPAIGHAIPS------NTRS 520

Query: 645 FLNG-LHANRVAHMPGFPRVPPLMLNATSPAHH-HIGSAPAVNPSLWDRQHAYAGESPET 702
              G L+  R A + G          +    HH H+GSAP+  P  ++    +  ESPET
Sbjct: 521 QGQGLLYGGRQASLFG----------SQDQLHHHHVGSAPSGAP--FESHFGFLPESPET 568

Query: 703 SNF------HLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNV--GMRSPQQI 754
           S        ++G++GSG        +    AS N +S + GN  D   +    + SP ++
Sbjct: 569 SYMNQVRFGNIGNIGSGRNGTGLMLNMAARASVNPVSALSGNMSDNNSSSFRPILSP-RL 627

Query: 755 CHLFPGRNPMMSMQTSF--DSSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDDS 811
              F G NP      SF  D+S ER RN   RR +S+   AD KKQY+LD+++I +GDD+
Sbjct: 628 GQSFYG-NPTYQGPGSFGLDNSIERGRN---RRVDSSVFQADSKKQYQLDLEKIRKGDDT 683

Query: 812 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFK 851
           RTTLMIKNIPNKYTSKMLLAAIDE  +GTYDF YLPIDFK
Sbjct: 684 RTTLMIKNIPNKYTSKMLLAAIDEFHKGTYDFFYLPIDFK 723

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 =  434 bits (1117), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 326/871 (37%), Positives = 458/871 (52%), Gaps = 112/871 (12%)

Query: 24  PAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFSPVGIPSVDWLELQ--QSTL 81
           P ERQ+GFW   +M D +GS         K V +SP+E   P G       E    Q+  
Sbjct: 34  PTERQVGFWNSESMVDHKGS---------KSVFASPLEKIQPNGANHAGDPETPGGQAFK 84

Query: 82  ARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLA------VQPGI--NSLSGNRSG 133
             D +    ++ +E A+     SW  +  +P S   L+      V+P      + G   G
Sbjct: 85  GLDILSLSNLMRQENASGSPSLSWGEILTNPISRLGLSTRETAFVEPTTADQHVPGYGKG 144

Query: 134 INGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASH---HQPEEPFESLKEIEA 190
           ++         SSSLS++F+ K +    EI+S     +  +H   +  +EP ES++ IEA
Sbjct: 145 LS---------SSSLSEVFSGKSR----EIVSGVLCQSTGTHTSIYDSDEPLESMEAIEA 191

Query: 191 QTIG-NLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKN 249
           QTIG  L  D+DDL SG+ D       +   DD  D D+F +GGGMELE +D +    K 
Sbjct: 192 QTIGDLLPDDDDDLISGIADGFEFTGMSTNQDD-ADEDIFCTGGGMELENNDSV----KG 246

Query: 250 SDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT 309
                G     +S+G     H   + PSRTL VRNI +N+EDS+L  LF+Q+GDIR +YT
Sbjct: 247 DKVQDGSFKSQISSG-----HSINKQPSRTLVVRNITANIEDSDLTVLFQQYGDIRMLYT 301

Query: 310 ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFN 369
           + KH GFV +SYYDIRAA+NAM+AL +KPL   KLD+ +S PK+N   KD ++G LVV N
Sbjct: 302 SFKHHGFVTVSYYDIRAAQNAMRALHSKPLGLMKLDVQFSFPKENVPGKDIDKGMLVVSN 361

Query: 370 LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI 429
           +DSS+S ++L Q+  +YG+++EI  +      KF+EFYD+RAAE AL  LN+  ++G + 
Sbjct: 362 IDSSISNDDLLQMLSVYGDVKEISSSPISCTKKFVEFYDVRAAEEALHDLNKGGISGPKF 421

Query: 430 KLEASRPGGARRFMVQS---EQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQV 486
           K+E S+ G A   + Q    E +QD L     P    +S    + G + + C DN ++  
Sbjct: 422 KVELSQHGEAGSCLRQQHSREWKQDSL-----PHQPKNSSPG-TIGKLGTKCQDNSTVHN 475

Query: 487 LHSATRSPAIALTESHQTSSVPNGLPSLARVGSI---GKQFGHYEPNLSLDEMKFGNQHP 543
           L S       + T+   T+  P  L S  R+ S      Q    + +  L +  FG    
Sbjct: 476 LFSPVNQQLESPTQCISTTG-PQILSSPIRIKSTLQHNNQASVGDLSGPLGQGNFGRGIQ 534

Query: 544 SFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDS--RHIRGVSSNGHLMEP 601
           + HP SLPE+H+ + N    NS S    ++    +  +DG+D   + +      GH  + 
Sbjct: 535 TLHPRSLPEHHNRICN----NSKSMT--VSGRNASSRQDGVDHNIQKVGPAGFCGHSFDQ 588

Query: 602 TGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFP 661
               FG    GS  LHG  Y WN++N   Q PS+P++W N              H+  +P
Sbjct: 589 NNEAFGFTEIGSCPLHGYHYTWNHTNVFPQSPSAPILWSN---------LQHPMHVHSYP 639

Query: 662 RVPPLMLNATSPA--HHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRS 719
            VPP MLN  S     HH+GSAP              G      +FH GSLGS G  G  
Sbjct: 640 GVPPHMLNTGSYPMDQHHLGSAP-----------DNGGSFGNVHSFHPGSLGSIGLHGSP 688

Query: 720 ---PSHHVDIAS------QNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTS 770
              PS     AS      + + S VGG         G +S QQ+C+   GRNPM+ + TS
Sbjct: 689 QLYPSELSAFASSRGNFREALFSPVGG---------GFQSLQQMCNAINGRNPMIHVSTS 739

Query: 771 FDSSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKML 829
           +D++N+RMR+   RR++ N   ++ K+Q+ELDIDRI +G+DSRTTLMIKNIPNKY  K+L
Sbjct: 740 YDATNDRMRS---RRHDGNPAQSENKRQFELDIDRIAKGEDSRTTLMIKNIPNKYNCKLL 796

Query: 830 LAAIDEHCRGTYDFIYLPIDFKASL-FGFFF 859
           LA IDE+ RGTYDFIYLPIDFK     G+ F
Sbjct: 797 LAVIDENHRGTYDFIYLPIDFKNKCNVGYAF 827

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 =  423 bits (1087), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 300/742 (40%), Positives = 409/742 (55%), Gaps = 107/742 (14%)

Query: 134 INGIQSESSLFSSSLSDIFTRKMKLSGNEI-LSRQPLNAV-ASHHQP---EEPFESLKEI 188
           +NG  S++ LFSSSL  +  +  KL G E   + QP + +     QP       + + ++
Sbjct: 38  VNG-SSDAVLFSSSLPSVL-QFGKLPGKEREYNAQPKDDMFPMMKQPGTNARVADPMDDV 95

Query: 189 EAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD---DRLFA 245
               IGNLLPD+++L +GV +D  H      V++ E++D+F + GGMEL+ D      F 
Sbjct: 96  AQHLIGNLLPDDEELLAGVIEDFDHVKLRTQVEESEEYDVFRNSGGMELDIDPLESITFG 155

Query: 246 VQKNS--DFVGGVSNQGV---SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQ 300
             K S  +  G  +NQ      AG+V GEHPYGEHPSRTLFVRNINSNVEDSEL++LFE 
Sbjct: 156 TAKASLVNGTGSSTNQYSIQNGAGTVTGEHPYGEHPSRTLFVRNINSNVEDSELRSLFEP 215

Query: 301 FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDA 360
           FGDIR++YTA KHRGFVMISYYDIR ARNA  ALQ+KPLRRRKLDIHYSIPK+NPS+KD 
Sbjct: 216 FGDIRSMYTATKHRGFVMISYYDIRHARNAKTALQSKPLRRRKLDIHYSIPKENPSDKDM 275

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           NQGTLV+FNL+ +VS EEL QIFG +GE+REIR+T HK +H+FIEFYD+RAAE+ALR+LN
Sbjct: 276 NQGTLVIFNLEPAVSNEELLQIFGAFGEVREIRETPHKRHHRFIEFYDVRAAESALRSLN 335

Query: 421 RSDVAGKQIKLEASRPGGARRFMVQS-----EQEQDDLNLCQIPFDDLSSGQMVSSGVIT 475
           +SD+AGK++KLE SRPGGARR  +Q      EQ++   N  QI     +S   + S + +
Sbjct: 336 KSDIAGKRVKLEPSRPGGARRSFIQHFNHEFEQDETKHNSFQIGSPSANSPPSLWSQLGS 395

Query: 476 STCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDE 535
            T  D   +  L+    +  ++   S+  S   +G P +     +GK    Y  N + D 
Sbjct: 396 PT--DENKLNALNETAFNGGMSPLGSNHLSGFSSGYPPMK--SPVGK--SSYWNNRA-DN 448

Query: 536 MKFGNQHPSFH-PHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSS 594
           +  G+  P+ H  HS PE+H  + +  P  S +  +   +S                   
Sbjct: 449 IFHGS--PTLHNSHSFPEHHGGIISASPLVSSAASSASTAS------------------- 487

Query: 595 NGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQH--PSSPMVWPNSPSFLNGLHAN 652
                            G  +L G  ++W N+N+ + H  PSS      S S        
Sbjct: 488 -----------------GFTALTGTSFLWGNNNNLRDHGQPSSIQSQALSNSLFPNNQPQ 530

Query: 653 RVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGS 712
           R +++  +  +      +   +  ++GSAP+V P  ++    Y  +SP+TS    G  G 
Sbjct: 531 RQSNL--YQNLRGSFGASEHFSQFNVGSAPSVFP--FESNFGYFSDSPDTSYMRQGKFGG 586

Query: 713 GGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQ---T 769
            G                  + V G+ M    N G          +P  N + SMQ    
Sbjct: 587 TG-----------------PTRVSGSLM---TNFGA---------YPRIN-VASMQNGSV 616

Query: 770 SFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKML 829
            F+   +R RN +     S      + QY+LD+++I+ G D+RTTLMIKNIPNKYTS ML
Sbjct: 617 GFEGLLDRGRNQTV--GNSGCQEDSRVQYQLDLEKIIAGKDTRTTLMIKNIPNKYTSNML 674

Query: 830 LAAIDEHCRGTYDFIYLPIDFK 851
           L  IDE   GTYDF YLPIDFK
Sbjct: 675 LEVIDETHEGTYDFFYLPIDFK 696

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: 139 SESSLFSSSLSDIFTR-KMKLSGN-EILSRQPLNAVASHHQPEEPFESLKEIEAQTIGNL 196
           S+++LFSSSL  +F R K++LS N +  S     AV+  ++  E   S  + E+ +IGNL
Sbjct: 26  SDATLFSSSLP-VFPRGKLQLSDNRDGFSLIDDTAVSRTNKFNE---SADDFESHSIGNL 81

Query: 197 LPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDR------------LF 244
           LPDE+DL +G+ DD+        + D +D+DLF SGGGMEL+ D R            L 
Sbjct: 82  LPDEEDLLTGMMDDL----DLGELPDADDYDLFGSGGGMELDADFRDNLSMSGPPRLSLS 137

Query: 245 AVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI 304
           ++  N+     + N    AG+V GEHPYGEHPSRTLFVRNINSNVEDSEL ALFEQ+GDI
Sbjct: 138 SLGGNAIPQFNIPN---GAGTVAGEHPYGEHPSRTLFVRNINSNVEDSELTALFEQYGDI 194

Query: 305 RTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT 364
           RT+YT CKHRGFVMISYYDIR+AR AM++LQNKPLRRRKLDIH+SIPKDNPSEKD NQGT
Sbjct: 195 RTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKDNPSEKDMNQGT 254

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 424
           LVVFNLD S+S ++LH IFG +GEI+EIR+T HK +HKF+EFYD+R AE AL+ LNR ++
Sbjct: 255 LVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAEAALKALNRCEI 314

Query: 425 AGKQIKLEASRPGGARR-FMVQSEQEQDDLNLCQIPF 460
           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: 163 ILSRQPLNAVASHHQPEEPFES------------LKEIEAQTIGNLLPD-EDDLFSGVTD 209
           ++  Q +N   S+HQ  +   S            L + ++  IGN+LPD E++LFSG+ D
Sbjct: 29  LIQHQNINPRDSYHQSVDEMASGLDHFSGGIGNMLDDGDSHPIGNMLPDDEEELFSGLMD 88

Query: 210 DMGHNFQANTVDDLEDFDLFSSGGGMELEGD---------DRLFAVQKNSDFV--GGVSN 258
           D+  +    T+DDLED+DLF SGGG+ELE D          R+     N D V    +  
Sbjct: 89  DLNLSSLPATLDDLEDYDLFGSGGGLELETDPYDSLNKGFSRMGFADSNVDNVMPQNIFQ 148

Query: 259 QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVM 318
            GV  GS+ GEHPYGEHPSRTLFVRNINSNVEDSEL+ALFEQ+G IRT+YTACK RGFVM
Sbjct: 149 NGV--GSIAGEHPYGEHPSRTLFVRNINSNVEDSELQALFEQYGHIRTLYTACKQRGFVM 206

Query: 319 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEE 378
           +SY DIRA+R AM+ALQ K L++RKLDIH+SIPKDNPSEKD NQGTLVVFNL  SVS  +
Sbjct: 207 VSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDNPSEKDVNQGTLVVFNLAPSVSNRD 266

Query: 379 LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG 438
           L  IFG+YGEI+EIR+T +K +HKF+EF+D+R+A+ AL+ LNR+++AGK+IKLE SRPGG
Sbjct: 267 LENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADAALKALNRTEIAGKRIKLEHSRPGG 326

Query: 439 ARRFM---VQSEQEQDD 452
           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 = 83.2 bits (204), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 45/58 (77%)

Query: 794 DKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFK 851
           D  +Y +D+DRI  GD+ RTTL+IKNIPNKYT KML+A IDE  +G YDF+ LP DFK
Sbjct: 661 DGGRYHIDLDRIASGDEIRTTLIIKNIPNKYTYKMLVAEIDEKHKGDYDFLCLPTDFK 718

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

Arabidopsis thaliana (taxid: 3702)

>sp|O65001|TE1_MAIZE Protein terminal ear1 OS=Zea mays GN=TE1 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/200 (23%), Positives = 98/200 (49%), Gaps = 38/200 (19%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTI-YTACKHRGFVMISYYDIRAARNAMKALQ 335
           SR + +  +  + +++++      FG IR++   A    G   + ++DIRAA  A+  ++
Sbjct: 86  SRVVVLGLVPPHAQEADVAQAMAPFGAIRSVDACAVASEGVATVHFFDIRAAELALTCVR 145

Query: 336 NKPLRRR-KLDIHYSI--------------------PKDNP----------------SEK 358
            + +R++ +L   Y+                     P D+                 ++ 
Sbjct: 146 EQHMRQQSRLGQLYAAAAVAPAWAPAPTPQAWDWPHPNDDGRGLVLGHAVWAHFATGADD 205

Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT 418
             N+G+LVV +    VS  +L Q+F  +G+++++R++  + +HKF++F+D R A  AL  
Sbjct: 206 GDNRGSLVVLSPLPGVSVADLRQVFQAFGDLKDVRESAQRPSHKFVDFFDTRDAARALAE 265

Query: 419 LNRSDVAGKQIKLEASRPGG 438
           LN  ++ G+++ +E +RP G
Sbjct: 266 LNGQELFGRRLVVEFTRPSG 285

Probable RNA-binding protein. Involved in the regulation of leaf initiation rate and shoot development. Seems to act more predominantly in the early stages of the leaf development, rather than in the later phase.

Zea mays (taxid: 4577)

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	861
255540053	972	RNA-binding protein, putative [Ricinus c	0.980	0.868	0.697	0.0
297734509	998	unnamed protein product [Vitis vinifera]	0.996	0.859	0.667	0.0
359491581	991	PREDICTED: protein MEI2-like 4-like [Vit	0.990	0.860	0.667	0.0
224134156	919	predicted protein [Populus trichocarpa]	0.911	0.854	0.632	0.0
296085525	986	unnamed protein product [Vitis vinifera]	0.962	0.840	0.558	0.0
359473863	965	PREDICTED: protein MEI2-like 4-like [Vit	0.938	0.837	0.551	0.0
224075455	976	predicted protein [Populus trichocarpa]	0.951	0.839	0.544	0.0
356507390	976	PREDICTED: protein MEI2-like 4-like [Gly	0.962	0.849	0.528	0.0
356527581	955	PREDICTED: protein MEI2-like 1-like [Gly	0.947	0.854	0.516	0.0
147775314	932	hypothetical protein VITISV_040729 [Viti	0.891	0.824	0.541	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 = 1193 bits (3086), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 600/860 (69%), Positives = 707/860 (82%), Gaps = 16/860 (1%)

Query: 6   MDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQ-GSDGTVPMLGGKFVASSPMENFS 64
           MD R G+A +H+ E++  PAERQIGFWKP++M D Q G+ G VP    K VA SP+E FS
Sbjct: 1   MDQRGGTASSHYFEDMLLPAERQIGFWKPHSMPDHQIGTGGMVPFPSSKLVAPSPLEKFS 60

Query: 65  PVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGI 124
           P G  SVD+++L  S LA D+ ++L I   EG+ N+ +NSWNSV+ + KSWS+L++QP  
Sbjct: 61  PGGALSVDYMQLPDSVLAMDQKEKLSI--GEGSTNMLKNSWNSVDQNAKSWSSLSMQPTS 118

Query: 125 NSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFES 184
            SL GNR+GI   Q ESSLFSSSLS++F  K++L  N+I SRQP   +A  ++ +EPFES
Sbjct: 119 YSLGGNRAGIGATQWESSLFSSSLSEVFNGKLRLLENDIQSRQPAKPIALPNEEDEPFES 178

Query: 185 LKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLF 244
           L+E+EAQTIGNLLP EDDLFSGVTD++GHN   N  DDLEDFDLF +GGGMELEGDDRL 
Sbjct: 179 LEELEAQTIGNLLPAEDDLFSGVTDELGHNAHTNGGDDLEDFDLFITGGGMELEGDDRLC 238

Query: 245 AVQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD 303
             Q+NSDFVG +SN QG S GSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQ+GD
Sbjct: 239 VGQRNSDFVGALSNLQGGSNGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQYGD 298

Query: 304 IRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
           IRT+YTACKHRGFVMISYYDIRAARNAM++LQNKPLRRRKLDIHYSIPKDNPSEKD NQG
Sbjct: 299 IRTLYTACKHRGFVMISYYDIRAARNAMRSLQNKPLRRRKLDIHYSIPKDNPSEKDINQG 358

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           TLV+FNLDSSVSTEELH+IFG+YGEI+EIR+T HK +HKFIE+YDIR+AE AL  LNRSD
Sbjct: 359 TLVIFNLDSSVSTEELHKIFGVYGEIKEIRETPHKRHHKFIEYYDIRSAEAALSALNRSD 418

Query: 424 VAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMV--SSGVITSTCMDN 481
           +AGKQIKLE SRPGG RR M + EQEQD+  LCQ PF+DLSSG++   S GVI S+CM+N
Sbjct: 419 IAGKQIKLEPSRPGGTRRLMTKPEQEQDESGLCQSPFEDLSSGRLATFSPGVIASSCMEN 478

Query: 482 GSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQ 541
           GS QV+HSA +SP  +  ESH++SSVPN LPS   V SI KQFG +EPN S+DEM FGNQ
Sbjct: 479 GSTQVIHSAIQSPVGSFIESHRSSSVPNNLPSPVSVTSISKQFGLHEPNRSMDEMMFGNQ 538

Query: 542 H-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLME 600
             PSFHPHSLPEY D LANG+P+NS S+I  +A SVG+K+ +G+ SRHI+ VSSNGHLME
Sbjct: 539 RIPSFHPHSLPEYPDGLANGVPFNSSSSIGGMAHSVGSKVTEGISSRHIQAVSSNGHLME 598

Query: 601 PTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGF 660
             GGVFGS  NG  SL G+ Y+WNNSN++QQH SS M+WPNS SF NG+HA+ + HMPGF
Sbjct: 599 LNGGVFGSSGNG--SLPGHHYMWNNSNTNQQHHSSRMIWPNSSSFTNGVHAHHLPHMPGF 656

Query: 661 PRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFLGRSP 720
           PR PP+MLN T PAHHH+GSAP+VNPS+W+R+HAYAGESPE S+FHLGSLGS G    SP
Sbjct: 657 PRAPPVMLN-TVPAHHHVGSAPSVNPSVWERRHAYAGESPEASSFHLGSLGSVG----SP 711

Query: 721 SHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRN 780
            H ++IAS NI SHVGGNCMDMTKN G+R+ Q +CH+FPGRNPM+SM  SFDS NER+RN
Sbjct: 712 -HPMEIASHNIFSHVGGNCMDMTKNAGLRTAQPMCHIFPGRNPMISMPASFDSPNERVRN 770

Query: 781 LSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGT 840
           LS+RR +SN NH+DKKQYELD+DRI+RG+DSRTTLMIKNIPNKYTSKMLLAAIDE+CRGT
Sbjct: 771 LSHRRIDSNPNHSDKKQYELDLDRIMRGEDSRTTLMIKNIPNKYTSKMLLAAIDEYCRGT 830

Query: 841 YDFIYLPIDFKASL-FGFFF 859
           YDFIYLPIDFK     G+ F
Sbjct: 831 YDFIYLPIDFKNKCNVGYAF 850

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 = 1095 bits (2832), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 581/871 (66%), Positives = 680/871 (78%), Gaps = 13/871 (1%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGS-DGTVPMLGGKFVASSP 59
           MPFE+MD R  SA +   ++I FPAERQ+GFWKP  MSD     DG   + G K V SSP
Sbjct: 1   MPFEVMDPRGVSASSPLFDDICFPAERQVGFWKPKIMSDHHAEGDGVARIPGSKSVTSSP 60

Query: 60  MENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLA 119
           +E   PVG  SVD+ E  +S LARD+ ++L +  EEG ANLS   W +V+H+ K+WSNL 
Sbjct: 61  LEKLLPVGSKSVDYSEGPESYLARDQKEKLQVNREEGTANLSRTPWRTVDHNSKTWSNLY 120

Query: 120 VQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPE 179
           VQP  + +   ++ ING   ESSLFSSSLS+IF RK+++S +++LS Q    VA H + E
Sbjct: 121 VQPASSYVEVKKTSINGALYESSLFSSSLSEIFNRKLRVSTSDVLSHQSAGTVAPHSEEE 180

Query: 180 EPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEG 239
           + F+SL+EIE QT+GNLLPDED+LFSGV DDMG+N  AN  DD EDFDLFSSGGGMELEG
Sbjct: 181 KLFKSLEEIEVQTLGNLLPDEDELFSGVVDDMGYNAHANNGDDFEDFDLFSSGGGMELEG 240

Query: 240 DDRLFAVQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALF 298
           DD L   Q++SDF GG+ N QG S GS+  EHPYGEHPSRTLFVRNINSNVEDSEL+ LF
Sbjct: 241 DDHLCISQRHSDFNGGIPNSQGGSNGSLASEHPYGEHPSRTLFVRNINSNVEDSELRDLF 300

Query: 299 EQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 358
           EQ+GDIRT+YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDNPSEK
Sbjct: 301 EQYGDIRTLYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPSEK 360

Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT 418
           D NQGTLVVFNLDSSVS ++L QIFGIYGEI+EIR+T HK +HKFIEF+D+RAAE ALR 
Sbjct: 361 DINQGTLVVFNLDSSVSNDDLRQIFGIYGEIKEIRETPHKRHHKFIEFFDVRAAEAALRA 420

Query: 419 LNRSDVAGKQIKLEASRPGGARRFMVQ---SEQEQDDLNLCQIPFDDLSSGQM-VSSGVI 474
           LNRSD+AGK+IKLE SRPGG+RR ++Q   SE EQD+  LCQ P D+LSSG M VS G+ 
Sbjct: 421 LNRSDIAGKRIKLEPSRPGGSRRCLMQLCSSELEQDESILCQSPDDNLSSGCMAVSPGIK 480

Query: 475 TSTCMDNGSIQVLHSATRSPAIALTE---SHQTSSVPNGLPSLARVGSIGKQFGHYEPNL 531
           TS+CMDN SIQ LHSA R P  +  E   SH +SSVPN LPS  RV SI  +FG  E + 
Sbjct: 481 TSSCMDNVSIQDLHSAVRMPIGSFVENATSHGSSSVPNTLPSPMRVVSIINEFGLGETSN 540

Query: 532 SLDEMKFGNQ-HPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIR 590
           +LD+MKFGNQ  P++HPHSLPEYHD+LAN + YNS STI D+   VG +I +G+D+RHI 
Sbjct: 541 TLDQMKFGNQSFPNYHPHSLPEYHDNLANAIRYNSSSTIGDMTGHVGPRITEGIDNRHIH 600

Query: 591 GVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLH 650
            V SNGH +E  GG FGS  NGS  +HG    W NS+S+Q H SSPM+WPNSPSF NG+H
Sbjct: 601 RVGSNGHPIELNGGAFGSSGNGSCPVHGLHRAWGNSSSYQHHSSSPMIWPNSPSFSNGVH 660

Query: 651 ANRVAHMPGFPRVPPLMLNATSPA-HHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGS 709
           A R   +PGFPR PP MLN  SP  HHH+GSAPAVNPSLWDR+HAY+GESPETS FHLGS
Sbjct: 661 AQRPTQVPGFPRPPPHMLNIVSPVHHHHVGSAPAVNPSLWDRRHAYSGESPETSGFHLGS 720

Query: 710 LGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQT 769
           LGS GF G SP H +++AS  I  HVGGNCMD++ NVG+RSPQQICH+FPGRN M+S+ +
Sbjct: 721 LGSVGFPGSSPLHPLEMASH-IFPHVGGNCMDISANVGLRSPQQICHVFPGRNSMLSIPS 779

Query: 770 SFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKML 829
           SFD   ER+RNLS+RR E+NSNH DKKQYELDIDRILRG+D RTTLMIKNIPNKYTSKML
Sbjct: 780 SFDLPMERVRNLSHRRTEANSNHTDKKQYELDIDRILRGEDCRTTLMIKNIPNKYTSKML 839

Query: 830 LAAIDEHCRGTYDFIYLPIDFKASL-FGFFF 859
           LAAIDEH RGTYDFIYLPIDFK     G+ F
Sbjct: 840 LAAIDEHHRGTYDFIYLPIDFKNKCNVGYAF 870

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 = 1088 bits (2814), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 577/864 (66%), Positives = 673/864 (77%), Gaps = 11/864 (1%)

Query: 6   MDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFSP 65
           MD R  SA +   ++I FPAERQ+GFWKP  MSD    DG   + G K V SSP+E   P
Sbjct: 1   MDPRGVSASSPLFDDICFPAERQVGFWKPKIMSDHHEGDGVARIPGSKSVTSSPLEKLLP 60

Query: 66  VGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLAVQPGIN 125
           VG  SVD+ E  +S LARD+ ++L +  EEG ANLS   W +V+H+ K+WSNL VQP  +
Sbjct: 61  VGSKSVDYSEGPESYLARDQKEKLQVNREEGTANLSRTPWRTVDHNSKTWSNLYVQPASS 120

Query: 126 SLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEEPFESL 185
            +   ++ ING   ESSLFSSSLS+IF RK+++S +++LS Q    VA H + E+ F+SL
Sbjct: 121 YVEVKKTSINGALYESSLFSSSLSEIFNRKLRVSTSDVLSHQSAGTVAPHSEEEKLFKSL 180

Query: 186 KEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFA 245
           +EIE QT+GNLLPDED+LFSGV DDMG+N  AN  DD EDFDLFSSGGGMELEGDD L  
Sbjct: 181 EEIEVQTLGNLLPDEDELFSGVVDDMGYNAHANNGDDFEDFDLFSSGGGMELEGDDHLCI 240

Query: 246 VQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI 304
            Q++SDF GG+ N QG S GS+  EHPYGEHPSRTLFVRNINSNVEDSEL+ LFEQ+GDI
Sbjct: 241 SQRHSDFNGGIPNSQGGSNGSLASEHPYGEHPSRTLFVRNINSNVEDSELRDLFEQYGDI 300

Query: 305 RTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT 364
           RT+YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDNPSEKD NQGT
Sbjct: 301 RTLYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPSEKDINQGT 360

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 424
           LVVFNLDSSVS ++L QIFGIYGEI+EIR+T HK +HKFIEF+D+RAAE ALR LNRSD+
Sbjct: 361 LVVFNLDSSVSNDDLRQIFGIYGEIKEIRETPHKRHHKFIEFFDVRAAEAALRALNRSDI 420

Query: 425 AGKQIKLEASRPGGARRFM--VQSEQEQDDLNLCQIPFDDLSSGQM-VSSGVITSTCMDN 481
           AGK+IKLE SRPGG+RR M    SE EQD+  LCQ P D+LSSG M VS G+ TS+CMDN
Sbjct: 421 AGKRIKLEPSRPGGSRRLMQLCSSELEQDESILCQSPDDNLSSGCMAVSPGIKTSSCMDN 480

Query: 482 GSIQVLHSATRSPAIALTE---SHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKF 538
            SIQ LHSA R P  +  E   SH +SSVPN LPS  RV SI  +FG  E + +LD+MKF
Sbjct: 481 VSIQDLHSAVRMPIGSFVENATSHGSSSVPNTLPSPMRVVSIINEFGLGETSNTLDQMKF 540

Query: 539 GNQ-HPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGH 597
           GNQ  P++HPHSLPEYHD+LAN + YNS STI D+   VG +I +G+D+RHI  V SNGH
Sbjct: 541 GNQSFPNYHPHSLPEYHDNLANAIRYNSSSTIGDMTGHVGPRITEGIDNRHIHRVGSNGH 600

Query: 598 LMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHM 657
            +E  GG FGS  NGS  +HG    W NS+S+Q H SSPM+WPNSPSF NG+HA R   +
Sbjct: 601 PIELNGGAFGSSGNGSCPVHGLHRAWGNSSSYQHHSSSPMIWPNSPSFSNGVHAQRPTQV 660

Query: 658 PGFPRVPPLMLNATSPA-HHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGGFL 716
           PGFPR PP MLN  SP  HHH+GSAPAVNPSLWDR+HAY+GESPETS FHLGSLGS GF 
Sbjct: 661 PGFPRPPPHMLNIVSPVHHHHVGSAPAVNPSLWDRRHAYSGESPETSGFHLGSLGSVGFP 720

Query: 717 GRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNE 776
           G SP H +++AS  I  HVGGNCMD++ NVG+RSPQQICH+FPGRN M+S+ +SFD   E
Sbjct: 721 GSSPLHPLEMASH-IFPHVGGNCMDISANVGLRSPQQICHVFPGRNSMLSIPSSFDLPME 779

Query: 777 RMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEH 836
           R+RNLS+RR E+NSNH DKKQYELDIDRILRG+D RTTLMIKNIPNKYTSKMLLAAIDEH
Sbjct: 780 RVRNLSHRRTEANSNHTDKKQYELDIDRILRGEDCRTTLMIKNIPNKYTSKMLLAAIDEH 839

Query: 837 CRGTYDFIYLPIDFKASL-FGFFF 859
            RGTYDFIYLPIDFK     G+ F
Sbjct: 840 HRGTYDFIYLPIDFKNKCNVGYAF 863

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 =  993 bits (2568), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 545/861 (63%), Positives = 636/861 (73%), Gaps = 76/861 (8%)

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

Query: 60  MENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNLA 119
                                            G EG+AN S+++W+S++HHPKSWS+L+
Sbjct: 43  ---------------------------------GCEGSANTSKHAWSSMDHHPKSWSSLS 69

Query: 120 VQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPE 179
           +QP   S   +R  I+G Q ESSLFSSS S+IF+RK++ S N+I S QP   + S H+ E
Sbjct: 70  MQPASYSTGRSRVDISGTQWESSLFSSSFSEIFSRKLRSSRNDIQSHQPAKTITSSHEEE 129

Query: 180 EPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEG 239
           EPFESL+E+EA+TIGNLLP ED+LFSGVT + G + Q N +DDLEDFDLF SGGGMELEG
Sbjct: 130 EPFESLEELEAKTIGNLLPTEDNLFSGVTTEFGRDAQINNLDDLEDFDLFGSGGGMELEG 189

Query: 240 DDRLFAVQKNSDFVGGVSN-QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALF 298
           D      + NS  + GVSN QG S GS+V  HP     SRTLFVRNINSNVE SELKALF
Sbjct: 190 D----VARGNSGLLRGVSNGQGDSNGSIVVGHP-----SRTLFVRNINSNVEVSELKALF 240

Query: 299 EQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 358
           EQ+GDIRT+YTACKHRGFVMISYYDIRAARNAM ALQNKPL+ R LDIHYSIPKDNPSEK
Sbjct: 241 EQYGDIRTLYTACKHRGFVMISYYDIRAARNAMSALQNKPLKHRNLDIHYSIPKDNPSEK 300

Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRDTQHKHNHKFIEFYDIRAAETALR 417
           D NQGTLVVFNLDSSV+ +EL QIFG+YGEI+E IR++ HKH+HKF+E+YDIRAAE AL 
Sbjct: 301 DMNQGTLVVFNLDSSVTIDELRQIFGVYGEIKEVIRESPHKHHHKFVEYYDIRAAEAALS 360

Query: 418 TLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMV--SSGVIT 475
            LNRSDVAGKQIK+E+S PGG R  M Q E EQ + NL Q PF+DLSSG +   S GV  
Sbjct: 361 ALNRSDVAGKQIKIESSHPGGTRSLMQQPEHEQAERNLLQSPFNDLSSGPLATFSPGVSA 420

Query: 476 STCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDE 535
           S+ M NGS QVLHSA  S   A  E H++SSV N LPS     S  KQF       S+DE
Sbjct: 421 SSYMANGSSQVLHSAIPSQLGAFAELHRSSSVSNNLPSPV-TASAAKQF-------SIDE 472

Query: 536 MKFGNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSS 594
           MKFGN+  PS HPHSLPEYHDS AN +PYNSPSTI D+ SS  +K+ +G++S HIRGV S
Sbjct: 473 MKFGNKCIPSIHPHSLPEYHDSFANTIPYNSPSTIRDMPSSFTSKVTEGINSLHIRGVGS 532

Query: 595 NGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRV 654
           NGH+ME  GGVFGSP  GS +L G+ YVW NS S QQHPS+ M+W NSPSF NG+HA+ V
Sbjct: 533 NGHMMELNGGVFGSPGTGSCTLPGHHYVWKNSKSGQQHPSNAMIWSNSPSFANGVHAHHV 592

Query: 655 AHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGG 714
            HMPGFPR   +MLN ++PA HHIGSAPAVNPSLWDR+  ++GESPE S+FHLG+LGS G
Sbjct: 593 PHMPGFPRGHTVMLN-SAPAPHHIGSAPAVNPSLWDRRQTFSGESPEASSFHLGALGSVG 651

Query: 715 FLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSS 774
           F G SP H ++IAS NI SH GG+CMDMTK  G+ +  Q+C +FPGRNPM+SM  SF S 
Sbjct: 652 FPGSSPPHPMEIASHNIFSH-GGSCMDMTKGTGLPASPQMCQMFPGRNPMISMPASFGSP 710

Query: 775 NERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAID 834
           NER+RN S+RR ESNSNH+DKKQYELDID ILRGDD+RTTLMIKNIPNKYTSKMLLAAID
Sbjct: 711 NERVRNFSHRRIESNSNHSDKKQYELDIDCILRGDDNRTTLMIKNIPNKYTSKMLLAAID 770

Query: 835 EHCRGTYDFIYLPIDFKASLF 855
           E CRGTYDFIYLPIDFKAS F
Sbjct: 771 EQCRGTYDFIYLPIDFKASEF 791

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 =  844 bits (2180), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 495/886 (55%), Positives = 602/886 (67%), Gaps = 57/886 (6%)

Query: 5   IMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPMENFS 64
           + D    S  ++FSEE   P+ERQ+GFWK  TM+D+          GGK +ASSPME   
Sbjct: 1   MTDLHGWSRSSYFSEEACLPSERQVGFWKAETMADRNA--------GGKSIASSPMEKLI 52

Query: 65  PVGIPSVDWLELQQSTLARDKMKRLG----IVGEEGAANLSENSWNSVNHHPKSWSNLAV 120
           P    +V+  E  +  L RD+   L      VG E     S + W +V H   + SN  V
Sbjct: 53  PTESQTVNCWEQSEPYLIRDQKVNLSSERHAVGAERVVRNSLDMWRTVEHDLGTRSNANV 112

Query: 121 QPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHHQPEE 180
                 + G++  + G Q E+ LFSSSLS++F RK++LS N  L    ++ VA HH+ E+
Sbjct: 113 HSASYFMEGDKINMTGSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPHHEEED 172

Query: 181 PFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD 240
            FESL+EIEAQTIGNLLP+EDDL SGV D + +  Q +  DDLED DLFSS GGM+L GD
Sbjct: 173 LFESLEEIEAQTIGNLLPNEDDLLSGVADVLDYVVQPSNGDDLEDIDLFSSVGGMDL-GD 231

Query: 241 DRLFAVQKNSDFVGGVSNQ--GVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALF 298
           D   A Q+NS++ GG+SN   G S GS VGEHPYGEHPSRTLFVRNINSNVEDSEL+ LF
Sbjct: 232 DGSSAGQRNSEYPGGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSELRILF 291

Query: 299 EQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 358
           EQ+GDIR +YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDNP EK
Sbjct: 292 EQYGDIRALYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDNPPEK 351

Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT 418
           D NQGTLVVFNLD SV+ +EL QIFG+YGEI+EIR+T H+ +HKF+EFYDIRAAE ALR 
Sbjct: 352 DVNQGTLVVFNLDPSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAEAALRA 411

Query: 419 LNRSDVAGKQIKLEASRPGGARRFMVQ--SEQEQDD--LNLCQIPFDDLSSGQM---VSS 471
           LNRSD+AGK+IKLE SRPGGARR M Q  SE E+D+  L L Q    + S+       S 
Sbjct: 412 LNRSDIAGKRIKLEPSRPGGARRLMQQFPSELEEDESGLYLQQNNTPNNSTTGFPGPASL 471

Query: 472 GVITSTCMDNGSIQVLHSATRSPAIALTE--SHQ--TSSVPNGLPSLARVGSIGKQFGHY 527
           G ITS+ M+NG+I  +HS    P     E  SH   +SSVPN LPSL  V S+G Q G  
Sbjct: 472 GAITSSSMENGTIMGVHSGIPFPIRPFLENVSHHGISSSVPNTLPSLLSVESVGSQSGLA 531

Query: 528 EPNLSLDEMKF---GNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGL 584
           E + S  ++KF   G Q  S HPHSLPEY+D LANG P N    +  +A+++  +  + +
Sbjct: 532 ESSRSQGQLKFDFRGTQ--SLHPHSLPEYNDGLANGAPCN---PVGTMAANINPR-PERI 585

Query: 585 DSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSP-MVWPNSP 643
           ++R + G +SNG  +E   GVFGS  NGS  L G+ Y+W+NS     HP SP M+WPNSP
Sbjct: 586 ENRQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNS----HHPQSPGMMWPNSP 641

Query: 644 SFLNGLHANRVAHMP----GFPRVPPLMLNAT-SPAHHHIGSAPAVNPSLWDRQHAYAGE 698
           SF+NG+     AH P    G PR P  MLN   S  +HH+GSAP VNPS+WDR+H YAGE
Sbjct: 642 SFMNGIG---TAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSIWDRRHTYAGE 698

Query: 699 SPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMT---KNVGMRSPQQIC 755
           S E S FH GSLGS      S  H ++ A  NI   VGGNC+D++   KNVG+ S  Q C
Sbjct: 699 SSEASGFHPGSLGSMRISNNS-LHPLEFAPHNIFPSVGGNCIDLSIPPKNVGLHSHHQRC 757

Query: 756 HLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDDSRTT 814
            +FPGR+ ++ M +SFD  NER R+   RRN+++SN  D KKQYELDIDRILRG+D+RTT
Sbjct: 758 LMFPGRSQLIPMMSSFDPPNERSRS---RRNDNSSNQVDNKKQYELDIDRILRGEDTRTT 814

Query: 815 LMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASL-FGFFF 859
           LMIKNIPNKYTSKMLLAAIDE  RGTYDFIYLPIDFK     G+ F
Sbjct: 815 LMIKNIPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAF 860

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 =  830 bits (2145), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 491/890 (55%), Positives = 598/890 (67%), Gaps = 82/890 (9%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPM 60
           MP ++ D    S  ++FSEE   P+ERQ+GFWK  TM+D+          GGK +ASSPM
Sbjct: 1   MPSKMTDLHGWSRSSYFSEEACLPSERQVGFWKAETMADRNA--------GGKSIASSPM 52

Query: 61  ENFSPVGIPSVDWLELQQSTLARDKMKRLG----IVGEEGAANLSENSWNSVNHHPKSWS 116
           E   P    +V+  E  +  L RD+   L      VG E +A+                 
Sbjct: 53  EKLIPTESQTVNCWEQSEPYLIRDQKVNLSSERHAVGAERSASYF--------------- 97

Query: 117 NLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHH 176
                     + G++  + G Q E+ LFSSSLS++F RK++LS N  L    ++ VA HH
Sbjct: 98  ----------MEGDKINMTGSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPHH 147

Query: 177 QPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGME 236
           + E+ FESL+EIEAQTIGNLLP+EDDL SGV D + +  Q +  DDLED DLFSS GGM+
Sbjct: 148 EEEDLFESLEEIEAQTIGNLLPNEDDLLSGVADVLDYVVQPSNGDDLEDIDLFSSVGGMD 207

Query: 237 LEGDDRLFAVQKNSDFVGGVSNQ--GVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSEL 294
           L GDD   A Q+NS++ GG+SN   G S GS VGEHPYGEHPSRTLFVRNINSNVEDSEL
Sbjct: 208 L-GDDGSSAGQRNSEYPGGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSEL 266

Query: 295 KALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
           + LFEQ+GDIR +YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKDN
Sbjct: 267 RILFEQYGDIRALYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKDN 326

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 414
           P EKD NQGTLVVFNLD SV+ +EL QIFG+YGEI+EIR+T H+ +HKF+EFYDIRAAE 
Sbjct: 327 PPEKDVNQGTLVVFNLDPSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAEA 386

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARRFMVQ--SEQEQDD--LNLCQIPFDDLSSGQM-- 468
           ALR LNRSD+AGK+IKLE SRPGGARR M Q  SE E+D+  L L Q    + S+     
Sbjct: 387 ALRALNRSDIAGKRIKLEPSRPGGARRLMQQFPSELEEDESGLYLQQNNTPNNSTTGFPG 446

Query: 469 -VSSGVITSTCMDNGSIQVLHSATRSPAIALTE--SHQ--TSSVPNGLPSLARVGSIGKQ 523
             S G ITS+ M+NG+I  +HS    P     E  SH   +SSVPN LPSL  V S+G Q
Sbjct: 447 PASLGAITSSSMENGTIMGVHSGIPFPIRPFLENVSHHGISSSVPNTLPSLLSVESVGSQ 506

Query: 524 FGHYEPNLSLDEMKF---GNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKI 580
            G  E + S  ++KF   G Q  S HPHSLPEY+D LANG P N    +  +A+++  + 
Sbjct: 507 SGLAESSRSQGQLKFDFRGTQ--SLHPHSLPEYNDGLANGAPCN---PVGTMAANINPR- 560

Query: 581 KDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSP-MVW 639
            + +++R + G +SNG  +E   GVFGS  NGS  L G+ Y+W+NS     HP SP M+W
Sbjct: 561 PERIENRQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNS----HHPQSPGMMW 616

Query: 640 PNSPSFLNGLHANRVAHMP----GFPRVPPLMLNAT-SPAHHHIGSAPAVNPSLWDRQHA 694
           PNSPSF+NG+     AH P    G PR P  MLN   S  +HH+GSAP VNPS+WDR+H 
Sbjct: 617 PNSPSFMNGIG---TAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSIWDRRHT 673

Query: 695 YAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMT---KNVGMRSP 751
           YAGES E S FH GSLGS      S  H ++ A  NI   VGGNC+D++   KNVG+ S 
Sbjct: 674 YAGESSEASGFHPGSLGSMRISNNS-LHPLEFAPHNIFPSVGGNCIDLSIPPKNVGLHSH 732

Query: 752 QQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHAD-KKQYELDIDRILRGDD 810
            Q C +FPGR+ ++ M +SFD  NER R+   RRN+++SN  D KKQYELDIDRILRG+D
Sbjct: 733 HQRCLMFPGRSQLIPMMSSFDPPNERSRS---RRNDNSSNQVDNKKQYELDIDRILRGED 789

Query: 811 SRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASL-FGFFF 859
           +RTTLMIKNIPNKYTSKMLLAAIDE  RGTYDFIYLPIDFK     G+ F
Sbjct: 790 TRTTLMIKNIPNKYTSKMLLAAIDERHRGTYDFIYLPIDFKNKCNVGYAF 839

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 =  774 bits (1999), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 471/865 (54%), Positives = 588/865 (67%), Gaps = 46/865 (5%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQQGSDGTVPMLGGKFVASSPM 60
           MP EIMD +  S+ + FSE+  FP+ERQ+GFWK +TM DQ+G    +    GK    SP 
Sbjct: 1   MPSEIMDLQGLSSSSFFSEDASFPSERQVGFWKSDTMPDQRGQ--YIRDTLGKSYVLSPS 58

Query: 61  ENFSPVGIPSVDWLELQQSTLARDKMKRLGI----VGEEGAANLSENSWNSVNHHPKSWS 116
           E    V + SV  LE  Q +L  D+     +    VG E A N S      V++   + +
Sbjct: 59  EKL--VAVESVQSLEHPQPSLMHDQKMNHSLDKHAVGAERALNRSFTLLRPVDNDTGTGT 116

Query: 117 NLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHH 176
           +L VQP        +      Q E+SLFSSSLS++F+RK++LS    L    ++ +ASH 
Sbjct: 117 SLNVQPTSYFAEVGKVNAMATQHENSLFSSSLSELFSRKLRLSSTNSLYGHSVDTIASHF 176

Query: 177 QPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGME 236
           + EEPF+SL+EIEAQTIGNLLP++DDLFSGVTD + +    +  DD+ED D FSS GGM+
Sbjct: 177 EEEEPFQSLEEIEAQTIGNLLPNDDDLFSGVTDRVENINHPSGGDDMEDLDFFSSVGGMD 236

Query: 237 LEGDDRLFAVQKNSDFVGGVSNQGVSAG--SVVGEHPYGEHPSRTLFVRNINSNVEDSEL 294
           L GDD   A Q +S+F GG SN  + A   SV GEHPYGEHPSRTLFVRNINSNVE+SEL
Sbjct: 237 L-GDDGSVA-QIDSEFHGGASNGQLGACNLSVAGEHPYGEHPSRTLFVRNINSNVEESEL 294

Query: 295 KALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
           +A+FEQ+GDIRT+YTACKHRGFVMISYYDIRAA+NAMKALQN+PLR RKLDIHYSIPKDN
Sbjct: 295 RAIFEQYGDIRTLYTACKHRGFVMISYYDIRAAKNAMKALQNRPLRCRKLDIHYSIPKDN 354

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 414
           PSEKD NQGTL VFNLDSSVS ++L +IFG+YGEI+EIR+T H+++HKF+EFYD+RAAE 
Sbjct: 355 PSEKDFNQGTLAVFNLDSSVSNDDLRRIFGVYGEIKEIRETPHRNHHKFVEFYDVRAAEA 414

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARRFMVQ--SEQEQDDLNLCQIPFDDLSSGQMVS-- 470
           AL  LN+SD+AGK+IKLEAS PGG RR + Q   E EQD+      PF   SS    S  
Sbjct: 415 ALHALNKSDIAGKRIKLEASCPGGLRRLLHQIPPELEQDEFG----PFVQQSSPPNNSTT 470

Query: 471 --SGVITSTCMDNGSIQVLHSATRSPAIALTESHQT-SSVPNGLPSLARVGSIGKQFGHY 527
             SG + ST MDNG I   HSAT++P       H   SSVPN + SL+RV S G Q G  
Sbjct: 471 EFSGTVISTGMDNGPILGAHSATQAPFFESALHHGISSSVPNSMSSLSRVESAGNQTGFA 530

Query: 528 EPNLSLDEMKFGNQHP-SFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDS 586
           E + S   +KF  Q   +FHPHSLPEY D L +G+  NSP     +A+++  ++ + +D+
Sbjct: 531 ELSHSPGHLKFDIQSTLNFHPHSLPEY-DGLNSGVHCNSPGA---MAANINPRLLERIDT 586

Query: 587 RHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFL 646
           RH+  +S NG+ +E + GVFGS RNGS S  G+ Y W NS  H Q P   M+WPNSPSF+
Sbjct: 587 RHLARISPNGNPIEFSEGVFGSARNGSCSRPGHHYTWGNS-YHHQPPG--MIWPNSPSFV 643

Query: 647 NGLHANRVAH----MPGFPRVPPLMLNATSPA-HHHIGSAPAVNPSLWDRQHAYAGESPE 701
           NG+    VAH    + G PR PP MLN   P  + H+GS PAVNPSLWDRQHAYAGESP+
Sbjct: 644 NGI---SVAHPGPRLHGPPRAPPPMLNPVLPINNQHVGSVPAVNPSLWDRQHAYAGESPD 700

Query: 702 TSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDM---TKNVGMRSPQQICHLF 758
            S FH  SLGS      S  H ++  S  +  HVGGNC+++    +NVG +S QQ   +F
Sbjct: 701 ASGFHPCSLGSMRISNNS-LHSMEFLSPKMFPHVGGNCLELPMPPQNVGFQSQQQRSMVF 759

Query: 759 PGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIK 818
           PGR  M+ M  +FD+  ER R+   RRNE +++ ADKKQYELDIDRIL+G+D+RTTLMIK
Sbjct: 760 PGRGQMIPMINTFDAPGERARS---RRNEGSTSQADKKQYELDIDRILQGEDNRTTLMIK 816

Query: 819 NIPNKYTSKMLLAAIDEHCRGTYDF 843
           NIPNKYTSKMLLAAIDE  +GTY+F
Sbjct: 817 NIPNKYTSKMLLAAIDERHKGTYNF 841

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 =  769 bits (1986), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 455/861 (52%), Positives = 576/861 (66%), Gaps = 32/861 (3%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQ--QGSDGTVPMLGGKFVASS 58
           MP EIM+ R  SA + F ++I + +E+  G  KP  + D   QG        G  F  SS
Sbjct: 1   MPSEIMEKRGVSASSRFLDDISYVSEKNTGLRKPKFIHDHFLQGKSEMAASPGIIFNTSS 60

Query: 59  PMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAAN-LSENSWNSVNHHPKSWSN 117
           P E  +  G      L + Q+TL+R+  + L    E G    L +++  S+N+H +SWSN
Sbjct: 61  PHETNAKTG------LLMSQTTLSREITEDLHFGREAGNIEMLKDSTTESLNYHKRSWSN 114

Query: 118 LAVQPGINS--LSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASH 175
           +  QP  +S  L G++   N    ESSLFSSSLSD+F++K++L GN +LS QP+  V S 
Sbjct: 115 VHRQPASSSYGLVGSKIVTNAASRESSLFSSSLSDMFSQKLRLLGNGVLSGQPI-TVGSL 173

Query: 176 HQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM 235
            + EEP++SL+EIEA+TIGNLLPDEDDLFSGV D++G + +    DD EDFDLFSS GGM
Sbjct: 174 PE-EEPYKSLEEIEAETIGNLLPDEDDLFSGVNDELGCSTRTRMNDDFEDFDLFSSSGGM 232

Query: 236 ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELK 295
           ELEGD+ L + ++ S         GVS G +    P+GE  SRTLFVRNINSNVEDSELK
Sbjct: 233 ELEGDEHLISGKRTSCGDEDPDYFGVSKGKI----PFGEQSSRTLFVRNINSNVEDSELK 288

Query: 296 ALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP 355
           ALFEQ+G+IRTIYTACK+RGFVMISYYD+RAA+NAMKALQN+ LR RKLDIHYSIPK N 
Sbjct: 289 ALFEQYGNIRTIYTACKYRGFVMISYYDLRAAQNAMKALQNRSLRSRKLDIHYSIPKGNS 348

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 415
            EKD   GTL++ NLDSSV  +EL QIFG YGEIREI +    ++ KFIEFYD+RAAE +
Sbjct: 349 PEKDIGHGTLMISNLDSSVLDDELKQIFGFYGEIREIYEYPQLNHVKFIEFYDVRAAEAS 408

Query: 416 LRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQM--VSSGV 473
           LR LN    AGK IKLE   P  A   M QS + +D+ ++     D++S      VSSG 
Sbjct: 409 LRALNGICFAGKHIKLEPGLPKIATCMMHQSHKGKDEPDVGHSLSDNISLRHKAGVSSGF 468

Query: 474 ITS-TCMDNGSIQVLHSATRSPA-IALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNL 531
           I S + ++NG  Q  HSAT+ PA I  +  H  SS+      + R  S GK  G +E + 
Sbjct: 469 IASGSSLENGYNQGFHSATQLPAFIDNSPFHVNSSIHK----ITRGASAGKVSGVFEASN 524

Query: 532 SLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRG 591
           + D MKF +    FHPHSLPEY +SLA G PYN  STI + AS++GT   +  +SRHI+G
Sbjct: 525 AFDAMKFASI-SRFHPHSLPEYRESLATGSPYNFSSTI-NTASNIGTGSTESSESRHIQG 582

Query: 592 VSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHA 651
           +SS G+L E   G FG   NG++  HG  ++WN SN HQQ  S+ M+W  +PSF+NG  +
Sbjct: 583 MSSTGNLAEFNAGDFGPSGNGNHPHHGLYHMWNGSNLHQQPSSNAMLWQKTPSFVNGACS 642

Query: 652 NRVAHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLG 711
             +  +P FPR PP +L A S   H +GSAP V  S WDRQH++ GESP+ S F LGS+G
Sbjct: 643 PGLPQIPSFPRTPPHVLRA-SHIDHQVGSAPVVTASPWDRQHSFLGESPDASGFRLGSVG 701

Query: 712 SGGFLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSF 771
           S GF G    H    AS NI SHVGGN  ++T N G  SP+Q+ H+FPG+ P M++ + F
Sbjct: 702 SPGFHGSWQLH--PPASHNIFSHVGGNGTELTSNAGQGSPKQLSHVFPGKLP-MTLVSKF 758

Query: 772 DSSNERMRNLSYRRNESNS-NHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLL 830
           D++NERMRNL  RR+E N+ N+ADKKQYELD+ RILRGDD+RTTLMIKNIPNKYTSKMLL
Sbjct: 759 DTTNERMRNLYSRRSEPNTNNNADKKQYELDLGRILRGDDNRTTLMIKNIPNKYTSKMLL 818

Query: 831 AAIDEHCRGTYDFIYLPIDFK 851
            AIDE CRGTYDF+YLPIDFK
Sbjct: 819 VAIDEQCRGTYDFLYLPIDFK 839

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 =  756 bits (1953), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 443/857 (51%), Positives = 562/857 (65%), Gaps = 41/857 (4%)

Query: 1   MPFEIMDHRSGSAPTHFSEEIRFPAERQIGFWKPNTMSDQ--QGSDGTVPMLGGKFVASS 58
           MPF+IMD R  SA +H+ ++I F +ER +G  KP +++D   QG++G V   G    A+ 
Sbjct: 1   MPFQIMDQRGVSASSHYFDDISFRSERNVGLRKPKSINDHYPQGNNGMVASPGNILNATP 60

Query: 59  PMENFSPVGIPSVDWLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSWSNL 118
           P++  +  G      L L Q++L  D +                +S  S N+  KS SN 
Sbjct: 61  PLDVNAKAG------LLLPQASLPGDNI----------------HSTESSNYRTKSLSNA 98

Query: 119 AVQ--PGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASHH 176
            +Q  P    L GN+   N    ESSLFSSS+S+IF++K++  GN++ S  P+ A +   
Sbjct: 99  CLQSAPTSYGLIGNKIVTNAAPFESSLFSSSMSEIFSQKLRFFGNDVRSDHPITAGSP-- 156

Query: 177 QPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGME 236
             EEP++SL+E+EA TIGNLLPDEDDLFSGV D++G +  A T DD EDFDLFSSGGGME
Sbjct: 157 PKEEPYKSLEEMEADTIGNLLPDEDDLFSGVVDELGCSSHARTNDDFEDFDLFSSGGGME 216

Query: 237 LEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKA 296
           +EGD+ L + ++ S   G     G S G +    P  E PSRTLFVRNINSNVEDSELKA
Sbjct: 217 MEGDEHLSSGKRMSALDGDFGFFGSSKGKL----PLVEQPSRTLFVRNINSNVEDSELKA 272

Query: 297 LFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
           LFEQ+GDIRTIYTA KHRGFVMISY D+RAA+NAM+ALQN+PL  RKLDIHYSIPK N  
Sbjct: 273 LFEQYGDIRTIYTASKHRGFVMISYQDLRAAQNAMQALQNRPLGSRKLDIHYSIPKVNAP 332

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL 416
           EKD   GTL++  LDS V  +EL QIFG YGEI+EI +    +NHKFIEFYD+RAAE AL
Sbjct: 333 EKDIGHGTLMLSGLDSPVLNDELKQIFGFYGEIKEIYEYSEMNNHKFIEFYDVRAAEAAL 392

Query: 417 RTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVS--SGVI 474
           R LN+ D+AGKQIKLE   P      M QS++ Q++ +L Q   D+LS  Q  +  SGVI
Sbjct: 393 RALNKIDIAGKQIKLEPGHPS----LMHQSQKGQEERDLGQSIIDNLSLRQKATLPSGVI 448

Query: 475 TSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLD 534
            S C++NG  Q   S  R P  A  + +    V +G+ +  R    GK     E +  +D
Sbjct: 449 GSGCLENGYNQRFQSTVRQPLNAFMD-NAFIHVNSGIHNTVRGAPAGKVSSVCESSNFVD 507

Query: 535 EMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSS 594
            MKF +    FHPHSLPEY DSLANG PYN  S+I+++A+++G    +  D RHI+G+ S
Sbjct: 508 AMKFASGS-RFHPHSLPEYRDSLANGSPYNFSSSISNMANNIGAGATEASDGRHIQGMGS 566

Query: 595 NGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPSSPMVWPNSPSFLNGLHANRV 654
            G+L E   G F S  NG     G  ++WN+SN  QQ  SS M+W  SPSF+N   +  +
Sbjct: 567 TGNLAEFNAGYFCSSGNGIRPHQGLYHMWNSSNLQQQPSSSTMLWQKSPSFVNDASSPGL 626

Query: 655 AHMPGFPRVPPLMLNATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSNFHLGSLGSGG 714
             M  F R PP ML       HH+GSAP V  S W+RQ++Y G SPE S F LGSLGSGG
Sbjct: 627 PQMSSFARTPPHMLRTPHMMDHHVGSAPVVTASPWERQNSYLGGSPEASGFRLGSLGSGG 686

Query: 715 FLGRSPSHHVDIASQNILSHVGGNCMDMTKNVGMRSPQQICHLFPGRNPMMSMQTSFDSS 774
           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: 775 NERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAID 834
           NERMRNL +R+NE+++N+ DKK YELD+ RILRG+DSRTTLMIKNIPNKYTSKMLLAAID
Sbjct: 746 NERMRNLYHRKNEASTNNVDKKLYELDLGRILRGEDSRTTLMIKNIPNKYTSKMLLAAID 805

Query: 835 EHCRGTYDFIYLPIDFK 851
           E C+GTYDF+YLPIDFK
Sbjct: 806 EQCKGTYDFLYLPIDFK 822

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  748 bits (1930), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 448/828 (54%), Positives = 547/828 (66%), Gaps = 60/828 (7%)

Query: 60  MENFSPVGIPSVDWLELQQSTLARDKMKRLG----IVGEEGAANLSENSWNSVNHHPKSW 115
           ME   P    +V+  E  +  L RD+   L      VG E     S + W +V H   + 
Sbjct: 1   MEKLIPTESQTVNCWEQSEXYLIRDQKVNLSSERHAVGAERVVRNSLDMWRTVEHDLGTR 60

Query: 116 SNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQPLNAVASH 175
           SN  V      + G++  + G Q E+ LFSSSLS++F RK++LS N  L    ++ VA H
Sbjct: 61  SNANVHSASYFMEGDKINMTGSQYENGLFSSSLSELFNRKLRLSSNNGLYGHSVDTVAPH 120

Query: 176 HQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM 235
           H+ E+ FESL+EIEAQTIGNLLP+EDDL SGV D + +  Q +  DDLED DLFSS GGM
Sbjct: 121 HEEEDLFESLEEIEAQTIGNLLPNEDDLLSGVADVLDYVVQPSNGDDLEDIDLFSSVGGM 180

Query: 236 ELEGDDRLFAVQKNSDFVGGVSNQ--GVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSE 293
           +L GDD   A Q+NS++ GG+SN   G S GS VGEHPYGEHPSRTLFVRNINSNVEDSE
Sbjct: 181 DL-GDDGSSAGQRNSEYPGGMSNGQLGGSNGSAVGEHPYGEHPSRTLFVRNINSNVEDSE 239

Query: 294 LKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD 353
           L+ LFEQ+GDIR +YTACKHRGFVMISYYDIRAARNAM+ALQNKPLRRRKLDIHYSIPKD
Sbjct: 240 LRILFEQYGDIRALYTACKHRGFVMISYYDIRAARNAMRALQNKPLRRRKLDIHYSIPKD 299

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 413
           NP EKD NQGTLVVFNLD SV+ +EL QIFG+YGEI+EIR+T H+ +HKF+EFYDIRAAE
Sbjct: 300 NPPEKDVNQGTLVVFNLDPSVTNDELLQIFGVYGEIKEIRETPHRSHHKFVEFYDIRAAE 359

Query: 414 TALRTLNRSDVAGKQIKLEASRPGGARRFMVQ--SEQEQDDLNL----------CQIPFD 461
            ALR LNRSD+AGK+IKLE SRPGGARR M Q  SE E+D+  L              F 
Sbjct: 360 AALRALNRSDIAGKRIKLEPSRPGGARRLMQQFPSELEEDESGLYLQQNNTPNNSTTGFP 419

Query: 462 DLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTE--SHQ--TSSVPNGLPSLARV 517
            L +G   S G ITS+ M+NG+I  +HS    P     E  SH   +SSVPN LPSL  V
Sbjct: 420 ALLTGP-ASLGAITSSSMENGTIMGVHSGIPFPIRPFLENVSHHGISSSVPNTLPSLLSV 478

Query: 518 GSIGKQFGHYEPNLSLDEMKF---GNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIAS 574
            S+G Q G  E + S  ++KF   G Q  S HPHSLPEY+D LANG P N    +  +A+
Sbjct: 479 ESVGSQSGLAESSRSQGQLKFDFRGTQ--SLHPHSLPEYNDGLANGAPCN---PVGTMAA 533

Query: 575 SVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWNNSNSHQQHPS 634
           ++  +  + +++R + G +SNG  +E   GVFGS  NGS  L G+ Y+W+NS     HP 
Sbjct: 534 NINPR-PERIENRQLSGANSNGLTVELNDGVFGSSGNGSCPLPGHHYMWSNS----HHPQ 588

Query: 635 SP-MVWPNSPSFLNGLHANRVAHMP----GFPRVPPLMLNAT-SPAHHHIGSAPAVNPSL 688
           SP M+WPNSPSF NG+     AH P    G PR P  MLN   S  +HH+GSAP VNPS+
Sbjct: 589 SPGMMWPNSPSFXNGIG---TAHPPPRLHGLPRAPSHMLNTMLSINNHHVGSAPTVNPSI 645

Query: 689 WDRQHAYAGESPETSNFHLGSLGSGGFLGRSPSHHVDIASQNILSHVGGNCMDMT---KN 745
           WDR+H YAGES E S FH GSLGS      S  H ++ A  NI   VGGNC+D++   KN
Sbjct: 646 WDRRHTYAGESSEASGFHPGSLGSMRISNNS-LHPLEFAPHNIFPSVGGNCIDLSIPPKN 704

Query: 746 VGMRSPQQICHLFPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHAD-KKQYELDIDR 804
           VG+ S  Q C +FPGR+ ++ M +SFD  NER R+   RRN+++SN  D KKQYELDIDR
Sbjct: 705 VGLHSHHQRCLMFPGRSQLIPMMSSFDPPNERSRS---RRNDNSSNQVDNKKQYELDIDR 761

Query: 805 ILRGDDSRTTLMIKNIPNKYTSKML------LAAIDEHCRGTYDFIYL 846
           ILRG+D+RTTLMIKNIPNK    +L         +   C   Y FI +
Sbjct: 762 ILRGEDTRTTLMIKNIPNKRELLILELHYCYSQCVLNKCNVGYAFINM 809

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	861
TAIR|locus:2182885	907	ML4 "MEI2-like 4" [Arabidopsis	0.778	0.738	0.512	1.2e-179
TAIR|locus:2156166	915	ML1 "MEI2-like protein 1" [Ara	0.702	0.661	0.492	3.9e-155
TAIR|locus:2013583	800	ML5 "MEI2-like protein 5" [Ara	0.413	0.445	0.530	6.4e-125
TAIR|locus:2117706	759	ML3 "MEI2-like 3" [Arabidopsis	0.440	0.499	0.493	5.7e-117
TAIR|locus:2045605	843	ML2 "MEI2-like 2" [Arabidopsis	0.486	0.497	0.456	2e-102
TAIR|locus:2090350	615	TEL1 "terminal EAR1-like 1" [A	0.119	0.167	0.436	2.1e-29
TAIR|locus:2008530	527	TEL2 "terminal EAR1-like 2" [A	0.106	0.174	0.413	1.4e-28
DICTYBASE|DDB_G0279255	1698	DDB_G0279255 [Dictyostelium di	0.239	0.121	0.309	2.3e-23
DICTYBASE|DDB_G0268266	689	DDB_G0268266 "RNA recognition	0.191	0.239	0.352	2.6e-20
DICTYBASE|DDB_G0276005	1984	DDB_G0276005 [Dictyostelium di	0.182	0.079	0.326	5.1e-16

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

 Score = 1675 (594.7 bits), Expect = 1.2e-179, Sum P(2) = 1.2e-179
 Identities = 356/694 (51%), Positives = 460/694 (66%)

Query:   164 LSRQPLNAVASHHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDL 223
             L R    A  S ++ EEP ESL+E+EAQTIGNLLPDEDDLF+ V  +  H  +AN  DDL
Sbjct:   105 LPRSDKLAFMSANREEEPSESLEEMEAQTIGNLLPDEDDLFAEVVGEGVHKSRANGGDDL 164

Query:   224 EDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVR 283
             +D DLFSS GGMEL+GD  +F+     D   G SN      S V EHP GE  SR LFVR
Sbjct:   165 DDCDLFSSVGGMELDGD--VFSSVSQRDGKRG-SNV-----STVAEHPQGEILSRILFVR 216

Query:   284 NINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK 343
             N++S++ED EL  LF+QFGD+R ++TA K+RGF+M+SYYDIRAA+ A +AL  + LR RK
Sbjct:   217 NVDSSIEDCELGVLFKQFGDVRALHTAGKNRGFIMVSYYDIRAAQKAARALHGRLLRGRK 276

Query:   344 LDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKF 403
             LDI YSIPK+NP E ++++G L V NLDSS+S EELH IF  YGEIRE+R T H+++  +
Sbjct:   277 LDIRYSIPKENPKE-NSSEGALWVNNLDSSISNEELHGIFSSYGEIREVRRTMHENSQVY 335

Query:   404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDL 463
             IEF+D+R A+ AL+ LN  +VAG+Q+KL  + P G   F  Q   +  +  L ++ F++L
Sbjct:   336 IEFFDVRKAKVALQGLNGLEVAGRQLKLAPTCPEGTS-FWPQFASDDGEGGLPKMAFNNL 394

Query:   464 SSGQMVSS--GVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIG 521
             SS  M     G++ ST +D GSI+ +H++  SP  +  E HQ+  VP GLP  ARV S  
Sbjct:   395 SSAHMGRHFPGILASTSIDGGSIRGMHNSVGSPMNSFIERHQSLDVPIGLPPSARVISAS 454

Query:   522 KQFGHYEPNLSLDEMKFGNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKI 580
             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:   581 KDGLDSRHIRGVSSNGHLMEPTGGVFGSPRN-GSYSLHGNPYVWXXXXXXXXXXXXXMVW 639
              +G    ++RGV  +G      GGV GSP N GS+   GN  +W             M+W
Sbjct:   513 NEGFMMSNVRGVGVDGF----NGGVIGSPINQGSH--RGNLNLWSNSNSQQHNQSSGMMW 566

Query:   640 PNSPSFLNGLHANRVAHMPGFPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGE 698
             PNSPS +NG+ + R+  +  F R  PLM+N A+SP HHHIGSAP +N   WDR+ AY  E
Sbjct:   567 PNSPSRVNGVPSQRIPPVTAFSRASPLMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAE 626

Query:   699 SPETSNFHXXXXXXXXXXXXXPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHL 757
             SPE+S FH             PSH +D  S  + SHVGGN M+  +KN  +RS +Q+ HL
Sbjct:   627 SPESSGFHLGSPGSMGFPGSSPSHPMDFGSHKVFSHVGGNRMEANSKNAVLRSSRQMPHL 686

Query:   758 FPGRNPMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMI 817
             F GR+PM+S+  SFD  NER RNLS+RR+ESNS++A+KK YELD+DRILRG+DSRTTLMI
Sbjct:   687 FTGRSPMLSVSGSFDLPNERYRNLSHRRSESNSSNAEKKLYELDVDRILRGEDSRTTLMI 746

Query:   818 KNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFK 851
             KNIPNKYTSKMLLAAIDE+C+GTYDF+YLPIDFK
Sbjct:   747 KNIPNKYTSKMLLAAIDEYCKGTYDFLYLPIDFK 780

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 = 1421 (505.3 bits), Expect = 3.9e-155, Sum P(2) = 3.9e-155
 Identities = 309/628 (49%), Positives = 403/628 (64%)

Query:   234 GMELEGDDRLFAV---QKNSDFVGGVSNQGVSAG--SVVGEHPYGEHPSRTLFVRNINSN 288
             G EL+  D   +V   + + D    VS++    G  + VGE   GE PSRTL V NI+SN
Sbjct:   168 GDELDEFDLFSSVGGMELDGDIFSSVSHRNGERGGNNSVGELNRGEIPSRTLLVGNISSN 227

Query:   289 VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY 348
             VED ELK LFEQFGDI+ ++TACK+RGF+M+SY DIRAA+NA +ALQNK LR  KLDI Y
Sbjct:   228 VEDYELKVLFEQFGDIQALHTACKNRGFIMVSYCDIRAAQNAARALQNKLLRGTKLDIRY 287

Query:   349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYD 408
             SI K+NPS+KD ++G L+V NLDSS+S +EL+++   YGE++EIR T H ++  +IEF+D
Sbjct:   288 SISKENPSQKDTSKGALLVNNLDSSISNQELNRLVKSYGEVKEIRRTMHDNSQIYIEFFD 347

Query:   409 IRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQM 468
             +RAA  AL  LN  +VAGK+++L  + P G R +  Q      +  L +  + + SSG +
Sbjct:   348 VRAAAAALGGLNGLEVAGKKLQLVPTYPEGTR-YTSQCAANDTEGCLPKTSYSNTSSGHI 406

Query:   469 VSS--GVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGH 526
                  G+I+ST  D GS++V+H++  SP  +  E H++ S+P G P  A   S  K  G 
Sbjct:   407 GRHFPGMISSTSSDGGSMRVIHNSIGSPVNSFIERHRSLSIPIGFPPSANGISASKPVGL 466

Query:   527 YEPNLSLDEMKFGNQH-PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLD 585
              E     D    G Q  P+ HPHS  EY D+ ANG PY S S  +++ S  G+K  +G  
Sbjct:   467 QEHGHHFDNSNMGIQSMPNLHPHSFSEYVDNFANGSPYTS-SAFSEMVSD-GSKANEGFM 524

Query:   586 SRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYVWXXXXXXXXXXXXXMVWPNSPSF 645
               ++RGV   G     +GG  GSP + S     N  +W             M+WPNSPS 
Sbjct:   525 IHNVRGVE--GF----SGGGIGSPMHQSSRRPIN--LWSNSNTQQQNPSSGMMWPNSPSH 576

Query:   646 LNGLHANRVAHMPGFPRVPPLMLN-ATSPAHHHIGSAPAVNPSLWDRQHAYAGESPETSN 704
             +N +   R   +  F R PP+M+N A+SP HHHIGSAP +N   WDR+ AY  ES E+S 
Sbjct:   577 INSIPTQRPP-VTVFSRAPPIMVNMASSPVHHHIGSAPVLNSPFWDRRQAYVAESLESSG 635

Query:   705 FHXXXXXXXXXXXXXPSHHVDIASQNILSHVGGNCMDM-TKNVGMRSPQQICHLFPGRNP 763
             FH             PSH +DI S    S VGGN MD+ ++N  +RSPQQ+ HLFPGR+P
Sbjct:   636 FHIGSHGSMGIPGSSPSHPMDIGSHKTFS-VGGNRMDVNSQNAVLRSPQQLSHLFPGRSP 694

Query:   764 MMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNK 823
             M SM  SFDS NER RNLS+RR+ES+S++ADKK YELD+DRILRG+D RTTLMIKNIPNK
Sbjct:   695 MGSMPGSFDSPNERYRNLSHRRSESSSSNADKKLYELDVDRILRGEDRRTTLMIKNIPNK 754

Query:   824 YTSKMLLAAIDEHCRGTYDFIYLPIDFK 851
             YTSKMLL+AIDEHC+GTYDF+YLPIDFK
Sbjct:   755 YTSKMLLSAIDEHCKGTYDFLYLPIDFK 782

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 = 6.4e-125, Sum P(2) = 6.4e-125
 Identities = 206/388 (53%), Positives = 261/388 (67%)

Query:   183 ESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD-- 240
             ES  + E+ +IGNLLPDE+DL +G+ DD+        + D +D+DLF SGGGMEL+ D  
Sbjct:    68 ESADDFESHSIGNLLPDEEDLLTGMMDDL----DLGELPDADDYDLFGSGGGMELDADFR 123

Query:   241 DRLFAV---QKNSDFVGGVS----NQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSE 293
             D L      + +   +GG +    N    AG+V GEHPYGEHPSRTLFVRNINSNVEDSE
Sbjct:   124 DNLSMSGPPRLSLSSLGGNAIPQFNIPNGAGTVAGEHPYGEHPSRTLFVRNINSNVEDSE 183

Query:   294 LKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD 353
             L ALFEQ+GDIRT+YT CKHRGFVMISYYDIR+AR AM++LQNKPLRRRKLDIH+SIPKD
Sbjct:   184 LTALFEQYGDIRTLYTTCKHRGFVMISYYDIRSARMAMRSLQNKPLRRRKLDIHFSIPKD 243

Query:   354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 413
             NPSEKD NQGTLVVFNLD S+S ++LH IFG +GEI+EIR+T HK +HKF+EFYD+R AE
Sbjct:   244 NPSEKDMNQGTLVVFNLDPSISNDDLHGIFGAHGEIKEIRETPHKRHHKFVEFYDVRGAE 303

Query:   414 TALRTLNRSDVAGKQIKLEASRPGGARR-FMVQSEQ--EQDDLNLCQIPFDDLSSGQMVS 470
              AL+ LNR ++AGK+IK+E SRPGGARR  M+Q  Q  E DDL+   +    +++   + 
Sbjct:   304 AALKALNRCEIAGKRIKVEPSRPGGARRSLMLQLNQDLENDDLHYLPMIGSPMANSPPMQ 363

Query:   471 SGVITSTCMDNGSIQVLHSATRSPAIAL--TESHQTSSVPNGL----PS--LARVG--SI 520
                  ++ ++   +Q + S  RSP   L  T +   S + + L    PS  LA +G   I
Sbjct:   364 GNWPLNSPVEGSPLQSVLS--RSPVFGLSPTRNGHLSGLASALNSQGPSSKLAPIGRGQI 421

Query:   521 G----KQFGHYEPNLSLDEMKFGNQHPS 544
             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 = 5.7e-117, Sum P(3) = 5.7e-117
 Identities = 203/411 (49%), Positives = 264/411 (64%)

Query:   185 LKEIEAQTIGNLLPD-EDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGD--D 241
             L + ++  IGN+LPD E++LFSG+ DD+  +    T+DDLED+DLF SGGG+ELE D  D
Sbjct:    63 LDDGDSHPIGNMLPDDEEELFSGLMDDLNLSSLPATLDDLEDYDLFGSGGGLELETDPYD 122

Query:   242 RL---FAVQKNSDF-VGGVSNQGV---SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSEL 294
              L   F+    +D  V  V  Q +     GS+ GEHPYGEHPSRTLFVRNINSNVEDSEL
Sbjct:   123 SLNKGFSRMGFADSNVDNVMPQNIFQNGVGSIAGEHPYGEHPSRTLFVRNINSNVEDSEL 182

Query:   295 KALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
             +ALFEQ+G IRT+YTACK RGFVM+SY DIRA+R AM+ALQ K L++RKLDIH+SIPKDN
Sbjct:   183 QALFEQYGHIRTLYTACKQRGFVMVSYNDIRASRAAMRALQGKLLKKRKLDIHFSIPKDN 242

Query:   355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 414
             PSEKD NQGTLVVFNL  SVS  +L  IFG+YGEI+EIR+T +K +HKF+EF+D+R+A+ 
Sbjct:   243 PSEKDVNQGTLVVFNLAPSVSNRDLENIFGVYGEIKEIRETPNKRHHKFVEFFDVRSADA 302

Query:   415 ALRTLNRSDVAGKQIKLEASRPGGARR-FMVQS--EQEQDD----LNLCQIPFDDLSSGQ 467
             AL+ LNR+++AGK+IKLE SRPGGARR  M+Q   E EQDD    LN  + P      G 
Sbjct:   303 ALKALNRTEIAGKRIKLEHSRPGGARRNMMLQMNPELEQDDSYSYLNHVESPLASSPIGN 362

Query:   468 MVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSI--GKQFG 525
               +S +      D+     L S ++SP        +    P      A V +   G++F 
Sbjct:   363 WRNSPI------DHP----LQSFSKSPIFGNLSPTKNIRYPEFSMKTASVNNDQEGRRFS 412

Query:   526 HYEPNLSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNS-PSTIADIASS 575
             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 = 2.0e-102, Sum P(2) = 2.0e-102
 Identities = 215/471 (45%), Positives = 284/471 (60%)

Query:   183 ESLKEIEAQTIGNLLP-DEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMEL--EG 239
             +SL+++E   +  LLP DE++L  G+ D++      + +DDLE+ D+F +GGGMEL  E 
Sbjct:    93 DSLEDVEPDALEILLPEDENELLPGLIDELNFTGLPDELDDLEECDVFCTGGGMELDVES 152

Query:   240 DDRLFAVQKNSDFVG--GVSNQGV------SAGSVVGEHPYGEHPSRTLFVRNINSNVED 291
              D   AV  +   +   G +N  V      +AG V  EHP GEHPSRTLFVRNINS+VED
Sbjct:   153 QDN-HAVDASGMQISDRGAANAFVPRKRPNTAGRVSVEHPNGEHPSRTLFVRNINSSVED 211

Query:   292 SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP 351
             SEL ALFE FG+IR++YTACK RGFVMISYYDIRAA  AM+ALQN  LR+R LDIH+SIP
Sbjct:   212 SELSALFEPFGEIRSLYTACKSRGFVMISYYDIRAAHAAMRALQNTLLRKRTLDIHFSIP 271

Query:   352 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRA 411
             K+NPSEKD NQGTLV+FN+D++VS +EL Q+FG YGEIREIR+T ++  H+FIE+YD+R 
Sbjct:   272 KENPSEKDMNQGTLVIFNVDTTVSNDELLQLFGAYGEIREIRETPNRRFHRFIEYYDVRD 331

Query:   412 AETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSS 471
             AETAL+ LNRS++ GK IKLE SRPGGARR  V S+ +  DL   ++     +    V S
Sbjct:   332 AETALKALNRSEIGGKCIKLELSRPGGARRLSVPSQSQ--DLERTEVT----NFYNQVGS 385

Query:   472 GVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSV-P---NGLPSLARV-GSIGKQFGH 526
              V  S     G+  +      SP+ A T  H    V P   + +P LA +  +    F  
Sbjct:   386 HVANSP---PGNWPIGSPVKGSPSHAFTRPHGLGMVRPVNSDNMPGLASILPAHPSSFHG 442

Query:   527 YEPNLSLDE--MKFGNQ--------HP-SF-HPHSLPEYHDSLANGLPYNSPSTIADIAS 574
             + P +S D+  +   NQ        H  S+  PHSLPE+   +  G+  NS   IA  +S
Sbjct:   443 FSP-VSNDQGLLNHSNQTILNKGLMHNISYGQPHSLPEH---ITGGIS-NSMRFIAPHSS 497

Query:   575 SVGTKIKDGLDSRHIRGVSSNGHLMEP--TG-GVFGSPRNGSYSL-HGNPY 621
               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 = 238 (88.8 bits), Expect = 2.1e-29, Sum P(4) = 2.1e-29
 Identities = 45/103 (43%), Positives = 65/103 (63%)

Query:   348 YSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFY 407
             + +P  +      NQGTLV+FNLD  VS+  L QIF +YG I+E+R+T +K + +F+EFY
Sbjct:   198 FVVPATSAVPGGCNQGTLVIFNLDPEVSSITLRQIFQVYGPIKELRETPYKKHQRFVEFY 257

Query:   408 DIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
             D+R A  A   +N  ++ GKQ+ +E SRPGG +     S Q Q
Sbjct:   258 DVRDAARAFDRMNGKEIGGKQVVIEFSRPGGIKNRFRSSRQPQ 300

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

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

 Score = 216 (81.1 bits), Expect = 1.4e-28, Sum P(3) = 1.4e-28
 Identities = 38/92 (41%), Positives = 62/92 (67%)

Query:   347 HYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEF 406
             H+  P+ N   +  NQG+LV+ NL+ +VS+  L  IF +YGE++++R+T  K   +F+EF
Sbjct:   167 HFVFPQLNAVPEGNNQGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEF 226

Query:   407 YDIRAAETALRTLNRSDVAGKQIKLEASRPGG 438
             +D+R A  ALR +N   ++GK + ++ SRPGG
Sbjct:   227 FDVRDAAKALRVMNGKVISGKPMVIQFSRPGG 258

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 = 228 (85.3 bits), Expect = 2.3e-23, Sum P(3) = 2.3e-23
 Identities = 70/226 (30%), Positives = 119/226 (52%)

Query:   274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-FVMISYYDIRAARNAMK 332
             E PSR LF+++I   +  +  K+  E  G I ++Y + K++G F++ISY DIR +  A  
Sbjct:   911 ESPSRYLFIKSIRG-INHNLFKSKIESIGQINSVYGSIKNKGGFLIISYLDIRHSIEAFN 969

Query:   333 ALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVV-FNLDSSVSTEELHQIFGIYGEIRE 391
              LQ       KL ++Y   KD   +K    GTL+  F+ D  +  + +   F  +GEI++
Sbjct:   970 ELQKVDFGS-KLIVNYCFDKDQTVDK----GTLIATFSNDDQI--KNIVNDFSKFGEIKD 1022

Query:   392 IRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQD 451
             IRD+ +K   KF+EFY+I +   A+  LN SD    +IK+  S  GG+ + +++    + 
Sbjct:  1023 IRDSPNKPLQKFVEFYNINSTLKAINNLN-SD----KIKVAFSHHGGSSKDLIKLNSTEA 1077

Query:   452 DLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIA 497
               N+    F+      + ++   T+T     S QV +S T+SP+ +
Sbjct:  1078 -FNVTTHYFNGT---YLPTTTTTTATASTPTSTQV-NSITKSPSFS 1118

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

DICTYBASE|DDB_G0268266 DDB_G0268266 "RNA recognition motif-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 272 (100.8 bits), Expect = 2.6e-20, Sum P(2) = 2.6e-20
 Identities = 61/173 (35%), Positives = 96/173 (55%)

Query:   264 GSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYD 323
             G V+GE    E   RTLFVRN+  ++++ ++ A+F + G+I+  ++  + RG   ISYYD
Sbjct:   175 GKVIGEK---EKLGRTLFVRNVAYSIKEVDIPAIFAKIGEIKKTFSLLESRGIAFISYYD 231

Query:   324 IRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIF 383
             +R A  A   +Q   L  R +DIH+SIPK+    +D N G + V N D  V   E+   F
Sbjct:   232 LRDAERAKNEIQGTTLDGRSIDIHFSIPKEESGLED-NAGFIHVKNRD--VPLNEVRIFF 288

Query:   384 GIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
               YG+I+++  T+   +   +EFYD+RA E AL   N   +  + + L+   P
Sbjct:   289 SSYGDIKDV--TEFNRDQVLVEFYDLRACEKALAEANGVKLGDQTLDLDYYTP 339

GO:0030587 "sorocarp development" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

DICTYBASE|DDB_G0276005 DDB_G0276005 [Dictyostelium discoideum (taxid:44689)]

 Score = 196 (74.1 bits), Expect = 5.1e-16, Sum P(3) = 5.1e-16
 Identities = 60/184 (32%), Positives = 93/184 (50%)

Query:   271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG--FVMISYYDIR--- 325
             P+G   SR L ++  N+N++   L   F++ G+I+++Y      G   V+ISY+DIR   
Sbjct:  1411 PHGGKASRNLLIKT-NANIDLRNLICKFKEHGEIKSVYQNITRSGTMHVVISYFDIRNSV 1469

Query:   326 -----------AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSV 374
                         + N+     N  +   +L I+Y + KD P +     GTLV+FN D+  
Sbjct:  1470 FALSANCNSSSCSNNSSTNKNNNDIINDRLSIYYCLNKD-PID----HGTLVLFNFDAVF 1524

Query:   375 STEE-LHQIFGI---YGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK 430
             ST    H +      +G+IREIR+   K+  KFIEFYDIR A  A+  L +    GK++ 
Sbjct:  1525 STNSNTHMLTSALNQFGQIREIREDL-KNKLKFIEFYDIRDAIAAVNALKKQVFFGKKLL 1583

Query:   431 LEAS 434
             +  S
Sbjct:  1584 VRLS 1587

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

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	0.4895	0.9581	0.8241	yes	no
Q8W4I9	AML1_ARATH	No assigned EC number	0.4836	0.9024	0.8491	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	861
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	4e-49
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-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
pfam04059	97	pfam04059, RRM_2, RNA recognition motif 2	4e-22
cd12531	86	cd12531, RRM3_MEI2_like, RNA recognition motif 3 i	5e-22
cd12277	86	cd12277, RRM3_MEI2_EAR1_like, RNA recognition moti	2e-15
cd12530	101	cd12530, RRM3_EAR1_like, RNA recognition motif 3 i	7e-15
smart00360	73	smart00360, RRM, RNA recognition motif	4e-13
cd12532	90	cd12532, RRM3_MEI2_fungi, RNA recognition motif 3	9e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-13
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	9e-13
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	1e-09
cd12525	72	cd12525, RRM1_MEI2_fungi, RNA recognition motif 1	2e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-08
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	3e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-08
cd12526	71	cd12526, RRM1_EAR1_like, RNA recognition motif 1 i	4e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	5e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	5e-08
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-08
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	6e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-07
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	1e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-07
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	3e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-07
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	3e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-07
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	5e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	6e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-07
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	9e-07
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-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
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	4e-06
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	4e-06
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	5e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	9e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	9e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	1e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	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
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-05
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	2e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	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
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	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
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	3e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	5e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	6e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	8e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	9e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	1e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-04
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	2e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	3e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	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
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	3e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	3e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	3e-04
cd12696	107	cd12696, RRM3_PTBP2, RNA recognition motif 3 in ve	4e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	4e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	4e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	5e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	5e-04
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	5e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	5e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	6e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	7e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	7e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	7e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-04
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	9e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.001
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	0.001
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.001
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.001
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.001
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.001
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.001
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.001
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	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
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.002
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.002
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.002
cd12752	87	cd12752, RRM1_RBM5, RNA recognition motif 1 in ver	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.003
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.003
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.003
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.003
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.003
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.003
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.003
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.003
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.003
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.004
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.004
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.004
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.004
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.004

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

 Score =  167 bits (424), Expect = 4e-49
 Identities = 63/77 (81%), Positives = 69/77 (89%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           SRTLFVRNINSNVED EL+ALFEQFGDIRT+YTACKHRGF+M+SYYDIRAAR A +ALQ 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 337 KPLRRRKLDIHYSIPKD 353
             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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score =  127 bits (322), Expect = 2e-35
 Identities = 52/71 (73%), Positives = 64/71 (90%)

Query: 362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 421
           QGTLVVFNLD SVS ++LHQIFG YGEI+EIR+T +K +HKFIEFYD+R+AE AL+ LNR
Sbjct: 1   QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 422 SDVAGKQIKLE 432
           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 =  107 bits (270), Expect = 3e-28
 Identities = 36/71 (50%), Positives = 52/71 (73%)

Query: 362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 421
           QGTL+VFNLDS +S +EL  +F  +GE+++IR+T  + + KF+EFYDIRAAE AL  LN 
Sbjct: 1   QGTLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 422 SDVAGKQIKLE 432
               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 (265), Expect = 1e-27
 Identities = 26/71 (36%), Positives = 44/71 (61%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           SR+LFV N+  +V +S L+ LFE +GD+R + T     G V + +YDIR A+ A++ L  
Sbjct: 1   SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCG 60

Query: 337 KPLRRRKLDIH 347
           + ++++ 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: 362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 421
           QGTLV+FNLD +VS+E L  IF +YG+++E+R+T  K   +F+EF+D+R A  ALR +N 
Sbjct: 1   QGTLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 422 SDVAGKQIKLE 432
            +++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|112856 pfam04059, RRM_2, RNA recognition motif 2

 Score = 91.1 bits (226), Expect = 4e-22
 Identities = 35/40 (87%), Positives = 37/40 (92%)

Query: 812 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFK 851
           RTTLMIKNIPNKYT KMLLAAIDE  +GTYDF+YLPIDFK
Sbjct: 1   RTTLMIKNIPNKYTQKMLLAAIDEKNKGTYDFLYLPIDFK 40

Length = 97

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

 Score = 90.5 bits (225), Expect = 5e-22
 Identities = 33/37 (89%), Positives = 33/37 (89%)

Query: 815 LMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFK 851
           LMIKNIPNKYT KMLLAAIDE  RGTYDF YLPIDFK
Sbjct: 1   LMIKNIPNKYTQKMLLAAIDEKHRGTYDFFYLPIDFK 37

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

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

 Score = 71.9 bits (177), Expect = 2e-15
 Identities = 26/38 (68%), Positives = 32/38 (84%), Gaps = 1/38 (2%)

Query: 815 LMIKNIPNKYTSKMLLAAIDEHCRG-TYDFIYLPIDFK 851
           +MI+NIPNKYT +MLL  +DEH +G  YDF+YLPIDFK
Sbjct: 1   VMIRNIPNKYTQEMLLQLLDEHGKGGAYDFLYLPIDFK 38

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 = 71.0 bits (174), Expect = 7e-15
 Identities = 29/53 (54%), Positives = 34/53 (64%), Gaps = 13/53 (24%)

Query: 812 RTTLMIKNIPNKYTSKMLLAAIDEHC-------------RGTYDFIYLPIDFK 851
           RTTLMIKNIPNKY+ K+LL  +D HC               +YDF+YLPIDFK
Sbjct: 1   RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHIEDSSQPVSSYDFVYLPIDFK 53

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|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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKA 333
           TLFV N+  +  + EL+ LF +FG + ++         K +GF  + +     A  A++A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 334 LQNKPLRRRKLDI 346
           L  K L  R L +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 64.5 bits (157), Expect = 9e-13
 Identities = 27/42 (64%), Positives = 32/42 (76%)

Query: 812 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKAS 853
           RTT+M+KNIPNK+T +ML   IDE   GTYDF+YL IDF  S
Sbjct: 1   RTTVMLKNIPNKFTQQMLRKYIDETNPGTYDFMYLRIDFNNS 42

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|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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARNAMKALQ 335
           LFV N+  +  + +L+ LF +FG+I ++        K +GF  + +     A  A++AL 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 336 NKPLRRRKLDIH 347
            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 = 9e-13
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 8/78 (10%)

Query: 279 TLFVRNINSNVEDSELK----ALFEQFGDIRTIYTACK---HRGFVMISYYDIRAARNAM 331
           TL++ N+N  ++  ELK    ALF QFG +  I  A K    RG   + + D+ +A NA+
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIV-ASKTLKMRGQAFVVFKDVESATNAL 59

Query: 332 KALQNKPLRRRKLDIHYS 349
           +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 = 62.7 bits (153), Expect = 2e-12
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           TL V N++S+V  EEL  +F  +G+IR +           + +YDIRAA  A R L  ++
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTE 62

Query: 424 VAGKQIKLEASRP 436
           + 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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 338
           TL V N++S + D EL++LF QFG+++ I           + +YDIRAA  A+ AL  +P
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRP 62

Query: 339 LRRRKLDI 346
               +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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHK--FIEFYDIRAAETALRT 418
           TL V NL    + EEL ++F  +G++  +R   D +   +    F+EF     AE AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 419 LNRSDVAGKQIKL 431
           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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLN 420
           L V NL    + E+L ++F  +GEI  +R             F+EF     AE AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 421 RSDVAGKQIKLE 432
             ++ 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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAMKALQ 335
           LFV N+  +  + +LK LF +FG I +I        + +GF  + + D   A  A++AL 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 336 NKPLRRRKL 344
            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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLN 420
           L V NL    + E+L  +F  +G I  IR    +T       F+EF D   AE AL  LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 421 RSDVAGKQIK 430
             ++ 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: 294 LKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS 349
           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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVMISYYDIRAARNAMKA 333
           +L+VRN+       +L+ LF ++G I  +Y          RGF  + + D+R A +A+  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 334 LQNKPLRRRKLDIHYS 349
           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 = 1e-09
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALR 417
             L V  L +  + +EL  +F  +G + E+   +     +     F+ F  +  A+ A+R
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 418 TLNRSDVAGKQIKLEASR 435
            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: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-RGFVMISYYDIRAARNAMKALQ 335
           +R L V  +  +V  S LK +FE+ GD++ I+      +G V++S++D+R A  A K LQ
Sbjct: 1   TRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLLSKGIVIVSFHDLRQAIKAYKDLQ 60

Query: 336 NKPL 339
           +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 = 3e-09
 Identities = 20/77 (25%), Positives = 43/77 (55%), Gaps = 9/77 (11%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDIRAARN 329
           R ++VRN++  +++ +L+ +F +FG++ +I    K        + GF  +++ D  +A N
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 330 AMKALQNKPLRRRKLDI 346
           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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 333
           TLFVRN+  +  D +L+  F + G I+  +        K RGF  +++     A+ A++ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 334 LQNKPLRRRKLDIHYSIPK 352
            +      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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 57.6 bits (139), Expect = 2e-08
 Identities = 52/205 (25%), Positives = 93/205 (45%), Gaps = 24/205 (11%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAAR 328
           E   RT+FV  +     + +L   F + G +R +       + + +G   + +YD+ +  
Sbjct: 86  ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVI 145

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN--QGT------LVVFNLDSSVSTEELH 380
            A+ AL  + L  R + +  S  + N + K A    G       L V NL  +++ +EL 
Sbjct: 146 KAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELR 204

Query: 381 QIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS- 434
           QIF  +G+I +++     +T       FI+F+D   A+ AL  +N  ++AG+ IK+  + 
Sbjct: 205 QIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ 264

Query: 435 ----RPGGARRFMVQSEQEQDDLNL 455
                   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|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: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI----------YTACKHRGFVMISYYDIRAA 327
            TLFV+N+N    +  LK  FE+ G +R++                 G+  + +    AA
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 328 RNAMKALQNKPLRRRKLDIHYS 349
           + 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|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 = 3e-08
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 279 TLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMK 332
           T+++ N+N  V+  ELK    A+F QFG I  I      K RG   + + DI +A NA++
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60

Query: 333 ALQNKPLRRRKLDIHYS 349
           ++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|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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRS 422
           L V NL   +S+EEL+ +FG YG IR+IR  +T+      F+ + DI  A+ A   L+  
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSGF 64

Query: 423 DVAGK 427
           +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|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal EAR1-like proteins

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 15/59 (25%), Positives = 34/59 (57%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           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|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 = 4e-08
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           T+ V NL   ++ EEL + F  +G I E+R       + F+ F    AA TA+  +N + 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVR-VFKDKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 424 VAGKQIK 430
           + 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 56.4 bits (136), Expect = 4e-08
 Identities = 62/325 (19%), Positives = 116/325 (35%), Gaps = 36/325 (11%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVMISYYDIRAARNAMKAL 334
           L+V+N++ +V + +L+ LF +FG+I T     K      RGF  +++     A  A++ +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEI-TSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 335 QNKPLRRRKL-DIHYSIPKDNPSEKDA----------------NQGT-LVVFNLDSSVST 376
             K +   K     Y       +E++A                 QG  L V NLD +V+ 
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299

Query: 377 EELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
           E+L ++F   GEI   +    +        F+ F +   A  A+  ++   + GK + + 
Sbjct: 300 EKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVA 359

Query: 433 ASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATR 492
            ++    RR  +Q +  Q    + Q+P      G M                Q       
Sbjct: 360 LAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQ----GPQQQFNGQPLG 415

Query: 493 SPAIAL---TESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQHPSFHPHS 549
            P +++            PNGL  +  V +  +   +      +  + +   + S  P S
Sbjct: 416 WPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYPPNYQS-LPLS 474

Query: 550 LPEYHDSLANGLPYNSPSTIADIAS 574
                          +      +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|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 = 5e-08
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH--RGFVMISYYDIRAARNAMKAL 334
           +R L+VRN+   +   EL  LF ++G IR I        RG   + Y DI  A+NA   L
Sbjct: 2   NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 335 QNKPLRRRKLDIHY 348
               +  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 = 5e-08
 Identities = 23/70 (32%), Positives = 36/70 (51%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
           V NL    +  EL   F  YG +R +   ++     F+EF D R AE A+R L+   + G
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRICG 63

Query: 427 KQIKLEASRP 436
            ++++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 = 50.3 bits (121), Expect = 5e-08
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL-RTLNRS 422
           TL V  L   V+ ++L   F  +GEIR I     +    F+ F    AAE A  R  N+ 
Sbjct: 3   TLYVGGLGERVTEKDLRDHFYQFGEIRSITVV-PRQQCAFVTFTTREAAEKAAERLFNKL 61

Query: 423 DVAGKQIKL 431
            + 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|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 = 50.4 bits (121), Expect = 6e-08
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           S TL++ +++  V + +LK LFE++G+I++I      RG   +     + A  A++ L+N
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI-DMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 337 KPLRRRKLDIHYSIPK 352
             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 = 49.5 bits (118), Expect = 1e-07
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTLN 420
           L V NLD  V+ + L QIF + G ++ ++          N+ F+E++    AE AL+TLN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 421 RSDVAGKQIKL 431
              +   +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 = 54.8 bits (132), Expect = 1e-07
 Identities = 42/175 (24%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           PS  + VRN+  +V +++L      FG + +       +   ++ + D  +A+  +    
Sbjct: 1   PSPVVHVRNLPQDVVEADLVEALIPFGPV-SYVMMLPGKRQALVEFEDEESAKACVNFAT 59

Query: 336 NKP--LRRRKLDIHYS----IPKDNPSEKDANQGTLV----VFNLDSSVSTEELHQIFGI 385
           + P  +R +    +YS    I +D  S+ D+     V    V N    ++ + L+QIF  
Sbjct: 60  SVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNP 119

Query: 386 YGEIREIRDTQHKHN--HKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEASRP 436
           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: 280 LFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           L+VRN+  +V + +L+  F  +G +   R +    + RGF  + +     A  A+K L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 337 KPLRRRKL 344
             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 = 3e-07
 Identities = 20/68 (29%), Positives = 38/68 (55%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 338
           TL V N++ +V + +L  +F  +G+I+ I      R    I +YD+R+A  A+KAL    
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 339 LRRRKLDI 346
           +  +++ +
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 = 3e-07
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 14/84 (16%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIR----TIYTACKH---RGFVMISYYDIRAARNA 330
           RT+F+RN+  +  + ELK LF QFG+++           H     FV   +    +A+  
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFV--KFKTKESAQKC 58

Query: 331 MKALQNKP-----LRRRKLDIHYS 349
           ++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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 52.6 bits (125), Expect = 3e-07
 Identities = 33/149 (22%), Positives = 56/149 (37%), Gaps = 7/149 (4%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAAR 328
           +  + TLFV N+  +V + +L+ LF++FG ++ +         K RGF  + +    +A 
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNP-SEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 387
            A++ L  K L  R L +  + P   P SE   N        L    +           G
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Query: 388 EIREIRDTQHKHNHKFIEFYDIRAAETAL 416
            +      +   +  F    DI  A    
Sbjct: 232 NLPLKTAEEELADL-FKSRGDIVRASLPP 259

Length = 306

>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 = 3e-07
 Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 6/80 (7%)

Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A N
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 330 AMKALQNKPLRRRKLDIHYS 349
           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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L V NL  +V+ E+L  +FG +GE+        R+T       F+E      A  A+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 419 LNRSDVAGKQIKLEASRP 436
           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|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 = 47.6 bits (114), Expect = 5e-07
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACK----HRGFVMISYYDIRAARNAMKAL 334
            L VRN+       EL+ LF  FG ++++    K    HRGF  + +   + A+NAM+AL
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 335 QNKPLRRRKLDIHYS 349
           ++  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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 47.6 bits (114), Expect = 5e-07
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQF-G--DIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           P++ LF++N+        L+ LF QF G  ++R +      RG   + +     A  A++
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV----PRRGIAFVEFETEEQATVALQ 56

Query: 333 ALQN 336
           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 = 6e-07
 Identities = 15/54 (27%), Positives = 31/54 (57%)

Query: 379 LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
           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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 52.5 bits (126), Expect = 7e-07
 Identities = 33/150 (22%), Positives = 68/150 (45%), Gaps = 9/150 (6%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAMKALQ 335
           +FV+N++ +V++  L   F +FG+I +   A     K RG+  + +    +A+ A++ + 
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 336 NKPLRRRKLDI-HYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD 394
              L  +++ +  +    +  +        L V NLD SV+ ++L ++F  +GEI     
Sbjct: 151 GMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV 210

Query: 395 TQHKHNHK----FIEFYDIRAAETALRTLN 420
            +          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|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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHKFIEFYDIRAAETALRTLN 420
           T+ V  +D S+S ++L + F   GE+  +R   D QH     F+EF D  +A +AL  L+
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALN-LS 60

Query: 421 RSDVAGKQIKLEASR 435
            + + 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|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 = 46.8 bits (112), Expect = 1e-06
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKA 333
            LFV  +++   + EL+ALF +FG +  +         + RGF  +++  +  A  A++ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 334 LQNKPLRRRKLDI 346
           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 = 46.5 bits (111), Expect = 1e-06
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 9/74 (12%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIR------DTQHKHNH--KFIEFYDIRAAETALRT 418
           V NLD  +  ++L  IF  +GE+  IR      + Q + N+   F+ F D  +AE AL+ 
Sbjct: 5   VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ- 63

Query: 419 LNRSDVAGKQIKLE 432
           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 = 1e-06
 Identities = 39/181 (21%), Positives = 87/181 (48%), Gaps = 21/181 (11%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC------KHRGFVMISYYDIRAARNAMK 332
           +L+V +++ +V +++L  LF+ FG + ++   C      +  G+  +++ +   A  A++
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSV-RVCRDSVTRRSLGYGYVNFQNPADAERALE 60

Query: 333 ALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI 392
            +  K L  + + I +S  + +PS + +  G + V NLD SV  + L   F  +G I   
Sbjct: 61  TMNFKRLGGKPIRIMWS--QRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSC 118

Query: 393 R----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQ 448
           +    +      + F+ F    +A+ A++ +N   +  K++ +         RF+ + E+
Sbjct: 119 KVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVG--------RFIKKHER 170

Query: 449 E 449
           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 = 46.9 bits (112), Expect = 1e-06
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRTL 419
           T+ V NLD + + ++L + F   GE++ +R    +TQ    + F+EF +  +   AL+ L
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPT-RYAFVEFAEQTSVINALK-L 63

Query: 420 NRSDVAGKQIKLEASR 435
           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|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKAL 334
           LFVRN+  + ++ +L+ LF +FG++  ++ A      K +GF  + + D   A  A K L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 335 QNKPLRRRKLDI 346
             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|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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHN-HKFIEFYDIRAAETALRTLNRS 422
           L V NLD +V+ + L ++F   G I+  +   +H ++ + F+E+YD R+A  AL+T+N  
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 423 DVAGKQIK 430
            + 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 45.7 bits (109), Expect = 4e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMK 332
           +TLFV  +N +  +S+L+  FE++G I+ I         K RG+  I +   R  + A K
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 333 ALQNKPL--RRRKLDI 346
               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|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: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAM 331
           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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           ++ V  L   V+ EEL++ F  +G+I E   I+   H +   FI+F   +AA  A+ + N
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 421 RSDVAGKQIKLE 432
            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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHN---HKFIEFYDIRAAETALRTLN 420
           TL + NL+ + +  +L + F  +GEI +I D + +     + FI++ DI +   A+R ++
Sbjct: 4   TLFIGNLEKTTTYSDLREAFERFGEIIDI-DIKKQGGNPAYAFIQYADIASVVKAMRKMD 62

Query: 421 RSDVAGKQIKL 431
              +   ++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|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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           + + NL   V+ + LHQ+F  YG + +I    ++      ++F  + +AE A + LN  +
Sbjct: 4   VTISNLLYPVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRN 63

Query: 424 VAGKQIKLE 432
           +      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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 45.4 bits (107), Expect = 5e-06
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 6/79 (7%)

Query: 277 SRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNA 330
           + T+++ N+N  ++  ELK    ALF QFG +  I      K RG   + + ++ +A NA
Sbjct: 1   NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNA 60

Query: 331 MKALQNKPLRRRKLDIHYS 349
           ++ 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 = 44.1 bits (105), Expect = 6e-06
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           L+V  +      +EL+  F++FG IR I      R +  I Y  I AA+ A +AL+  PL
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI-DYDPGRNYAYIEYESIEAAQAAKEALRGFPL 59

Query: 340 RR--RKLDIHYS 349
               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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 44.5 bits (106), Expect = 7e-06
 Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 12/73 (16%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC--------KHRGFVMISYYDIRAARNAM 331
           ++V+N+  +++D +LK LF ++G I    T+         K +GF  +++ +  AA+ A+
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKI----TSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59

Query: 332 KALQNKPLRRRKL 344
           + 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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 48.9 bits (116), Expect = 7e-06
 Identities = 46/175 (26%), Positives = 75/175 (42%), Gaps = 15/175 (8%)

Query: 257 SNQGVSAGSVVGEHPYGEHPSRT-LFVRNINSNVEDSELKALFEQFGDIRTI-----YTA 310
           S   +++    G      + S T L V  +  ++ D EL ALF   G I T      Y  
Sbjct: 86  STNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKT 145

Query: 311 CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNL 370
               G+  + +     ++ A+K L    +R ++L + Y+ P    S KD N   L V NL
Sbjct: 146 GYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP-GGESIKDTN---LYVTNL 201

Query: 371 DSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLN 420
             +++ ++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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKAL 334
           LFVRN+     + EL+ LFE FG+I  ++        + +GF  +S+     A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 335 QNKPLRRRKLDI 346
                + 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|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 = 9e-06
 Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 419
           L+V  L   ++ EEL  +F   G I   +  + +   +     F+++ D   A+ A+ TL
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 420 NRSDVAGKQIK 430
           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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMK 332
           +RTLF+ N+      S+L+  FE+FG+I  I    K +G    +  I Y DI +   AM+
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEIIDI--DIKKQGGNPAYAFIQYADIASVVKAMR 59

Query: 333 ALQNKPLRRRKL 344
            +  + 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|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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
           T+ V NL  S++  +LH+IF  YG++ ++   + K   K     FI F D   A   ++ 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 419 LNRSDVAGKQIK 430
           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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 9/61 (14%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARNAMKALQN 336
           LFV N+       EL+ALFE++G +    T C   K+ GFV +   +   A +A+KAL  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV----TECDVVKNYGFVHME--EEEDAEDAIKALNG 55

Query: 337 K 337
            
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|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: 279 TLFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAMKA 333
           TLFVRN+  +V   +L   F     I+     T     + RG+  +++  +  A+ A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 334 LQNKPL--RRRKLDI 346
           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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 44.0 bits (103), Expect = 1e-05
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 5/81 (6%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
           ++  L+V  L  +++ EEL  +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 416 LRTLNRSDVAGKQIKLEASRP 436
           + 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|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL 419
           +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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---D--TQHKHNHKFIEFYDIRAAETALRT 418
           +L V N+  +   ++L ++FG YG I ++    D  T+      +++F D+R AE AL  
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 419 LNRSDVAGKQIKLE 432
           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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 43.9 bits (103), Expect = 2e-05
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 418
           +L V N+  +   E+L + FG YG I ++       T+      +I+F D+R AE AL  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 419 LNRSDVAGKQIKLE 432
           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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 43.5 bits (102), Expect = 2e-05
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
           V NL +     EL + F  YG +R +   ++     F+EF D R AE A+R L+   + G
Sbjct: 4   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 63

Query: 427 KQIKLEASRPGGARR 441
            ++++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|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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 333
           +LFVRNI  +    +L+  F ++G I  +Y        + RGF  + + D+R A +A+  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 334 LQNKPLRRRKLDIHYS 349
           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|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: 367 VFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRTLNR 421
           V N+    + E+L +IF   G +   R     DT     + F EF DI  A +A+R LN 
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 422 SDVAGKQIKLE 432
            +  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|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 43.5 bits (102), Expect = 2e-05
 Identities = 22/68 (32%), Positives = 38/68 (55%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
           V NL ++ +  EL + FG YG +R +   ++     F+EF D R A  A+R L+   + G
Sbjct: 9   VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 68

Query: 427 KQIKLEAS 434
            ++++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|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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKAL 334
           L V N+       +L+ +FE++G++  +Y        + RGF  + +YD R A +AM A+
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 335 QNKPLRRRKL 344
             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|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 = 2e-05
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKAL 334
           LFV  +     + +++ALFE++G+I  +         + +G   + +     A+ A++AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 335 QNK 337
             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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 10/83 (12%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFG---DIRTIYT---ACKHRGFVMISYYDIRAARN 329
           P+R +FV  I  +  + EL+  F +FG   D++ I       K  GFV  ++     A  
Sbjct: 2   PNR-IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFV--TFETQEDAEK 58

Query: 330 AMKALQNKPLRRRKLDIHYSIPK 352
              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|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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           ++V N+       EL+  FE++G +R+++ A    GF  + + D R A +A++AL  + +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 340 RRRKL 344
              ++
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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETALRTLNR 421
           L V NL  SV+ E+L + F  YG++  +R  ++K   +   F+EF     AE AL+ LN 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 422 SDVAGKQIK 430
             + G+ ++
Sbjct: 61  LVLDGRTLR 69

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

>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 = 3e-05
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 5/74 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
           +L V N+     +E+L + FG YG I ++      +  +     +++F D+R AE AL  
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 419 LNRSDVAGKQIKLE 432
           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 = 42.6 bits (101), Expect = 3e-05
 Identities = 14/69 (20%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 337
           + L+VRN+  +  + +L+ LF ++G++  +    K + +  + + +   A  AM+ +  K
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK---KIKDYAFVHFEERDDAVKAMEEMNGK 58

Query: 338 PLRRRKLDI 346
            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|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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHNHKFIEFYDIRAAETALRTLNRS 422
           T+      +S    ++ ++F   G +R++   ++    H FI F ++ AA+ A+ TLN +
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 423 DVAGKQIKLE 432
            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 = 43.0 bits (102), Expect = 3e-05
 Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 10/89 (11%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIRAAETALRT 418
           TL V  L    + E L ++F  YG+IR +R  +         + F+E+   R A  A R 
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 419 LNRSDVAGKQI--KLEASR--PGG-ARRF 442
            ++  + 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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 17/72 (23%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           SR +++ NI+ ++ + +L+  F Q+G+I ++    + +    +++ +I  A  A+  +++
Sbjct: 3   SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNY-LREKNCAFVNFTNISNAIKAIDGVKS 61

Query: 337 KPLRRRKLDIHY 348
            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|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 22/69 (31%), Positives = 36/69 (52%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            LVV NL  S S + L ++F     IR  ++      + F+EF     A+ AL + N ++
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 424 VAGKQIKLE 432
           + 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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 42.5 bits (101), Expect = 4e-05
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 364 TLVVFNLDSSVSTEE----LHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALR 417
           TL + NL+  +  +E    L+ +F  +G + +I    T       F+ F D+ +A  ALR
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 418 TLNRSDVAGKQIKLEASR 435
            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|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 = 4e-05
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 418
            L+V N+    + +EL ++F  +G+++ +R     D  H+    F+EF   + A+ A+  
Sbjct: 2   KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHR-GFAFVEFVTKQEAQNAMEA 60

Query: 419 LNRSDVAGKQIKLE 432
           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|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: 365 LVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHNHKFIEFYDIRAAETALRTLNR 421
           L V NL  S + E+L ++F  YGE+   ++I+D      + F+ F +   A  A+  +N 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD------YAFVHFEERDDAVKAMEEMNG 57

Query: 422 SDVAGKQIKLEASRP 436
            ++ 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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIRAAETALRT 418
            L++  L  +++ EE   +F   G ++  +  + K     +   F+++     A+ A+RT
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 419 LNRSDVAGKQIKLEASRPGG 438
           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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI-YTACKHRGFVMISYYDIRAARNAMKALQN 336
            TL+V  +   V + +L+  F QFG+IR+I     +   FV  ++    AA  A + L N
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFV--TFTTREAAEKAAERLFN 59

Query: 337 K 337
           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 = 5e-05
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKH----NHKFIEFYDIRAAETALRTL 419
            L V  L  SV+ EEL ++F  +G ++ +R   ++        ++E+ +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 420 NRSDVAGKQIKLEASRPG 437
           + +++  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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-05
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAARNAMKA 333
           T+ V N++ + ++ +L+ LF  FG I  +Y A      + RGF  ++++    A  A++ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 334 LQ 335
           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|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 = 6e-05
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 281 FVRNINSNVEDSELKALFEQFGDI---RTIY--TACKHRGFVMISYYDIRAARNAMKALQ 335
           FV NI  +  + +L  +F + G +   R +      K +G+    + DI  A +A++ L 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 336 NKPLRRRKLDIHYS 349
                 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 = 6e-05
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 277 SRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           SR +FV N+N++ V   +L+ +F ++G I  I     H+G+  + + +   AR A+    
Sbjct: 1   SR-VFVGNLNTDKVSKEDLEEIFSKYGKILGISL---HKGYGFVQFDNEEDARAAVAGEN 56

Query: 336 NKPLRRRKLDI 346
            + +  +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 = 6e-05
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 12/71 (16%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA------ 333
           LFV N+ +++ + E K LF ++G++  ++   K +GF  I   D R   NA KA      
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVF-LNKEKGFGFIR-LDTRT--NAEKAKAELDG 59

Query: 334 --LQNKPLRRR 342
              + + 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 = 41.6 bits (98), Expect = 7e-05
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFG---DIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
           + L V NI     D +L+ +F QFG   D+  I+     +GF  +++ +   A  A + L
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 335 QNKPLRRRKLDIHYS 349
               +  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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 41.1 bits (96), Expect = 8e-05
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)

Query: 370 LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI 429
           L   V  +++ + FG YG++ EI     K+ + F+EF D R A+ A+  LN  D+ G+++
Sbjct: 7   LSYHVREKDIQRFFGGYGKLLEI---DLKNGYGFVEFEDSRDADDAVYELNGKDLCGERV 63

Query: 430 KLEASR 435
            +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 = 9e-05
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKAL 334
           LFV N++    + EL+A F + G IR +         K +GF  + + +I  A NA+K  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK-- 58

Query: 335 QNKPLRRRKLDIHY 348
             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|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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 333
           +LFVRN+       +L+  F ++G I  +Y        + RGF  I + D+R A +A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 334 LQNKPLRRRKLDIHYS 349
           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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEI--------REIRDTQHKHNHKFIEFYDIRAAETAL 416
           L V NL+  V+ E L Q FG +G +        R   + +   N  F+ F +   AE AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 417 RTLNRSDVAGKQIKL 431
             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|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 = 1e-04
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRA 326
            +  +  LFV  I  N+E+ +L+ LFEQFG I      +  YT   H+G   ++Y    +
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTG-MHKGCAFLTYCARES 59

Query: 327 ARNAMKALQNK 337
           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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRGFVMISYYDIRAARNAMKA 333
           + VRNI       EL+ LF  FG+++T+    K      HRGF  + +   + A+ A KA
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 334 LQ 335
           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|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 = 1e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQ 335
           T+FV  ++  V + EL++LF  FG+I  +Y      K  GFV   +    AA  A++ LQ
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEI--VYVKIPPGKGCGFV--QFVHRAAAEAAIQQLQ 58

Query: 336 NKPL 339
              +
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|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: 279 TLFVRNINSNVEDSELKALFEQFG---DIRTIY---TACKHRGFVMISYYDIRAARNAMK 332
            L+V N+  NV + +LK LF QFG     R I    T  + RGF  +       A  A++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETG-RSRGFGFVEMETAEEANAAIE 59

Query: 333 ALQNKPLRRRKL 344
            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|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 = 2e-04
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           T+ V  LD +V+ +EL  +FG +GEI  ++    K    F++F    AAE A++ L  + 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGC-GFVQFVHRAAAEAAIQQLQGTI 61

Query: 424 VAGKQIKL 431
           + 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|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: 364 TLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 422
           TL V   D  +   E++ ++F  +G +        +    F+EF D   A  AL  L+ S
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCD---IRKTFAFVEFEDSEDATKALEALHGS 57

Query: 423 DVAGKQIKLE 432
            + 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 40.9 bits (95), Expect = 2e-04
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 5/81 (6%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
           ++  L+V  L  +++ EE   +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 416 LRTLNRSDVAGKQIKLEASRP 436
           + 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|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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
           L V  L  +V+ + L +IF  YG ++++     R+      + ++EF     AE A++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 420 NRSDVAGKQIKLE 432
           +   + 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|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: 365 LVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           L+V NL+   V+ + L  +FG+YG++  ++   +K +   I+  D + A+TAL  LN   
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61

Query: 424 VAGKQIKLEASR 435
           + 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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIR-TIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           +RTLFV+N+  N+   ELK +FE   DIR         +G   I+Y + +    A KAL+
Sbjct: 3   ARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKG---IAYIEFKTEAEAEKALE 59

Query: 336 NK 337
            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 = 2e-04
 Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNR 421
           V N+D   + EEL + F   G I  I     + T       +IEF D  + E AL  LN 
Sbjct: 4   VGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLNE 62

Query: 422 SDVAGKQIK 430
           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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 4/61 (6%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIY-TACK-HRGFVMISYYDIRAARNAMKALQN 336
           TL + N++  V    L+++F+ +GD++ +  T CK  + FV   ++D+R A  A++A+  
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFV--EFFDVRDAAKALRAMNG 60

Query: 337 K 337
           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|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 39.6 bits (92), Expect = 3e-04
 Identities = 17/60 (28%), Positives = 34/60 (56%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           ++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|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: 369 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ 428
            L       ++ + F  YG IREI     K+   F+EF D R A+ A+  LN  ++ G++
Sbjct: 6   RLPYRARERDVERFFKGYGRIREI---NLKNGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 429 IKLEASRP 436
           + +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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI---RD--TQHKHNHKFIEFYDIRAAETALRTL 419
           L V NL  +++ ++L  IF  +GEI  +   RD  T     + FI+F D   A+ AL  L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 420 NRSDVAGKQIKL 431
           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|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 = 3e-04
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 7/61 (11%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRAARNAMKA 333
           L+V N++ N+ + +L+ +FE FG+I      R   T  + +G+  I + D   A+ A++ 
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETG-RSKGYGFIQFADAEDAKKALEQ 59

Query: 334 L 334
           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|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: 363 GTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALR 417
           G L +  L    + + L Q+F  YG+I E+     R+TQ      F+ F +   A+ A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 418 TLNRSDVAGKQIKLE 432
            +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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 369 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN-RSDVAGK 427
           NL  S S EEL +    +G I +I+  + K N  F+ F  I  A   + TL    D A +
Sbjct: 10  NLPESYSEEELREDLEKFGPIDQIKIVKEK-NIAFVHFLSIANAIKVVTTLPCEPDYASR 68

Query: 428 QI 429
           +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|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: 367 VFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 424
           V NL   +   ++  +F  YG I+ I  ++ +      F+EF D R AE A+R  +  D 
Sbjct: 4   VGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGYDF 63

Query: 425 AGKQIKLE 432
            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|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 = 3e-04
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           LFV N+  ++ + E++ LFE++G    I+   K +GF  I       A  A   L N PL
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIH-KDKGFGFIRLETRTLAEIAKAELDNMPL 62

Query: 340 RRRKLDIHY 348
           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|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 = 3e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           TL V NL   V+   + Q+F   G  +    I DT     + F+EF++ R A  +L  +N
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60

Query: 421 RSDVAGKQIKL 431
              + 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|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: 355 PSEKDANQGTLVVFNL-DSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 413
           P         L+V NL +  V+ + L  +FG+YG+++ ++   +K +   I+  D   ++
Sbjct: 6   PGVSAGGNTVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQ 65

Query: 414 TALRTLNRSDVAGKQIKLEASR 435
            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|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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----RGFVMISYYDIRAARNAMKALQ 335
           + V+N+       +++ LF  +G ++++    K     RGF  + +   + A NAM AL+
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 336 NKPLRRRKLDIHYS 349
           +  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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 424
           L V NL ++V+ E L + FG +G++  ++  +   ++ FI F +   A  A+  +N  ++
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLK---DYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 425 AGKQIKLEASRP 436
            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 = 4e-04
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRAARNAMKA 333
           +FV +++  ++   L+A F  FG+I      + + T  K +G+  +S+     A NA+++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTG-KSKGYGFVSFVKKEDAENAIQS 60

Query: 334 LQNKPLRRRKL 344
           +  + 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|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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           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|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 = 5e-04
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
           L V NL    + ++L ++F  YGE+ ++     R T+      F+ FYD R AE A+  +
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 420 NRSDVAGKQIK 430
           +  ++ 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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 39.3 bits (92), Expect = 5e-04
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMK 332
           +RTLFV N+   + + EL+  FE++G +  +      RG    +  + + ++  A  A  
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61

Query: 333 ALQNKPLRRRKLDIHY 348
           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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 373 SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
            VS E+L +IF  YGE+ +I     K+ + F++F    +   A+       + G+++ LE
Sbjct: 11  RVSKEDLFRIFSTYGELAQI---VLKNAYGFVQFDSPESCANAINCEQGKMIRGRKLHLE 67

Query: 433 ASRP 436
            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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMI-----SYYDIRAARNAMKAL 334
           LFV N+ +++ + + K LFE++G+   ++   + RGF  I     +  +I  A      L
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 62

Query: 335 QNKPLRRR 342
           +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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 39.2 bits (92), Expect = 6e-04
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 7/67 (10%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDI------RTIYTACKHRGFVMISYYDIRAARN 329
           P  TLFV  ++    +  L+ +F ++GDI      R I T    +G+  + Y   R A  
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTG-FSKGYAFVEYEHERDALR 60

Query: 330 AMKALQN 336
           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 = 6e-04
 Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 277 SRTLFVRNINSNVED-SELKALFEQFGDIRTIYTACKH----RGFVMISYYDIRAARNAM 331
           SR LFV  +     D S L+ LF Q G       A       RGF  + Y     A  A 
Sbjct: 2   SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 332 KALQNKPLRRRKLDIHYSIP 351
           +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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 42.6 bits (100), Expect = 6e-04
 Identities = 47/192 (24%), Positives = 83/192 (43%), Gaps = 26/192 (13%)

Query: 277 SRT-LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRA 326
           S+T L V  +   +   E+++LF   G+I +    CK           G+  ++Y     
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIES----CKLVRDKVTGQSLGYGFVNYVRPED 57

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 386
           A  A+ +L    L+ + + + Y+ P  + S K AN   L V  L  +++  EL  IF  +
Sbjct: 58  AEKAVNSLNGLRLQNKTIKVSYARPS-SDSIKGAN---LYVSGLPKTMTQHELESIFSPF 113

Query: 387 GEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAG--KQIKLE-ASRPGG 438
           G+I   R              FI F     A+ A++TLN +  +G  + I ++ A+ P  
Sbjct: 114 GQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSS 173

Query: 439 ARRFMVQSEQEQ 450
           +    + 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKF-----IEFYDIRAAETALRTL 419
           L V NL      + +++ FG YGEI  +R      + +      +EF    AA+ AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 420 NRSDVAGKQIKLE 432
             +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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 38.9 bits (91), Expect = 7e-04
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 5/76 (6%)

Query: 279 TLFVRNINSNVEDSELKALFEQFG---DIRTIYT--ACKHRGFVMISYYDIRAARNAMKA 333
           TLFV N++ +V+D  LKA FE+FG     R I      + RGF  + +     A+ A++A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 334 LQNKPLRRRKLDIHYS 349
           +  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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 38.7 bits (91), Expect = 7e-04
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI---RD--TQHKHNHKFIEFYDIRAAETALRTL 419
           L V +L   V+   L++IF   G +  I   RD  T+    + ++ F +   AE AL TL
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 420 NRSDVAGKQIKL 431
           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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 39.2 bits (92), Expect = 7e-04
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI 307
           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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI---RDTQHKHNHK---FIEFYDIRAAETALRT 418
           L V  L   V  + LH  F  +G+I++I    D      H+   F+EF +   A  A+  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLD-YETQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 419 LNRSDVAGKQIK 430
           +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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 38.8 bits (91), Expect = 8e-04
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 9/73 (12%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGD------IRTIYT-ACKHRGFVMISYYDIRAARNAM 331
            +FV N+  + ++S L  LF  FG       IR + T  CK  GFV ++ Y+   A +A+
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE--EAYSAI 60

Query: 332 KALQNKPLRRRKL 344
            +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|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 = 8e-04
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 5/68 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-HKHNHK---FIEFYDIRAAETALRTL 419
           T+ V NLD SV  +EL ++F   GEI ++R  + +K   K   ++EF +  + + AL  L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-KL 59

Query: 420 NRSDVAGK 427
           +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|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 = 9e-04
 Identities = 18/68 (26%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 365 LVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           L+V+ LD   ++ ++L  +F +YG +  I+  + K     ++  D +AAE A+  LN   
Sbjct: 2   LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVV 61

Query: 424 VAGKQIKL 431
           + 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMK 332
             L V  +  ++   EL++LFE  G I +          +  G+  + Y D   A+ A+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 333 ALQNKPLRRRKLDIHY 348
            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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 12/77 (15%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDI--------RTIYTACKHR--GFVMISYYDIRAARN 329
           L+V N+N  V +  L   F +FG +        RT     ++R  GFV  ++ +   A  
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFV--AFMNRADAER 61

Query: 330 AMKALQNKPLRRRKLDI 346
           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|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: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRT-IYTACKHRGFVMISYYDIRAARNAMKALQ 335
           SRTLF   +  N+ + +L++ F +FG++++ I    K   FV +  Y+ R A NA +A++
Sbjct: 3   SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKM--YNRRDAENAREAME 60

Query: 336 NKP 338
              
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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----RGFVMISYYDIRAARNAMKAL 334
           TLFV N++ + E  +L+  F++ G++  +  A       +GF  + +     A+ A+   
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59

Query: 335 QNKPLRRRKL 344
             + 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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 42.4 bits (99), Expect = 0.001
 Identities = 36/169 (21%), Positives = 87/169 (51%), Gaps = 17/169 (10%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAARNAMKAL 334
           ++V +I+  + +  ++  F+ FG I++I  +      KH+GF  + Y    AA+ A++ +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 335 QNKPL--RRRKLDIHYSIPKDNP----SEKDANQGTLV-VFNLDSSVSTEELHQIFGIYG 387
             + L  R  K+    ++P+  P     +++A +   + V ++   +S  ++  +F  +G
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229

Query: 388 EIREIR----DTQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
           EI + +     T   H  + FIE+ ++++   A+ ++N  D+ G+ +++
Sbjct: 230 EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 38.6 bits (89), Expect = 0.001
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHN--HKFIEFYDIRAAETALRTLN 420
           TL V NL   V+   + Q+F   G  +  +  T+H  N  + F+EFY+ R A  AL  +N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 421 RSDVAGKQIKLE-ASRPGGAR 440
              + 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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK----FIEFYDIRAAETALRTLN 420
           L+V NL    +  +L ++F  +G + E+   +     K    F++F     AE A++ +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 421 RSDVAGKQI 429
              + 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|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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
           TL + +L+  +    ++  F   GE+  ++  ++K   K     F+EF    AAE AL++
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 419 LNRSDVAGKQIKLEASRPGGARRF 442
           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|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 = 0.001
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           LFV N+ +++ + E K LF ++G+   ++   K +GF  I       A  A   L + P+
Sbjct: 4   LFVGNLPADITEDEFKKLFAKYGEPGEVFIN-KGKGFGFIKLESRALAEIAKAELDDTPM 62

Query: 340 RRRKLDIHY 348
           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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
            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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARNAMKAL 334
            LFV  +  +V   EL+ LF++ G ++++      + K +G   + Y +  +A  A+  +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 335 QNKPLRRRKLDIHYSIP 351
               ++ + + +  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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARNAMKALQ 335
           L VRN+     +++LK LF  FG +  +        K +GF  + +     A  A+K + 
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 336 NKPLRRRKLDIHYSI 350
            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|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: 280 LFVRNINSNVEDSELKALFEQFGDIRTI--------YTACKHRGFVMISYYDIRAARNAM 331
           L+V N++    + ++  LF + GDI+ I         T C   GF  + YY    A NA+
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPC---GFCFVEYYTREDAENAV 57

Query: 332 KAL 334
           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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 419
           L V NL    + E+++++F   G+I+ I     +         F+E+Y    AE A++ L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 420 NRSDVAGKQIKLE 432
           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|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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALRTLNR 421
           T+ V NL   +   E+  +F  YG I +I  +       + FIEF D R AE A+R  + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 422 SDVAGKQIKLE 432
            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|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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAM 331
            +++ ++     + ELK  F QFG ++ +  A        KH GF  I + +   A  A 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGF--IQFLNPEVAAIAA 58

Query: 332 KALQNKPLRRRKLDIHY 348
           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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK--------HNHKFIEFYDIRAAETA 415
            L + NLDS ++   L ++F  YG+I++     HK          + F+ F     AE A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 416 LRTLNRSDVAGKQI 429
           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 = 0.002
 Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 7/86 (8%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQF-----GDIRTIYTACK-HRGFVMISYYDIRAA 327
           E  S+T+ +R +  N+ +++++ L E F      D+R +       RGF  + +Y ++ A
Sbjct: 2   EKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDA 61

Query: 328 RNAMKALQNK-PLRRRKLDIHYSIPK 352
            + 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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           TL + +L   V+ E+L  +F  YGEI+ I D        ++     + A  AL+ L    
Sbjct: 4   TLWIGHLSKKVTEEDLKNLFEEYGEIQSI-DMIPPRGCAYVCMETRQDAHRALQKLRNVK 62

Query: 424 VAGKQIKL 431
           +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 = 0.003
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG---FVMISYYDIRAARNAMKAL 334
           RT++V N++      +L   F Q G+++ +  A        +  + + +  +  NA+K L
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALK-L 63

Query: 335 QNKPLRRRKLDIHYSI 350
                  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 = 0.003
 Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 18/89 (20%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
           TL V  L+   +  +L + F  YG I+ IR  + K   K     FIEF   R  + A + 
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK- 61

Query: 419 LNRSDVAGKQIKLEASRPGGARRFMVQSE 447
                  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 = 0.003
 Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           ++V N+ +     EL+  F  +G +RT++ A    GF  + + D R A +A++ L  K +
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 340 --RRRKLDIHYSIPK 352
              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 = 36.9 bits (85), Expect = 0.003
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 337
           + LFVRN+ + V +  L+  F QFG +  +    K + +  I + +   A  AM+ +  K
Sbjct: 2   KVLFVRNLANTVTEEILEKAFGQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGK 58

Query: 338 PLRRRKLDIHYSIP 351
            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|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: 280 LFVRNINSNVEDSELKALFEQFG---DIR-TIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           +FV  I  ++ + EL  LFE+ G   ++R  +  +  +RG+  ++Y +  AA+ A+K L 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 336 NKPLRRRKL 344
           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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 37.4 bits (86), Expect = 0.003
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETALRTL 419
           L+V  L  +++ +EL  +F   GE+     IRD    H   + F+ + + + AE A+ TL
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 420 NRSDVAGKQIKLEASRP 436
           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 = 0.003
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMK 332
           +RTLF+ N++  V +++L+  F++FG I  +      RG    +  + + ++  A  A  
Sbjct: 7   NRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKL 66

Query: 333 ALQNKPLRRRKLDIHY 348
           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

>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 = 0.003
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIR--TIYT--ACKHRGFVMISYYDIRAARNAMKA 333
           RTLFV N+++ V +  L  LF Q G +    I      K + F  +++    +   A++ 
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 334 LQNKPLRRRKLDI 346
           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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEFYDIRAAETALR 417
           TL V NL    + E+L + F   G I+    ++D   K   +   ++ F     A+ AL 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSK-KCRGFGYVTFALEEDAKRALE 59

Query: 418 TLNRSDVAGKQIKLEASRP 436
              ++   G++I +E ++ 
Sbjct: 60  EKKKTKFGGRKIHVEFAKK 78

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 = 36.8 bits (86), Expect = 0.004
 Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 10/81 (12%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK----------FIEFYDIRAAE 413
           TL V NL+   + E L + F   G +R +   + K              F+EF    AA+
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 414 TALRTLNRSDVAGKQIKLEAS 434
            AL+ L  + + G  ++L+ S
Sbjct: 62  KALKRLQGTVLDGHALELKLS 82

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

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIR--TIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           T++     ++   S++K LFE  G +R  T+ +    +    I++ ++ AA+ A++ L  
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR-TVQPHAFITFENLEAAQLAIETLNG 59

Query: 337 KPLRRRKLDIHY 348
             +    + +  
Sbjct: 60  ASVDGNCIKVQR 71

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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 36.8 bits (86), Expect = 0.004
 Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAMKALQ 335
           +F++N++ ++++  L   F  FG+I +   A       +G+  + +    AA  A++ + 
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 336 NKPLRRRKL 344
              L  +K+
Sbjct: 65  GMLLNDKKV 73

This subfamily corresponds to the RRM2 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 mammalian, such as ovary and testis. It may play an important role in germ cell development. 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 = 77

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDI-RTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 338
           L +RN+  +V +S+L AL   FG +   +    K++  V      + +A++ +      P
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALV--EMDSVESAKSMVDYYLTVP 59

Query: 339 LRRRKLDIH--YS 349
              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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	861
KOG4660	549	consensus Protein Mei2, essential for commitment t	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.93
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.92
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.91
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.91
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.91
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.91
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.91
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.9
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	99.89
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.89
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.88
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.87
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.87
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.86
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.86
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.86
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.86
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.84
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.83
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.82
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.82
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.79
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.77
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.75
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.74
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.69
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.66
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.66
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.65
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.64
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.62
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.61
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.58
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.54
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.47
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.47
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.43
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.39
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.37
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.36
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.36
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.34
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.32
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.31
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.31
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.31
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.26
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.24
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.22
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.2
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.19
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.18
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.16
PLN03120	260	nucleic acid binding protein; Provisional	99.15
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.14
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.14
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.13
PLN03120	260	nucleic acid binding protein; Provisional	99.12
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.11
PLN03213	759	repressor of silencing 3; Provisional	99.1
PLN03213	759	repressor of silencing 3; Provisional	99.09
smart00362	72	RRM_2 RNA recognition motif.	99.09
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.08
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.08
smart00362	72	RRM_2 RNA recognition motif.	99.07
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.05
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.05
KOG0122	270	consensus Translation initiation factor 3, subunit	99.05
KOG0122	270	consensus Translation initiation factor 3, subunit	99.04
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.03
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.03
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.01
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.0
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.99
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.97
smart00360	71	RRM RNA recognition motif.	98.97
PLN03121	243	nucleic acid binding protein; Provisional	98.96
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.96
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.94
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.94
PLN03121	243	nucleic acid binding protein; Provisional	98.93
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.93
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.93
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.91
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.9
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.9
smart00360	71	RRM RNA recognition motif.	98.9
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.89
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.88
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.82
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.81
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.8
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.8
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.77
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.76
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.76
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.76
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.75
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.73
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.73
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.7
smart00361	70	RRM_1 RNA recognition motif.	98.63
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.59
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.57
smart00361	70	RRM_1 RNA recognition motif.	98.56
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.56
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.54
KOG0226	290	consensus RNA-binding proteins [General function p	98.49
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.48
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.47
KOG4210	285	consensus Nuclear localization sequence binding pr	98.46
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.36
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.34
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.27
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.26
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.13
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.09
KOG0151	877	consensus Predicted splicing regulator, contains R	98.07
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.04
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.02
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.01
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.96
KOG0151	877	consensus Predicted splicing regulator, contains R	97.91
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.88
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.85
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.85
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.84
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.83
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.81
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.73
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.73
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.68
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.62
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.62
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.62
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.62
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.54
KOG0226	290	consensus RNA-binding proteins [General function p	97.47
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.45
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.4
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.27
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.12
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.68
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.66
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.63
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.6
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.52
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.46
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.42
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.41
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.37
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.36
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.12
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.11
KOG4210	285	consensus Nuclear localization sequence binding pr	95.8
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.73
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	95.7
KOG3152	278	consensus TBP-binding protein, activator of basal	95.58
KOG3152	278	consensus TBP-binding protein, activator of basal	95.51
KOG2314	698	consensus Translation initiation factor 3, subunit	95.2
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.19
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.83
KOG2314	698	consensus Translation initiation factor 3, subunit	94.73
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.54
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.45
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	94.15
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.0
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	93.93
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	93.79
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	93.14
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	92.79
KOG2591	684	consensus c-Mpl binding protein, contains La domai	92.73
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	92.73
KOG2135	526	consensus Proteins containing the RNA recognition	91.67
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	91.51
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.4
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	91.12
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	90.31
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	88.89
KOG1996	378	consensus mRNA splicing factor [RNA processing and	88.33
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	85.84
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	85.11
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	84.24
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	83.87
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	83.7
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	83.64
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	82.82
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	82.74
KOG2135	526	consensus Proteins containing the RNA recognition	82.39
KOG2068	327	consensus MOT2 transcription factor [Transcription	82.14
KOG2068	327	consensus MOT2 transcription factor [Transcription	81.08
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	80.57

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

Probab=100.00  E-value=5.9e-49  Score=438.58  Aligned_cols=429  Identities=46%  Similarity=0.613  Sum_probs=298.0

Q ss_pred             ccccccccCCccccccCcchhhhccCCCcCCCccCCCCCCCcccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCC
Q 002974          224 EDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD  303 (861)
Q Consensus       224 ee~Dvf~s~GGmEle~d~~~s~~~s~s~~~gg~~~~~~~ng~~~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~  303 (861)
                      |++|+|+++||||++.+.-.+...+++.        ...++...+++|..+  +++ ||         .+|..+|++|+ 
T Consensus         2 ~d~~lf~~~G~~el~~~~~~~~~~~~~~--------~n~~~~~~~~~P~~~--s~~-~~---------~~l~a~f~~~~-   60 (549)
T KOG4660|consen    2 EDCDLFSSGGGMELDADSFDNLSVRNSD--------RNSAGFVFPEHPPGE--SRT-FV---------SELSALFEPFN-   60 (549)
T ss_pred             CccccccCCCCCCcccccccchhhcccc--------cCCCccccCCCCCCC--CCC-Ch---------hhHHhhhhccC-
Confidence            6789999999999998873222221111        133456677877777  777 87         78889999881 


Q ss_pred             EEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHh
Q 002974          304 IRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIF  383 (861)
Q Consensus       304 I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelF  383 (861)
                                                       +.+.           ++++.+++.++++|+|.|||..|++++|+++|
T Consensus        61 ---------------------------------~p~~-----------~~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f   96 (549)
T KOG4660|consen   61 ---------------------------------KPLR-----------PDNPSEKDMNQGTLVVFNLPRSVSNDTLLRIF   96 (549)
T ss_pred             ---------------------------------CCCC-----------cCCCCcccCccceEEEEecCCcCCHHHHHHHH
Confidence                                             1111           15667788999999999999999999999999


Q ss_pred             cccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchhhhchhhhhhhccccCCCCCCCCC
Q 002974          384 GIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDL  463 (861)
Q Consensus       384 skfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~rrl~qq~eq~q~E~~vgkNLp~s~  463 (861)
                      +.||+|++|+.+...+|.+||+|+|..+|++|+++|++.+|.|++|+    ++...++.+.-+....--..++..+.+++
T Consensus        97 ~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k----~~~~~~~~~~~~~~~~~~~~~~~p~a~s~  172 (549)
T KOG4660|consen   97 GAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK----RPGGARRAMGLQSGTSFLNHFGSPLANSP  172 (549)
T ss_pred             HhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc----CCCcccccchhcccchhhhhccchhhcCC
Confidence            99999999999999999999999999999999999999999999999    66666652211111111111334444444


Q ss_pred             CccccCCcccEEEEeCCCCCcceeecCCCCCcccccccccccccCCCCCCCCcccccCccccccCCCCcccccccCCC-C
Q 002974          464 SSGQMVSSGVITSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLDEMKFGNQ-H  542 (861)
Q Consensus       464 tee~Ls~fG~I~Sv~~enG~srGF~S~~~~p~~~~~~~~~~s~~p~~~ssp~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  542 (861)
                      ++.+.                |+   ....+|.|...    +                   .+.++..+++.-.=+ + .
T Consensus       173 pgg~~----------------~~---~~~g~l~P~~s----~-------------------~~~~~~~~~~~~~~~-~~~  209 (549)
T KOG4660|consen  173 PGGWP----------------RG---QLFGMLSPTRS----S-------------------ILLEHISSVDGSSPG-RET  209 (549)
T ss_pred             CCCCc----------------CC---cceeeeccchh----h-------------------hhhhcchhccCcccc-ccc
Confidence            44432                11   01111333331    1                   111221111111000 1 1


Q ss_pred             CCCCCCCCccccCCCCCCCCCCCCccccccccccCCccccCCCCccccccCCCCCCCCCCCCccCCCCCCCccCCCCCcc
Q 002974          543 PSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKDGLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHGNPYV  622 (861)
Q Consensus       543 ~~~~~hs~pe~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~g~~~~~~~~~~~~~~~~~~~~~g~~~~  622 (861)
                      +..+.    .+....+...+|..+  .                    .+ +  |.+        .++..++.+++|+   
T Consensus       210 ~~~~h----q~~~~~~~~~s~a~~--~--------------------~~-~--G~~--------~s~~~~v~t~S~~---  249 (549)
T KOG4660|consen  210 PLLNH----QRFVEFADNRSYAFS--E--------------------PR-G--GFL--------ISNSSGVITFSGP---  249 (549)
T ss_pred             cchhh----hhhhhhccccchhhc--c--------------------cC-C--cee--------cCCCCceEEecCC---
Confidence            12111    222333444444211  1                    00 1  332        3334455556555   


Q ss_pred             CCCCCCCCCCCCCCcccCCCCccCCCCcCCCCCCCCCCCCCCCcccCCCCC-CCcCcCCCCCCCCCccccccccCCCCCC
Q 002974          623 WNNSNSHQQHPSSPMVWPNSPSFLNGLHANRVAHMPGFPRVPPLMLNATSP-AHHHIGSAPAVNPSLWDRQHAYAGESPE  701 (861)
Q Consensus       623 w~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~hvgsap~~~~~~~~r~~~~~~~~~~  701 (861)
                                   .++|       |++.+++            ++-+.... .|||||+||+                  
T Consensus       250 -------------~g~~-------n~~~~~r------------~~~~~~~~~~~~hi~~~Ps------------------  279 (549)
T KOG4660|consen  250 -------------GGVW-------NPFPSRR------------QRQNSSSSHYEHHIGSAPS------------------  279 (549)
T ss_pred             -------------Cccc-------CCccccc------------cccccCcccccCccCCCcc------------------
Confidence                         2566       4454433            11112111 2999999998                  


Q ss_pred             CcccccccCCCCCCCCCCCCcccccc--ccccccCCCCCccCCC-CCcCCCCCcccCCCCCCCCCCccccCCCCcchHhh
Q 002974          702 TSNFHLGSLGSGGFLGRSPSHHVDIA--SQNILSHVGGNCMDMT-KNVGMRSPQQICHLFPGRNPMMSMQTSFDSSNERM  778 (861)
Q Consensus       702 ~~~~~~~~~~~~g~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~g~~s~~~~~~~f~g~~~~~~~~~~~~~~~~~~  778 (861)
                        ..|+.+-++++|.+..+.+.+..+  .+..|.+..||++|.. +++++.+.++....|-++.-+.   ..+|...+..
T Consensus       280 --~~~l~~~~~~~f~~~s~~~~~~~~~~~n~g~~~~t~~~~e~~s~n~~~e~~~rv~~~f~~~~~~~---~~~~~~~~~~  354 (549)
T KOG4660|consen  280 --MHHLLSRISVGFNGGSGALEMNSNGQANQGFLTKTGNVTEFNSKNVGMESSPRVPKNFEGRRSYT---SQNDYPVELI  354 (549)
T ss_pred             --cccccccCccccCCCCCCccccccccCCCCccccCcccccccCCCccccccCCCCcccccccccc---cccccccccc
Confidence              446677788899988888877665  4567888999999999 9999999999999999887433   3456666644


Q ss_pred             hhcccccCCCCCCcccccccccchhhhhcCCCcceeEEEeccCCCCCHHHHHHHHhhhCCCcccEEeecccCCCCC-eEE
Q 002974          779 RNLSYRRNESNSNHADKKQYELDIDRILRGDDSRTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASL-FGF  857 (861)
Q Consensus       779 r~~~~rr~~~~~~~~~~~~~~~~~~~i~~g~d~rtT~MirnIPn~~t~~~l~~~i~~~~~~~ydf~ylp~Df~~~~-~Gy  857 (861)
                      .+...||...+..+.+++++++|+.+|++|++.|||+||||||||||++||+++ ||.++|+||||||||||+||| |||
T Consensus       355 ~~~~~~Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~-d~~~~gtYDFlYLPiDF~nkcNvGY  433 (549)
T KOG4660|consen  355 LNYRDRRTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAA-DEKNKGTYDFLYLPIDFKNKCNVGY  433 (549)
T ss_pred             cccccchhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhh-hccccCccceEEeccccccccccce
Confidence            444559999888888899999999999999999999999999999999999999 999999999999999999999 999


Q ss_pred             Eee
Q 002974          858 FFH  860 (861)
Q Consensus       858 aFi  860 (861)
                      |||
T Consensus       434 AFI  436 (549)
T KOG4660|consen  434 AFI  436 (549)
T ss_pred             eEE
Confidence            998

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

Probab=99.96  E-value=6.9e-29  Score=290.26  Aligned_cols=291  Identities=19%  Similarity=0.262  Sum_probs=215.3

Q ss_pred             HhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-ccccCcchhhhccCCCcCCCc--cCCCCCCCccc
Q 002974          192 TIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEGDDRLFAVQKNSDFVGGV--SNQGVSAGSVV  267 (861)
Q Consensus       192 ~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~d~~~s~~~s~s~~~gg~--~~~~~~ng~~~  267 (861)
                      +||||.++. ++-|..++..+|.+.......|..    ....-|+ -++.....++..++..+++..  ++.....+...
T Consensus         4 ~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~----t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         4 YVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSV----TRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             EEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC----CCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            689999988 888888988888765554444321    1111122 122222223333344443211  11111111111


Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcce
Q 002974          268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  343 (861)
Q Consensus       268 Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~  343 (861)
                       +........++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..+.++.
T Consensus        80 -~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~  158 (562)
T TIGR01628        80 -DPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKE  158 (562)
T ss_pred             -cccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCce
Confidence             11112234678999999999999999999999999999985    4678999999999999999999999999999999


Q ss_pred             eeeeecCCCCCC-CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHH
Q 002974          344 LDIHYSIPKDNP-SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRT  418 (861)
Q Consensus       344 L~V~~a~~k~~~-~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~  418 (861)
                      |.|.....+... .......++|||+||+.++|+++|+++|++||+|.++++    .++.+|||||+|.+.++|.+|++.
T Consensus       159 i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~  238 (562)
T TIGR01628       159 VYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE  238 (562)
T ss_pred             EEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHH
Confidence            999887765544 223455678999999999999999999999999999876    345689999999999999999999


Q ss_pred             hCCCeeC----CcEEEEEeccCCchhh--hchhhhhhhcc-------ccCC-CCCCCCCCcccc----CCcccEEEEe--
Q 002974          419 LNRSDVA----GKQIKLEASRPGGARR--FMVQSEQEQDD-------LNLC-QIPFDDLSSGQM----VSSGVITSTC--  478 (861)
Q Consensus       419 LNG~~I~----Gr~IkVe~Akpk~~rr--l~qq~eq~q~E-------~~vg-kNLp~s~tee~L----s~fG~I~Sv~--  478 (861)
                      |+|..|.    |+.|.|.+++.+.++.  +....++.+.+       ..++ +||+.++++++|    ..||.|++++  
T Consensus       239 l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~  318 (562)
T TIGR01628       239 MNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVM  318 (562)
T ss_pred             hCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEE
Confidence            9999999    9999999998887664  11112211111       1133 999999999999    8999999998  


Q ss_pred             -CCCCCccee
Q 002974          479 -MDNGSIQVL  487 (861)
Q Consensus       479 -~enG~srGF  487 (861)
                       +.+|.++||
T Consensus       319 ~d~~g~~~g~  328 (562)
T TIGR01628       319 LDEKGVSRGF  328 (562)
T ss_pred             ECCCCCcCCe
Confidence             677889987

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.96  E-value=5.4e-29  Score=258.43  Aligned_cols=214  Identities=19%  Similarity=0.389  Sum_probs=182.0

Q ss_pred             HHHHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCccccccCcchhhhccCCCcCCCccCCCCCCCccc
Q 002974          189 EAQTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVV  267 (861)
Q Consensus       189 eaq~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGmEle~d~~~s~~~s~s~~~gg~~~~~~~ng~~~  267 (861)
                      ...++|||++++ ||||+.++.++|.+..++.+-|  |..+.-.       ..+                          
T Consensus         7 rtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~--e~~v~wa-------~~p--------------------------   51 (321)
T KOG0148|consen    7 RTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD--ELKVNWA-------TAP--------------------------   51 (321)
T ss_pred             ceEEeeccChhhHHHHHHHHHHhccccccceeehh--hhccccc-------cCc--------------------------
Confidence            357899999999 9999999999999999988775  2111000       000                          


Q ss_pred             CCCC-CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCc
Q 002974          268 GEHP-YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR  341 (861)
Q Consensus       268 Ge~~-~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G  341 (861)
                      +... ......-.+||+.|.+.++-++|++.|.+||+|.++++     |+|+|||+||.|...++|++||..|+|+.|.+
T Consensus        52 ~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~  131 (321)
T KOG0148|consen   52 GNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGR  131 (321)
T ss_pred             ccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeecc
Confidence            1001 12223668999999999999999999999999999985     89999999999999999999999999999999


Q ss_pred             ceeeeeecCCCCCCCC------------cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCH
Q 002974          342 RKLDIHYSIPKDNPSE------------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDI  409 (861)
Q Consensus       342 r~L~V~~a~~k~~~~~------------k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~  409 (861)
                      |.|+.+|+..|.....            ....+++|||+|++.-++|++||+.|++||.|.+||+. +.+||+||+|.++
T Consensus       132 R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvF-k~qGYaFVrF~tk  210 (321)
T KOG0148|consen  132 RTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVF-KDQGYAFVRFETK  210 (321)
T ss_pred             ceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEe-cccceEEEEecch
Confidence            9999999987753211            12457899999999999999999999999999999987 5689999999999


Q ss_pred             HHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          410 RAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       410 eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      |+|..||..+|+++|.|..++|.|.+...
T Consensus       211 EaAahAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  211 EAAAHAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             hhHHHHHHHhcCceeCceEEEEeccccCC
Confidence            99999999999999999999999998765

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=3.2e-28  Score=267.33  Aligned_cols=159  Identities=23%  Similarity=0.409  Sum_probs=143.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      +.++|||+|||.+++|++|+++|++||+|..|++     +++++|||||+|.+.++|++||+.|+|+.|.|+.|+|.|+.
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            4789999999999999999999999999999985     57899999999999999999999999999999999999997


Q ss_pred             CCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       351 ~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                      ++..    .....+|||+|||..+++++|+++|++||.|..+++     .+..+|||||+|.+.++|++|++.|||..+.
T Consensus        82 ~~~~----~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~  157 (352)
T TIGR01661        82 PSSD----SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS  157 (352)
T ss_pred             cccc----ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccC
Confidence            6543    234568999999999999999999999999998775     3456899999999999999999999999988


Q ss_pred             C--cEEEEEeccCCc
Q 002974          426 G--KQIKLEASRPGG  438 (861)
Q Consensus       426 G--r~IkVe~Akpk~  438 (861)
                      |  ++|+|.++....
T Consensus       158 g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       158 GCTEPITVKFANNPS  172 (352)
T ss_pred             CCceeEEEEECCCCC
Confidence            7  678999886544

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=2.6e-27  Score=262.16  Aligned_cols=163  Identities=24%  Similarity=0.413  Sum_probs=146.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ......++|||+|||+++||++|+++|++||+|+.|++     +++++|||||+|.++++|++|++.|+++.|.+++|+|
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            34557899999999999999999999999999999985     5778999999999999999999999999999999999


Q ss_pred             eecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCC
Q 002974          347 HYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNR  421 (861)
Q Consensus       347 ~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG  421 (861)
                      .|+.+...    ....++|||+|||..+++++|+++|++||+|+.|++     ++++|+||||+|.+.++|++||+.||+
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    234578999999999999999999999999999876     455689999999999999999999999


Q ss_pred             CeeCC--cEEEEEeccCCc
Q 002974          422 SDVAG--KQIKLEASRPGG  438 (861)
Q Consensus       422 ~~I~G--r~IkVe~Akpk~  438 (861)
                      ..+.+  ++|+|.+++...
T Consensus       258 ~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       258 VIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CccCCCceeEEEEECCccc
Confidence            98876  789999998764

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).

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

Probab=99.95  E-value=2.5e-27  Score=277.23  Aligned_cols=203  Identities=20%  Similarity=0.325  Sum_probs=174.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      +|||+|||+++||++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            7999999999999999999999999999985     57889999999999999999999999999999999999986432


Q ss_pred             CCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       354 ~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                        ..+....++|||+||+.++++++|+++|++||.|.+|++    .++++|||||+|.+.++|++|++.|||..+.|+.|
T Consensus        82 --~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i  159 (562)
T TIGR01628        82 --SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEV  159 (562)
T ss_pred             --cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceE
Confidence              223334678999999999999999999999999999876    34678999999999999999999999999999999


Q ss_pred             EEEeccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe---CCCCCccee
Q 002974          430 KLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC---MDNGSIQVL  487 (861)
Q Consensus       430 kVe~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~---~enG~srGF  487 (861)
                      .|.....+..+.    .........++ +||+.++++++|    ..||.|+++.   ..+|+++||
T Consensus       160 ~v~~~~~~~~~~----~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~  221 (562)
T TIGR01628       160 YVGRFIKKHERE----AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGF  221 (562)
T ss_pred             EEeccccccccc----cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccE
Confidence            998877665432    11111122344 999999999998    8999999887   667888776

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=99.94  E-value=2.8e-26  Score=252.00  Aligned_cols=244  Identities=16%  Similarity=0.212  Sum_probs=177.7

Q ss_pred             HHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-ccccCcchhhhccCCCcCCCccCCCCCCCcccC
Q 002974          191 QTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVG  268 (861)
Q Consensus       191 q~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~d~~~s~~~s~s~~~gg~~~~~~~ng~~~G  268 (861)
                      -+||||.++. ++-|..++..+|.+.......|...    ...-|+ -++.....++..++..+++..-......-..+ 
T Consensus         6 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-   80 (352)
T TIGR01661         6 LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVT----GQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA-   80 (352)
T ss_pred             EEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCC----CccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee-
Confidence            3589997777 8888889998988777766554321    111122 12222222333334444431111000000001 


Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCc--
Q 002974          269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--  341 (861)
Q Consensus       269 e~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G--  341 (861)
                      .........++|||+|||..+++++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++.|+|..+.|  
T Consensus        81 ~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~  160 (352)
T TIGR01661        81 RPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCT  160 (352)
T ss_pred             cccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCc
Confidence            11112335779999999999999999999999999998874     46789999999999999999999999999876  


Q ss_pred             ceeeeeecCCCCCCCC----------------c-----------------------------------------------
Q 002974          342 RKLDIHYSIPKDNPSE----------------K-----------------------------------------------  358 (861)
Q Consensus       342 r~L~V~~a~~k~~~~~----------------k-----------------------------------------------  358 (861)
                      ++|.|.|+........                .                                               
T Consensus       161 ~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (352)
T TIGR01661       161 EPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHA  240 (352)
T ss_pred             eeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccc
Confidence            5788888753321000                0                                               


Q ss_pred             -------------------------ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECC
Q 002974          359 -------------------------DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYD  408 (861)
Q Consensus       359 -------------------------~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d  408 (861)
                                               .....+|||+|||+++++++|+++|++||.|++|++     ++.+||||||+|.+
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~  320 (352)
T TIGR01661       241 AQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTN  320 (352)
T ss_pred             cccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECC
Confidence                                     000125999999999999999999999999999986     56789999999999


Q ss_pred             HHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          409 IRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       409 ~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      .++|.+|++.|||..|.||+|+|.|...+..
T Consensus       321 ~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       321 YDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            9999999999999999999999999998864

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.93  E-value=3.4e-25  Score=258.18  Aligned_cols=164  Identities=19%  Similarity=0.377  Sum_probs=145.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...++|||+|||+++++++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|||+.|.||.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            45789999999999999999999999999999985     6789999999999999999999999999999999999876


Q ss_pred             CCCCCC-------CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHH
Q 002974          350 IPKDNP-------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALR  417 (861)
Q Consensus       350 ~~k~~~-------~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~  417 (861)
                      ......       ........+|||+||+.++++++|+++|++||+|++|++     ++++||||||+|.+.++|.+||+
T Consensus       185 ~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~  264 (612)
T TIGR01645       185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  264 (612)
T ss_pred             ccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHH
Confidence            432211       011223579999999999999999999999999999986     34679999999999999999999


Q ss_pred             HhCCCeeCCcEEEEEeccCCc
Q 002974          418 TLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       418 ~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      .||+..|+|+.|+|.++.++.
T Consensus       265 amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       265 SMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             HhCCCeeCCeEEEEEecCCCc
Confidence            999999999999999988653

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.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.92  E-value=1.2e-24  Score=250.72  Aligned_cols=161  Identities=20%  Similarity=0.315  Sum_probs=138.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHc--CccccCcceeeeeecCCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL--QNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaL--nG~~L~Gr~L~V~~a~~k~  353 (861)
                      |+++|||+|||++++|++|+++|++||.|..|++ .+.|+||||+|++.++|++|++.+  ++..|.|++|+|+|+..+.
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i-~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~   79 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMM-LPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQE   79 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE-ECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcc
Confidence            5899999999999999999999999999999987 357899999999999999999874  7789999999999997653


Q ss_pred             CCCCc--------ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCC-ccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          354 NPSEK--------DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-HNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       354 ~~~~k--------~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgks-KGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      .....        .....+|||+||++.+|+++|+++|++||+|.+|.+..+. +++|||+|.+.++|.+|++.|||..|
T Consensus        80 ~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i  159 (481)
T TIGR01649        80 IKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADI  159 (481)
T ss_pred             cccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcc
Confidence            21111        0122479999999999999999999999999999874333 47999999999999999999999999


Q ss_pred             CC--cEEEEEeccCC
Q 002974          425 AG--KQIKLEASRPG  437 (861)
Q Consensus       425 ~G--r~IkVe~Akpk  437 (861)
                      .|  ++|+|+|++++
T Consensus       160 ~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       160 YNGCCTLKIEYAKPT  174 (481)
T ss_pred             cCCceEEEEEEecCC
Confidence            65  58999998763

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).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.91  E-value=7.4e-24  Score=241.32  Aligned_cols=163  Identities=26%  Similarity=0.450  Sum_probs=144.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .+.+.++|||+|||..+++++|+++|++||.|..|++     +++++|||||+|.+.++|++||. |+|+.+.|++|.|.
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            4567899999999999999999999999999999985     57889999999999999999996 99999999999999


Q ss_pred             ecCCCCCCCC--------cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHH
Q 002974          348 YSIPKDNPSE--------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAET  414 (861)
Q Consensus       348 ~a~~k~~~~~--------k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~k  414 (861)
                      ++........        .....++|||+|||..+++++|+++|++||.|..|.+.     ++.+|||||+|.+.++|.+
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            8754432211        11235799999999999999999999999999998763     4678999999999999999


Q ss_pred             HHHHhCCCeeCCcEEEEEeccC
Q 002974          415 ALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       415 AL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      |++.|||..|.|++|+|.++..
T Consensus       244 A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       244 ALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHhcCCcEECCEEEEEEEccC
Confidence            9999999999999999999884

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=99.91  E-value=1.1e-23  Score=230.77  Aligned_cols=197  Identities=20%  Similarity=0.290  Sum_probs=169.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccC-cceeeeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHY  348 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~-Gr~L~V~~  348 (861)
                      ...+.||||.||.++.|+||.-+|++.|+|.++++     ++.+||||||.|.+.++|++|++.||++.|+ |+.|.|..
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            55899999999999999999999999999999984     7999999999999999999999999999997 99999987


Q ss_pred             cCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCc-EEEEEe------CCCCccEEEEEECCHHHHHHHHHHhCC
Q 002974          349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRD------TQHKHNHKFIEFYDIRAAETALRTLNR  421 (861)
Q Consensus       349 a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGe-I~sVri------tgksKGfAFVeF~d~eaA~kAL~~LNG  421 (861)
                      +.          .+++|||+|||..+++++|++.|++.++ |+.|.+      ..++||||||+|+++.+|..|.++|-.
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            75          3578999999999999999999999986 555543      346799999999999999999988754


Q ss_pred             C--eeCCcEEEEEeccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEeCCCCCccee
Q 002974          422 S--DVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTCMDNGSIQVL  487 (861)
Q Consensus       422 ~--~I~Gr~IkVe~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~~enG~srGF  487 (861)
                      .  .+.|..+.|.||.|..+-.    .+.....+.++ +||+.++|+|.|    ..||.|+.|+.-.  --+|
T Consensus       231 g~~klwgn~~tVdWAep~~e~d----ed~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r--DYaF  297 (506)
T KOG0117|consen  231 GKIKLWGNAITVDWAEPEEEPD----EDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPR--DYAF  297 (506)
T ss_pred             CceeecCCcceeeccCcccCCC----hhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeeccc--ceeE
Confidence            4  5679999999999986433    22344555666 999999999999    7889999998442  2566

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.91  E-value=1.8e-23  Score=241.06  Aligned_cols=165  Identities=16%  Similarity=0.284  Sum_probs=138.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcC------------CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCcccc
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQF------------GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL  339 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqf------------G~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L  339 (861)
                      ......++|||||||+.+|+++|+++|.+|            +.|..+.+ ++.+|||||+|.+.++|++|| +|+|+.|
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            356678999999999999999999999975            34555555 678999999999999999999 5999999


Q ss_pred             CcceeeeeecCCCCCCC-------------------------CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe
Q 002974          340 RRRKLDIHYSIPKDNPS-------------------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD  394 (861)
Q Consensus       340 ~Gr~L~V~~a~~k~~~~-------------------------~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri  394 (861)
                      .|+.|+|..........                         ......++|||+|||..+++++|+++|+.||.|+.+.+
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            99999997543221000                         00122468999999999999999999999999998875


Q ss_pred             -----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          395 -----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       395 -----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                           ++.++|||||+|.+.++|..|++.|||..|.|++|+|.++....
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~  376 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGA  376 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCC
Confidence                 46679999999999999999999999999999999999986543

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.91  E-value=1.6e-23  Score=243.71  Aligned_cols=193  Identities=21%  Similarity=0.288  Sum_probs=159.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccC-cceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~-Gr~L~V~~a  349 (861)
                      ...++|||+|||++++|++|+++|++||.|..|++    ++++||||||+|.+.++|++||+.||+..+. |+.|.|.++
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            34699999999999999999999999999999985    6889999999999999999999999999986 788888665


Q ss_pred             CCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCc-EEEEEe------CCCCccEEEEEECCHHHHHHHHHHhCCC
Q 002974          350 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRD------TQHKHNHKFIEFYDIRAAETALRTLNRS  422 (861)
Q Consensus       350 ~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGe-I~sVri------tgksKGfAFVeF~d~eaA~kAL~~LNG~  422 (861)
                      .          ..++|||+|||.++++++|++.|+++++ ++++.+      ..+++|||||+|.++++|.+|++.|+..
T Consensus       136 ~----------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~g  205 (578)
T TIGR01648       136 V----------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPG  205 (578)
T ss_pred             c----------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhcc
Confidence            3          2578999999999999999999999864 444332      2356899999999999999999988643


Q ss_pred             --eeCCcEEEEEeccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCc--ccEEEEeCCC
Q 002974          423 --DVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSS--GVITSTCMDN  481 (861)
Q Consensus       423 --~I~Gr~IkVe~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~f--G~I~Sv~~en  481 (861)
                        .+.|+.|+|+|+.++....    .+.....+.++ +||+.++++++|    ..|  |+|+.|+...
T Consensus       206 ki~l~Gr~I~VdwA~p~~~~d----~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r  269 (578)
T TIGR01648       206 RIQLWGHVIAVDWAEPEEEVD----EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR  269 (578)
T ss_pred             ceEecCceEEEEeeccccccc----ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec
Confidence              6789999999998765221    11112223344 999999999999    788  9999997443

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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.91  E-value=1.6e-23  Score=243.87  Aligned_cols=235  Identities=20%  Similarity=0.296  Sum_probs=173.6

Q ss_pred             HHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-ccccCcchhhhccCCCcCCCccCCCCCCCcccC
Q 002974          191 QTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVG  268 (861)
Q Consensus       191 q~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~d~~~s~~~s~s~~~gg~~~~~~~ng~~~G  268 (861)
                      -.||||.++. ++-|..++..++.+.......|..     ...-|+ -++.....++..++..+++..-.    ++...+
T Consensus        61 lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~s-----G~sRGfaFV~F~~~e~A~~Ai~~lng~~i~----~Gr~l~  131 (578)
T TIGR01648        61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-----GQNRGYAFVTFCGKEEAKEAVKLLNNYEIR----PGRLLG  131 (578)
T ss_pred             EEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCC-----CCccceEEEEeCCHHHHHHHHHHcCCCeec----CCcccc
Confidence            5689998877 777888888888766665544421     122233 22222222233334444431111    011100


Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEe------CCCcccEEEEEeCCHHHHHHHHHHcCc--ccc
Q 002974          269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD-IRTIYT------ACKHRGFVMISYYDIRAARNAMKALQN--KPL  339 (861)
Q Consensus       269 e~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~-I~svki------tgksrGyAFVeF~d~e~A~kALkaLnG--~~L  339 (861)
                      -  ......++|||+|||+++++++|.+.|++++. +..+.+      +++++|||||+|.+.++|.+|++.|+.  ..+
T Consensus       132 V--~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l  209 (578)
T TIGR01648       132 V--CISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQL  209 (578)
T ss_pred             c--cccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEe
Confidence            0  11234789999999999999999999999964 333322      357899999999999999999998864  457


Q ss_pred             CcceeeeeecCCCCCCCCcc-cCCcceEEecccCCCcHHHHHHHhccc--CcEEEEEeCCCCccEEEEEECCHHHHHHHH
Q 002974          340 RRRKLDIHYSIPKDNPSEKD-ANQGTLVVFNLDSSVSTEELHQIFGIY--GEIREIRDTQHKHNHKFIEFYDIRAAETAL  416 (861)
Q Consensus       340 ~Gr~L~V~~a~~k~~~~~k~-~~~~tLfVgNLp~svTeedLrelFskf--GeI~sVritgksKGfAFVeF~d~eaA~kAL  416 (861)
                      .|+.|.|.|+.++....+.. ...++|||+||+.++++++|+++|++|  |+|++|++.   ++||||+|.+.++|++|+
T Consensus       210 ~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---rgfAFVeF~s~e~A~kAi  286 (578)
T TIGR01648       210 WGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---RDYAFVHFEDREDAVKAM  286 (578)
T ss_pred             cCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---cCeEEEEeCCHHHHHHHH
Confidence            89999999998876543322 234789999999999999999999999  999999864   689999999999999999


Q ss_pred             HHhCCCeeCCcEEEEEeccCCch
Q 002974          417 RTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       417 ~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      +.||+.+|.|+.|+|.|++++..
T Consensus       287 ~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       287 DELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHhCCCEECCEEEEEEEccCCCc
Confidence            99999999999999999998753

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=99.90  E-value=3.9e-23  Score=238.31  Aligned_cols=164  Identities=21%  Similarity=0.289  Sum_probs=142.1

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          274 EHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       274 ~~~srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ..++++|||+||++ .+++++|+++|++||.|..|++-...+|||||+|.+.++|++|++.|||..|.|++|+|.+++.+
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            45789999999998 69999999999999999999975556899999999999999999999999999999999988543


Q ss_pred             CCCCC------------c---------------------ccCCcceEEecccCCCcHHHHHHHhcccCc--EEEEEeCCC
Q 002974          353 DNPSE------------K---------------------DANQGTLVVFNLDSSVSTEELHQIFGIYGE--IREIRDTQH  397 (861)
Q Consensus       353 ~~~~~------------k---------------------~~~~~tLfVgNLp~svTeedLrelFskfGe--I~sVritgk  397 (861)
                      .....            +                     .....+|||+|||.++++++|+++|+.||.  |+.|++...
T Consensus       352 ~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~  431 (481)
T TIGR01649       352 NVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPK  431 (481)
T ss_pred             cccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecC
Confidence            11000            0                     012458999999999999999999999998  888887543


Q ss_pred             C---ccEEEEEECCHHHHHHHHHHhCCCeeCCcE------EEEEeccCC
Q 002974          398 K---HNHKFIEFYDIRAAETALRTLNRSDVAGKQ------IKLEASRPG  437 (861)
Q Consensus       398 s---KGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~------IkVe~Akpk  437 (861)
                      .   +++|||+|.+.++|.+||..||+..|.++.      |+|.+++++
T Consensus       432 ~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       432 DNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            3   789999999999999999999999999875      999999875

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).

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

Probab=99.89  E-value=3.6e-24  Score=196.37  Aligned_cols=49  Identities=61%  Similarity=1.127  Sum_probs=48.6

Q ss_pred             ceeEEEeccCCCCCHHHHHHHHhhhCCCcccEEeecccCCCCC-eEEEee
Q 002974          812 RTTLMIKNIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKASL-FGFFFH  860 (861)
Q Consensus       812 rtT~MirnIPn~~t~~~l~~~i~~~~~~~ydf~ylp~Df~~~~-~GyaFi  860 (861)
                      ||||||||||||||++||+++||+.|+|+||||||||||+++| +|||||
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFV   50 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFV   50 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEE
Confidence            8999999999999999999999999999999999999999999 999998

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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.89  E-value=5.2e-23  Score=224.58  Aligned_cols=165  Identities=21%  Similarity=0.414  Sum_probs=145.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccc-cCc--ceee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKP-LRR--RKLD  345 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~-L~G--r~L~  345 (861)
                      +.+.-+|||+-||..++|+||+++|++||.|.+|.     .++.++|||||.|.+.++|.+|+.+|+++. |.|  .+|.
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            35678999999999999999999999999999986     378899999999999999999999998865 555  5788


Q ss_pred             eeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCC
Q 002974          346 IHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNR  421 (861)
Q Consensus       346 V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG  421 (861)
                      |+|+.....+   -...++|||+-|+..++|.+++++|++||.|++|.+    .+.+||||||+|.+.+.|..||++|||
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            8888654332   244789999999999999999999999999999976    567899999999999999999999999


Q ss_pred             C-eeCC--cEEEEEeccCCchhh
Q 002974          422 S-DVAG--KQIKLEASRPGGARR  441 (861)
Q Consensus       422 ~-~I~G--r~IkVe~Akpk~~rr  441 (861)
                      . .+.|  .+|.|+||+++..|.
T Consensus       188 ~~tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  188 TQTMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             ceeeccCCCceEEEecccCCCch
Confidence            8 5666  689999999887665

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=5.3e-22  Score=217.72  Aligned_cols=164  Identities=22%  Similarity=0.426  Sum_probs=145.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEe------CCCcccEEEEEeCCHHHHHHHHHHcC-c-cccCcceee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGD-IRTIYT------ACKHRGFVMISYYDIRAARNAMKALQ-N-KPLRRRKLD  345 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~-I~svki------tgksrGyAFVeF~d~e~A~kALkaLn-G-~~L~Gr~L~  345 (861)
                      ...++|||||||++.++++|.+.|++.++ |+.|.+      +.++||||||+|++...|..|.+.|- + ..++|..+.
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~t  241 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAIT  241 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcce
Confidence            46899999999999999999999999986 555542      57899999999999999999998764 3 458899999


Q ss_pred             eeecCCCCCCCCcccC-CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          346 IHYSIPKDNPSEKDAN-QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       346 V~~a~~k~~~~~k~~~-~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      |.||.++....+.... -+.|||+||+.++|+|.|+++|++||+|+.|+..   |.||||.|.+.++|.+|++.+||++|
T Consensus       242 VdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~---rDYaFVHf~eR~davkAm~~~ngkel  318 (506)
T KOG0117|consen  242 VDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP---RDYAFVHFAEREDAVKAMKETNGKEL  318 (506)
T ss_pred             eeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecc---cceeEEeecchHHHHHHHHHhcCcee
Confidence            9999998887655333 4679999999999999999999999999999854   77999999999999999999999999


Q ss_pred             CCcEEEEEeccCCchhh
Q 002974          425 AGKQIKLEASRPGGARR  441 (861)
Q Consensus       425 ~Gr~IkVe~Akpk~~rr  441 (861)
                      .|..|.|.+|+|..+++
T Consensus       319 dG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  319 DGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             cCceEEEEecCChhhhc
Confidence            99999999999987655

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.87  E-value=1.1e-21  Score=202.93  Aligned_cols=161  Identities=24%  Similarity=0.425  Sum_probs=145.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      +...++|.|.-||..+|++||+.||...|+|++|+     +++.+.||+||.|-++++|++|+..|||..|+.+.|+|.|
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            44567899999999999999999999999999998     4899999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEE-----eCCCCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       349 a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVr-----itgksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      +.|..+    .+...+|||.+||..+|..||.++|++||.|..-+     +++.+||.+||.|....+|++||+.|||..
T Consensus       118 ARPSs~----~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  118 ARPSSD----SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             ccCChh----hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence            987543    34567899999999999999999999999987654     367889999999999999999999999998


Q ss_pred             eCC--cEEEEEeccCCc
Q 002974          424 VAG--KQIKLEASRPGG  438 (861)
Q Consensus       424 I~G--r~IkVe~Akpk~  438 (861)
                      -.|  .+|.|+++....
T Consensus       194 P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  194 PSGCTEPITVKFANNPS  210 (360)
T ss_pred             CCCCCCCeEEEecCCcc
Confidence            776  689999986544

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.87  E-value=1.3e-21  Score=218.36  Aligned_cols=195  Identities=20%  Similarity=0.287  Sum_probs=169.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      ..||||   +++||..|.++|+.+|+|+++++   .. +.|||||.|.++++|++||++||...+.|++|+|.|+.....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~   77 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDAT-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS   77 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCC-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc
Confidence            468999   99999999999999999999874   33 999999999999999999999999999999999999975332


Q ss_pred             CCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Q 002974          355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL  431 (861)
Q Consensus       355 ~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkV  431 (861)
                      .         |||.||+++++..+|.++|+.||+|.+|++.   ..+||| ||+|+++++|.+|+..+||..+.|++|.|
T Consensus        78 ~---------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~v  147 (369)
T KOG0123|consen   78 L---------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYV  147 (369)
T ss_pred             e---------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEE
Confidence            2         9999999999999999999999999999872   237899 99999999999999999999999999999


Q ss_pred             EeccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe---CCCCCccee
Q 002974          432 EASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC---MDNGSIQVL  487 (861)
Q Consensus       432 e~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~---~enG~srGF  487 (861)
                      ....++.+|...... ..+....+. ++++.+.+.+.+    ..||.|+++.   ...|+++||
T Consensus       148 g~~~~~~er~~~~~~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~  210 (369)
T KOG0123|consen  148 GLFERKEEREAPLGE-YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGF  210 (369)
T ss_pred             eeccchhhhcccccc-hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCc
Confidence            999988876522222 444555555 888888888888    8999999997   677878887

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.86  E-value=4e-21  Score=221.62  Aligned_cols=162  Identities=20%  Similarity=0.336  Sum_probs=136.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...++|||+|||..+++++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|+|..|.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999998874     5779999999999999999999999999999999999998


Q ss_pred             CCCCCCCC------------------------cccCCcceEEecccCC--C--------cHHHHHHHhcccCcEEEEEeC
Q 002974          350 IPKDNPSE------------------------KDANQGTLVVFNLDSS--V--------STEELHQIFGIYGEIREIRDT  395 (861)
Q Consensus       350 ~~k~~~~~------------------------k~~~~~tLfVgNLp~s--v--------TeedLrelFskfGeI~sVrit  395 (861)
                      ........                        ......+|+|.|+...  +        ..++|+++|++||.|+.|.+.
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            64322110                        0123467899999532  1        236899999999999999873


Q ss_pred             C--------CCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          396 Q--------HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       396 g--------ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .        ..+|+|||+|.+.++|++|+.+|||..|+|+.|.|.|...
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            2        2368999999999999999999999999999999999764

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.86  E-value=4.4e-21  Score=218.67  Aligned_cols=162  Identities=22%  Similarity=0.386  Sum_probs=137.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..++|||+|||..+++++|+++|++||.|..|.+     +++++|||||+|.+.++|.+|++.|+|..|.|+.|.|.|+.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            3799999999999999999999999999999985     35789999999999999999999999999999999999953


Q ss_pred             CCCCCC----------------------------------C---------------------------------------
Q 002974          351 PKDNPS----------------------------------E---------------------------------------  357 (861)
Q Consensus       351 ~k~~~~----------------------------------~---------------------------------------  357 (861)
                      ......                                  .                                       
T Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (457)
T TIGR01622       265 DSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGAL  344 (457)
T ss_pred             CCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccccccccc
Confidence            210000                                  0                                       


Q ss_pred             -------------cccCCcceEEecccCCCc----------HHHHHHHhcccCcEEEEEeC-CCCccEEEEEECCHHHHH
Q 002974          358 -------------KDANQGTLVVFNLDSSVS----------TEELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAE  413 (861)
Q Consensus       358 -------------k~~~~~tLfVgNLp~svT----------eedLrelFskfGeI~sVrit-gksKGfAFVeF~d~eaA~  413 (861)
                                   ......+|+|.||-...+          .+||++.|++||.|++|.+. +...|++||+|.++++|.
T Consensus       345 ~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~  424 (457)
T TIGR01622       345 AIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAAL  424 (457)
T ss_pred             ccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHHHH
Confidence                         012235788888854433          37899999999999999875 677899999999999999


Q ss_pred             HHHHHhCCCeeCCcEEEEEeccCC
Q 002974          414 TALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       414 kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      +|++.|||+.|+|+.|.|.+....
T Consensus       425 ~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       425 AAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             HHHHHhcCcccCCeEEEEEEEcHH
Confidence            999999999999999999998653

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.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.86  E-value=1.4e-21  Score=193.98  Aligned_cols=163  Identities=23%  Similarity=0.342  Sum_probs=144.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ....||||+||+..++++.|++||-+.|+|..+++     +.+.+|||||+|.++++|+-|++.|+...|.||+|+|..+
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            45789999999999999999999999999999984     6789999999999999999999999999999999999988


Q ss_pred             CCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEE----E--eCCCCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          350 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI----R--DTQHKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       350 ~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sV----r--itgksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      ... .  ..-....+|||+||.+.+++..|.+.|+.||.|...    +  .++++++||||.|.+.+++.+|+..+||..
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-Q--KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQY  163 (203)
T ss_pred             ccc-c--ccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccch
Confidence            721 1  122334799999999999999999999999988762    2  367889999999999999999999999999


Q ss_pred             eCCcEEEEEeccCCchh
Q 002974          424 VAGKQIKLEASRPGGAR  440 (861)
Q Consensus       424 I~Gr~IkVe~Akpk~~r  440 (861)
                      +..++|.|.++..++.+
T Consensus       164 l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  164 LCNRPITVSYAFKKDTK  180 (203)
T ss_pred             hcCCceEEEEEEecCCC
Confidence            99999999999876543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.86  E-value=3.3e-21  Score=215.14  Aligned_cols=288  Identities=20%  Similarity=0.284  Sum_probs=214.0

Q ss_pred             HHHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-ccccCcchhhhccCCCcCCCccCCCCCCCccc
Q 002974          190 AQTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVV  267 (861)
Q Consensus       190 aq~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~d~~~s~~~s~s~~~gg~~~~~~~ng~~~  267 (861)
                      ..++|   |++ ++.|-+++...+.+-....-.|. .      .=|. -+-.....++..++..++.     ...+++..
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t------slgy~yvnf~~~~da~~A~~~~n~-----~~~~~~~~   67 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T------SLGYAYVNFQQPADAERALDTMNF-----DVLKGKPI   67 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C------ccceEEEecCCHHHHHHHHHHcCC-----cccCCcEE
Confidence            34677   788 88888888888777666554443 1      1122 1111222333444555543     22222111


Q ss_pred             CCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCccee
Q 002974          268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  344 (861)
Q Consensus       268 Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L  344 (861)
                      -- -...++...|||.||+++++..+|.++|+.||+|++|++   ...++|| ||+|+++++|++|++.+||..+.+++|
T Consensus        68 ri-m~s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki  145 (369)
T KOG0123|consen   68 RI-MWSQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKI  145 (369)
T ss_pred             Ee-ehhccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCee
Confidence            00 011223333999999999999999999999999999996   2348999 999999999999999999999999999


Q ss_pred             eeeecCCCCCCCCcc----cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHH
Q 002974          345 DIHYSIPKDNPSEKD----ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETAL  416 (861)
Q Consensus       345 ~V~~a~~k~~~~~k~----~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL  416 (861)
                      .|.....+..+....    ...+.++|.|++.+++++.|..+|..||.|..+.+    .++.++|+||+|++.++|..|+
T Consensus       146 ~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av  225 (369)
T KOG0123|consen  146 YVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAV  225 (369)
T ss_pred             EEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHH
Confidence            999888776543322    33578999999999999999999999999999875    4567899999999999999999


Q ss_pred             HHhCCCeeCCcEEEEEeccCCchhh--hchhhhhhhccc-------cCC-CCCCCCCCcccc----CCcccEEEEe---C
Q 002974          417 RTLNRSDVAGKQIKLEASRPGGARR--FMVQSEQEQDDL-------NLC-QIPFDDLSSGQM----VSSGVITSTC---M  479 (861)
Q Consensus       417 ~~LNG~~I~Gr~IkVe~Akpk~~rr--l~qq~eq~q~E~-------~vg-kNLp~s~tee~L----s~fG~I~Sv~---~  479 (861)
                      +.|++..+.+..+.|..+..+.++.  +..+.++...+.       .++ +|++..++.+.|    ..||+|++++   +
T Consensus       226 ~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~  305 (369)
T KOG0123|consen  226 ETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD  305 (369)
T ss_pred             HhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEec
Confidence            9999999999999999999876665  333322222221       233 889999999999    7999999988   8


Q ss_pred             CCCCccee-ecCCCCC
Q 002974          480 DNGSIQVL-HSATRSP  494 (861)
Q Consensus       480 enG~srGF-~S~~~~p  494 (861)
                      +.|+++|| +-....+
T Consensus       306 ~~g~skG~gfV~fs~~  321 (369)
T KOG0123|consen  306 ENGKSKGFGFVEFSSP  321 (369)
T ss_pred             cCCCccceEEEEcCCH
Confidence            88999998 4433333

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.84  E-value=3.1e-21  Score=202.57  Aligned_cols=149  Identities=24%  Similarity=0.397  Sum_probs=139.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE  357 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~~~  357 (861)
                      -+|||||||..+++.+|+.||++||+|.+|.+   -|.||||..++..+|+.|++.|+|..|+|..|.|+-++.|     
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDI---vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK-----   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDI---VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK-----   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeee---ecccceEEeecccccHHHHhhcccceecceEEEEEecccc-----
Confidence            36999999999999999999999999999997   5789999999999999999999999999999999988766     


Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                       .+..++|+|+||.+.++.++|+..|++||.|.+|++.   |+|+||.|.-.++|..|++.|++.++.|++++|..+..+
T Consensus        75 -sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv---kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   75 -SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV---KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             -CCCccccccCCCCccccCHHHhhhhcccCCceeeeee---cceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence             3356899999999999999999999999999999975   789999999999999999999999999999999998765


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      -
T Consensus       151 l  151 (346)
T KOG0109|consen  151 L  151 (346)
T ss_pred             c
Confidence            4

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.83  E-value=3.2e-20  Score=207.34  Aligned_cols=164  Identities=20%  Similarity=0.351  Sum_probs=146.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .||||++||++++.++|.++|+.+|+|..|.+     +..+|||+||.|.-.+++++|++.+.+..+.||.|.|.++.++
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            79999999999999999999999999999985     4578999999999999999999999999999999999998765


Q ss_pred             CCCCC--------------------c--ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEE
Q 002974          353 DNPSE--------------------K--DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEF  406 (861)
Q Consensus       353 ~~~~~--------------------k--~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF  406 (861)
                      ....+                    .  +....+|.|+|||+.+.+.+|+.+|+.||.|.+|.|.    ++-.|||||+|
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            33210                    0  1125689999999999999999999999999999874    33469999999


Q ss_pred             CCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchhh
Q 002974          407 YDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR  441 (861)
Q Consensus       407 ~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~rr  441 (861)
                      .+..+|..|++.+|+..|.||+|.|.||.++....
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye  200 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYE  200 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeeccccccc
Confidence            99999999999999999999999999999988554

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=9e-20  Score=188.87  Aligned_cols=245  Identities=17%  Similarity=0.239  Sum_probs=178.9

Q ss_pred             HHHHHhcCCCCCc--chhhhccccccCCCCCCCCCCCcccccccccCCcccc-ccCcchhhhccCCCcCCCccCCCCCCC
Q 002974          188 IEAQTIGNLLPDE--DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMEL-EGDDRLFAVQKNSDFVGGVSNQGVSAG  264 (861)
Q Consensus       188 ~eaq~IGnLlpdd--DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGmEl-e~d~~~s~~~s~s~~~gg~~~~~~~ng  264 (861)
                      -..-.|=|.||..  .|-+..++..+|....++.+.|.    +....=|+.+ -.....++..++..++|..-..+-...
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDK----itGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKV  115 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDK----ITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKV  115 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeecc----ccccccccceeeecChHHHHHHHhhhcceeeccceEEE
Confidence            3455677888876  55556666667777777777763    4444333321 111112334445666652222111111


Q ss_pred             cccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCcccc
Q 002974          265 SVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPL  339 (861)
Q Consensus       265 ~~~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L  339 (861)
                      ..+ ....+.....+|||.+||+.+|..||+.+|++||.|..-+     +++.+||.+||.|....+|+.||+.|||..-
T Consensus       116 SyA-RPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P  194 (360)
T KOG0145|consen  116 SYA-RPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKP  194 (360)
T ss_pred             Eec-cCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCC
Confidence            111 1112344578999999999999999999999999987766     4799999999999999999999999999887


Q ss_pred             Cc--ceeeeeecCCCCCCC-------------C----------------------------------------------c
Q 002974          340 RR--RKLDIHYSIPKDNPS-------------E----------------------------------------------K  358 (861)
Q Consensus       340 ~G--r~L~V~~a~~k~~~~-------------~----------------------------------------------k  358 (861)
                      .|  .+|.|+|+.......             .                                              .
T Consensus       195 ~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~  274 (360)
T KOG0145|consen  195 SGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGG  274 (360)
T ss_pred             CCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCC
Confidence            65  478998885321100             0                                              0


Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      .....+|||-||.++.+|.-|+++|++||.|..|++     +.+.|||+||.+.+.++|..||..|||..+++|.|.|.+
T Consensus       275 ~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsF  354 (360)
T KOG0145|consen  275 PGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF  354 (360)
T ss_pred             CCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEE
Confidence            001358999999999999999999999999999876     467899999999999999999999999999999999998


Q ss_pred             ccCC
Q 002974          434 SRPG  437 (861)
Q Consensus       434 Akpk  437 (861)
                      ...+
T Consensus       355 Ktnk  358 (360)
T KOG0145|consen  355 KTNK  358 (360)
T ss_pred             ecCC
Confidence            7654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=1.7e-19  Score=201.63  Aligned_cols=168  Identities=23%  Similarity=0.403  Sum_probs=144.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      +.-+|.|+|||+.+.+.+|+.+|++||.|..|.+    .++-+|||||+|.+..+|.+|++.+|+..|.||+|-|.||.+
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            4779999999999999999999999999999986    456679999999999999999999999999999999999965


Q ss_pred             CCCCC-----------------------------------------Cc--cc----------------------------
Q 002974          352 KDNPS-----------------------------------------EK--DA----------------------------  360 (861)
Q Consensus       352 k~~~~-----------------------------------------~k--~~----------------------------  360 (861)
                      ++.-.                                         +.  +.                            
T Consensus       196 Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~  275 (678)
T KOG0127|consen  196 KDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKE  275 (678)
T ss_pred             cccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCc
Confidence            42100                                         00  00                            


Q ss_pred             ---------------CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHh-
Q 002974          361 ---------------NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTL-  419 (861)
Q Consensus       361 ---------------~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~L-  419 (861)
                                     ...+|||+|||+++|+++|.+.|++||+|.++.+     ++.++|.|||.|.+..+|..||.+. 
T Consensus       276 ~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  276 SDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             ccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence                           0258999999999999999999999999999764     7889999999999999999999976 


Q ss_pred             ----CC-CeeCCcEEEEEeccCCchhhhc
Q 002974          420 ----NR-SDVAGKQIKLEASRPGGARRFM  443 (861)
Q Consensus       420 ----NG-~~I~Gr~IkVe~Akpk~~rrl~  443 (861)
                          .| ..|.||.|+|..+..+.+...+
T Consensus       356 pa~e~g~~ll~GR~Lkv~~Av~RkeA~dm  384 (678)
T KOG0127|consen  356 PASEDGSVLLDGRLLKVTLAVTRKEAADM  384 (678)
T ss_pred             ccCCCceEEEeccEEeeeeccchHHHHHH
Confidence                23 5678999999999998766644

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

Probab=99.79  E-value=4.2e-19  Score=185.22  Aligned_cols=197  Identities=19%  Similarity=0.284  Sum_probs=152.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      ....|||||+||+.+|||+-|..||.+.|.|..|++          .|+                    .|+|.|+....
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~----------i~~--------------------e~~v~wa~~p~   52 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKV----------IFD--------------------ELKVNWATAPG   52 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhcccccccee----------ehh--------------------hhccccccCcc
Confidence            456899999999999999999999999999999986          121                    67788887665


Q ss_pred             CCCCcccC-CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCc
Q 002974          354 NPSEKDAN-QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGK  427 (861)
Q Consensus       354 ~~~~k~~~-~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr  427 (861)
                      +.++.... .-.+||+.|...++.++||+.|.+||+|.++++     ++++|||+||.|.+.++|+.||..|||..|++|
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            55444433 457999999999999999999999999999775     678999999999999999999999999999999


Q ss_pred             EEEEEeccCCchhh-hchh-hhh-----hhccccCC-CCCCCCCCcccc----CCcccEEEEeCCCCCccee--ecCCCC
Q 002974          428 QIKLEASRPGGARR-FMVQ-SEQ-----EQDDLNLC-QIPFDDLSSGQM----VSSGVITSTCMDNGSIQVL--HSATRS  493 (861)
Q Consensus       428 ~IkVe~Akpk~~rr-l~qq-~eq-----~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~~enG~srGF--~S~~~~  493 (861)
                      .|+-.||..|..+. ..+. .++     .-+...|+ .+++.-++++.+    ++||.|..+|.-..+-..|  ++....
T Consensus       133 ~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEa  212 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEA  212 (321)
T ss_pred             eeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhh
Confidence            99999998776443 1111 221     12222355 788887787777    9999999999443333334  555554


Q ss_pred             Ccccccc
Q 002974          494 PAIALTE  500 (861)
Q Consensus       494 p~~~~~~  500 (861)
                      .-.++.+
T Consensus       213 AahAIv~  219 (321)
T KOG0148|consen  213 AAHAIVQ  219 (321)
T ss_pred             HHHHHHH
Confidence            4444443

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.77  E-value=9.2e-19  Score=187.84  Aligned_cols=162  Identities=20%  Similarity=0.404  Sum_probs=143.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      --|+||||.|.+.+.|+.|+..|..||+|+++.     +++++||||||+|+-++.|+-|++.|||..+.||.|+|....
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            378999999999999999999999999999997     489999999999999999999999999999999999998553


Q ss_pred             CCCC--C-----CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHH
Q 002974          351 PKDN--P-----SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRT  418 (861)
Q Consensus       351 ~k~~--~-----~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~  418 (861)
                      .-..  +     .++.....+|||..+.++++++||+..|+.||+|+.|.+     ....|||+||+|.+..+-..|+..
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            2111  1     122234679999999999999999999999999999986     345689999999999999999999


Q ss_pred             hCCCeeCCcEEEEEeccCC
Q 002974          419 LNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       419 LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ||-..++|.-|+|..+...
T Consensus       272 MNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  272 MNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             cchhhcccceEecccccCC
Confidence            9999999999999777543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.75  E-value=3.2e-18  Score=196.75  Aligned_cols=163  Identities=24%  Similarity=0.431  Sum_probs=141.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCC--------CcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC--------KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svkitg--------ksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .++|||.||+++++.++|..+|...|.|.++.+..        .+.|||||+|.+.++|++|++.|+|+.|.|+.|.|.+
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            34499999999999999999999999999997621        1349999999999999999999999999999999999


Q ss_pred             cCCCCCC-----CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCC-----CccEEEEEECCHHHHHHHHHH
Q 002974          349 SIPKDNP-----SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH-----KHNHKFIEFYDIRAAETALRT  418 (861)
Q Consensus       349 a~~k~~~-----~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgk-----sKGfAFVeF~d~eaA~kAL~~  418 (861)
                      +..+...     ...+...++|.|+|||+..+..+++++|..||.|++|++..+     .+|||||+|-++++|..|+.+
T Consensus       595 S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~a  674 (725)
T KOG0110|consen  595 SENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDA  674 (725)
T ss_pred             ccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHh
Confidence            9722111     011222578999999999999999999999999999997433     378999999999999999999


Q ss_pred             hCCCeeCCcEEEEEeccCCch
Q 002974          419 LNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       419 LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      |..+-++||+|.++|++....
T Consensus       675 l~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  675 LGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             hcccceechhhheehhccchH
Confidence            999999999999999998764

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.74  E-value=4.1e-17  Score=191.01  Aligned_cols=156  Identities=16%  Similarity=0.242  Sum_probs=107.0

Q ss_pred             HHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-ccccCcchhhhccCCCcCCCccC--C---CCC-
Q 002974          191 QTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEGDDRLFAVQKNSDFVGGVSN--Q---GVS-  262 (861)
Q Consensus       191 q~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~d~~~s~~~s~s~~~gg~~~--~---~~~-  262 (861)
                      -+||||..+. ++-|..++..+|.+.......|..    ....-|+ .++.+....+..++..+++..-.  .   ... 
T Consensus       110 LfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~----TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPA----TGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             EEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCC----CCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            3599998877 888899999898877766655421    1222333 22223222333334444431111  0   000 


Q ss_pred             CC----cccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHH
Q 002974          263 AG----SVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKA  333 (861)
Q Consensus       263 ng----~~~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALka  333 (861)
                      +.    .............++|||+|||+++++++|+++|+.||.|..|++     ++++||||||+|.+.++|.+|++.
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            00    000011112234689999999999999999999999999999985     467999999999999999999999


Q ss_pred             cCccccCcceeeeeecC
Q 002974          334 LQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       334 LnG~~L~Gr~L~V~~a~  350 (861)
                      ||+..|.|+.|+|.++.
T Consensus       266 mNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             hCCCeeCCeEEEEEecC
Confidence            99999999999998765

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.

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.69  E-value=4.5e-16  Score=160.07  Aligned_cols=163  Identities=26%  Similarity=0.454  Sum_probs=143.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHH----HhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKA----LFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~e----lFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      +..+..||||.||+..+..++|++    ||++||+|..|..  +.+.||.|||.|.+.+.|-.|+++|+|..+.|+.++|
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            345667999999999999999988    9999999999985  7899999999999999999999999999999999999


Q ss_pred             eecCCCCCCCCc----------------------------------------------ccCCcceEEecccCCCcHHHHH
Q 002974          347 HYSIPKDNPSEK----------------------------------------------DANQGTLVVFNLDSSVSTEELH  380 (861)
Q Consensus       347 ~~a~~k~~~~~k----------------------------------------------~~~~~tLfVgNLp~svTeedLr  380 (861)
                      +||..+.+.-.+                                              ...+..||+.|||..++.+.|.
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            999754321000                                              1234579999999999999999


Q ss_pred             HHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeC-CcEEEEEecc
Q 002974          381 QIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA-GKQIKLEASR  435 (861)
Q Consensus       381 elFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~-Gr~IkVe~Ak  435 (861)
                      .+|.+|.--++|+.....++.|||+|.+...|..|...|.+..|. ...++|.+++
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            999999999999988888999999999999999999999999887 7888887764

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=1.3e-16  Score=166.14  Aligned_cols=166  Identities=22%  Similarity=0.419  Sum_probs=140.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccc-cCc--ceeeeee
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKP-LRR--RKLDIHY  348 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~-L~G--r~L~V~~  348 (861)
                      +.++||||-|.+.-.|+|++.+|..||.|.+|.+    .+.+||||||.|.+..+|+.||..|+|.. +.|  ..|.|+|
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            5789999999999999999999999999999985    68899999999999999999999999964 333  3455555


Q ss_pred             cCCCCCCC------------------------------------------------------------------------
Q 002974          349 SIPKDNPS------------------------------------------------------------------------  356 (861)
Q Consensus       349 a~~k~~~~------------------------------------------------------------------------  356 (861)
                      +...+++.                                                                        
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            43211000                                                                        


Q ss_pred             --------------------------------------------------------------------------------
Q 002974          357 --------------------------------------------------------------------------------  356 (861)
Q Consensus       357 --------------------------------------------------------------------------------  356 (861)
                                                                                                      
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence                                                                                            


Q ss_pred             ----------------------CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCH
Q 002974          357 ----------------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDI  409 (861)
Q Consensus       357 ----------------------~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~  409 (861)
                                            .+..+.++|||-.||.+..+.||.++|-.||.|++.++     ++.+|.|+||.|.+.
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                                  00001368999999999999999999999999999765     678999999999999


Q ss_pred             HHHHHHHHHhCCCeeCCcEEEEEeccCCchhh
Q 002974          410 RAAETALRTLNRSDVAGKQIKLEASRPGGARR  441 (861)
Q Consensus       410 eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~rr  441 (861)
                      .+|++||.+|||..|+-|+|+|...+||++.|
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            99999999999999999999999999987543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.66  E-value=2.3e-16  Score=171.94  Aligned_cols=163  Identities=15%  Similarity=0.351  Sum_probs=143.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..++|||++|+++++++.|++.|.+||+|..|.+     +++++||+||+|++.+...+++. .....|.|+.|.+..+.
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            6899999999999999999999999999999984     68899999999999999999985 55677999999999999


Q ss_pred             CCCCCCCcc--cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          351 PKDNPSEKD--ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       351 ~k~~~~~k~--~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      ++....+..  ....+|||++|+..++++++++.|.+||.|..+.+     +.+.++|+||.|.+++++.+++. ..-+.
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            887654332  23568999999999999999999999998887653     45678999999999999999988 67889


Q ss_pred             eCCcEEEEEeccCCchh
Q 002974          424 VAGKQIKLEASRPGGAR  440 (861)
Q Consensus       424 I~Gr~IkVe~Akpk~~r  440 (861)
                      |.|+++.|..|.|++..
T Consensus       163 ~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             ecCceeeEeeccchhhc
Confidence            99999999999998743

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=3.3e-16  Score=171.84  Aligned_cols=244  Identities=16%  Similarity=0.278  Sum_probs=173.8

Q ss_pred             HHHHHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-cccc--Ccchhhhcc----CCCcCCCccCC
Q 002974          188 IEAQTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEG--DDRLFAVQK----NSDFVGGVSNQ  259 (861)
Q Consensus       188 ~eaq~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~--d~~~s~~~s----~s~~~gg~~~~  259 (861)
                      .-..++|-+--.- +.-|-.++..+|.+-..+.++|.    .....-|- .+..  ....+.+..    .-.+.|...  
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk----~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~--  107 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDK----STGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHH--  107 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeeccc----ccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCc--
Confidence            3344566553333 66677888888888888888874    32333332 1111  111111111    111111100  


Q ss_pred             CCCCCcccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcC
Q 002974          260 GVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQ  335 (861)
Q Consensus       260 ~~~ng~~~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLn  335 (861)
                       ...-+.+..........++||||-|++.++|.|++++|.+||.|++|++    .+.+||||||.|.+.+-|..||++||
T Consensus       108 -pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~n  186 (510)
T KOG0144|consen  108 -PVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALN  186 (510)
T ss_pred             -ceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhc
Confidence             0001111111122235889999999999999999999999999999985    57899999999999999999999999


Q ss_pred             ccc-cCc--ceeeeeecCCCCCCCCcc-----------------------------------------------------
Q 002974          336 NKP-LRR--RKLDIHYSIPKDNPSEKD-----------------------------------------------------  359 (861)
Q Consensus       336 G~~-L~G--r~L~V~~a~~k~~~~~k~-----------------------------------------------------  359 (861)
                      |.. +.|  .+|.|+|+.+++++..+.                                                     
T Consensus       187 g~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L  266 (510)
T KOG0144|consen  187 GTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPL  266 (510)
T ss_pred             cceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCC
Confidence            965 554  578998886553211000                                                     


Q ss_pred             --------------------------------------------------------------------------------
Q 002974          360 --------------------------------------------------------------------------------  359 (861)
Q Consensus       360 --------------------------------------------------------------------------------  359 (861)
                                                                                                      
T Consensus       267 ~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n  346 (510)
T KOG0144|consen  267 GPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYN  346 (510)
T ss_pred             CCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcc
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------------------------------cCCcc
Q 002974          360 ---------------------------------------------------------------------------ANQGT  364 (861)
Q Consensus       360 ---------------------------------------------------------------------------~~~~t  364 (861)
                                                                                                 ..-.+
T Consensus       347 ~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGan  426 (510)
T KOG0144|consen  347 LAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGAN  426 (510)
T ss_pred             cccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccc
Confidence                                                                                       00137


Q ss_pred             eEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          365 LVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       365 LfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      |||.+||.+.-+.+|-..|..||.|++.++     ++-+|.|+||.|++..+|..||..|||..|+.++++|...+.+.
T Consensus       427 lfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~  505 (510)
T KOG0144|consen  427 LFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRN  505 (510)
T ss_pred             eeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccC
Confidence            999999999999999999999999998654     56679999999999999999999999999999999999988765

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.64  E-value=1.9e-15  Score=150.72  Aligned_cols=149  Identities=19%  Similarity=0.303  Sum_probs=128.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCc--ccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH--RGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgks--rGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      +.+++|||+|||.++.|.||.+||.+||.|+.|.++...  -.||||+|+++.+|+.||..-+|..+.|..|+|+++..-
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            458999999999999999999999999999999875443  469999999999999999999999999999999998654


Q ss_pred             CCCC----------------------CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHH
Q 002974          353 DNPS----------------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR  410 (861)
Q Consensus       353 ~~~~----------------------~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~e  410 (861)
                      ....                      .......+|.|.+||++-+++||++...+-|+|....+.  .-+++.|+|...|
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~--rDg~GvV~~~r~e  161 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQ--RDGVGVVEYLRKE  161 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeee--cccceeeeeeehh
Confidence            2111                      111235689999999999999999999999999888765  3569999999999


Q ss_pred             HHHHHHHHhCCCeeC
Q 002974          411 AAETALRTLNRSDVA  425 (861)
Q Consensus       411 aA~kAL~~LNG~~I~  425 (861)
                      +.+-|++.|....+.
T Consensus       162 DMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  162 DMKYAVRKLDDQKFR  176 (241)
T ss_pred             hHHHHHHhhcccccc
Confidence            999999999877654

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.62  E-value=2.3e-15  Score=173.63  Aligned_cols=214  Identities=21%  Similarity=0.317  Sum_probs=165.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .++..+.|+|+|||..+..++|..+|..||+|..+.+. ..---|+|.|.+..+|++|++.|....+...++++.|+...
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            45567899999999999999999999999999999764 22235999999999999999999999999888888776311


Q ss_pred             CC--------------------CCC------------cc--------------cCCcceEEecccCCCcHHHHHHHhccc
Q 002974          353 DN--------------------PSE------------KD--------------ANQGTLVVFNLDSSVSTEELHQIFGIY  386 (861)
Q Consensus       353 ~~--------------------~~~------------k~--------------~~~~tLfVgNLp~svTeedLrelFskf  386 (861)
                      .-                    +.+            ++              ...++|||.||+++.+.++|...|.++
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            00                    000            00              012349999999999999999999999


Q ss_pred             CcEEEEEeCCC--------CccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchhhhchh-hhhhhccccCCC
Q 002974          387 GEIREIRDTQH--------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQ-SEQEQDDLNLCQ  457 (861)
Q Consensus       387 GeI~sVritgk--------sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~rrl~qq-~eq~q~E~~vgk  457 (861)
                      |.|.+|.|..+        +.|||||+|.+.++|+.|++.|+|+.|.|+.|.|+++..+.+-..-.+ ...+.--+.+-+
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            99999876322        239999999999999999999999999999999999983332221111 111111223449


Q ss_pred             CCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          458 IPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       458 NLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      |+|...+-..+    .+||+|.+|+    ...+-+|||
T Consensus       620 NipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF  657 (725)
T KOG0110|consen  620 NIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGF  657 (725)
T ss_pred             ccchHHHHHHHHHHHhcccceeeeccchhhcchhhccc
Confidence            99999987777    8999999999    234456776

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.61  E-value=3.6e-16  Score=176.27  Aligned_cols=165  Identities=23%  Similarity=0.361  Sum_probs=143.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ..++..+|+|+--|...++..+|.++|+.+|+|+.|++     +..++|.|||+|.|.+....|+ +|.|+.+.|.+|.|
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            45678999999999999999999999999999999974     6789999999999999999999 69999999999999


Q ss_pred             eecCCCCCCCCc----------ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHH
Q 002974          347 HYSIPKDNPSEK----------DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRA  411 (861)
Q Consensus       347 ~~a~~k~~~~~k----------~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~ea  411 (861)
                      +......+....          ...-..|||+||..++++++|+.+|+.||.|+.|.+     ++..|||+||+|.+.++
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            876543332100          011223999999999999999999999999999864     67889999999999999


Q ss_pred             HHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          412 AETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       412 A~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      |.+|++.|||.+|.|+.|+|..-..+
T Consensus       333 ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  333 ARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             HHHHHHHhccceecCceEEEEEeeee
Confidence            99999999999999999999876543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.58  E-value=6.5e-15  Score=163.75  Aligned_cols=120  Identities=24%  Similarity=0.326  Sum_probs=103.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||+++|+++|+++|+.||+|++|++     +++++|||||+|.++++|++||+.||+..|.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            345789999999999999999999999999999876     456789999999999999999999999999999999999


Q ss_pred             ccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          434 SRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       434 Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      +++....         .....++ .||+.++++++|    .+||.|+.++    ..+|+++||
T Consensus       184 a~p~~~~---------~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~  237 (346)
T TIGR01659       184 ARPGGES---------IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGV  237 (346)
T ss_pred             ccccccc---------cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceE
Confidence            9875311         1122344 999999999999    8999998887    458888886

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).

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.54  E-value=2.4e-14  Score=161.69  Aligned_cols=162  Identities=23%  Similarity=0.367  Sum_probs=130.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..|-+.||||||..+++|++|+.+|+.||.|..|.+     ++.++||+||+|.+.++|++|++.|||..|.||.|+|..
T Consensus       275 ~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~  354 (549)
T KOG0147|consen  275 TGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSV  354 (549)
T ss_pred             ccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEE
Confidence            345555999999999999999999999999999873     789999999999999999999999999999999999854


Q ss_pred             cCCCCCCCC--------------------------------------------------------------------cc-
Q 002974          349 SIPKDNPSE--------------------------------------------------------------------KD-  359 (861)
Q Consensus       349 a~~k~~~~~--------------------------------------------------------------------k~-  359 (861)
                      -..+-...+                                                                    +. 
T Consensus       355 v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~  434 (549)
T KOG0147|consen  355 VTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPAD  434 (549)
T ss_pred             eeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccc
Confidence            322110000                                                                    00 


Q ss_pred             ------cCCcceEEecc--cCCCc--------HHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          360 ------ANQGTLVVFNL--DSSVS--------TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       360 ------~~~~tLfVgNL--p~svT--------eedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                            ....++.+.|+  |...|        .+++.+.+.+||+|..|.+...+-|+.||.|.+.++|..|+.+|||.+
T Consensus       435 ~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrW  514 (549)
T KOG0147|consen  435 ASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRW  514 (549)
T ss_pred             cccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhh
Confidence                  01123333443  11111        278889999999999999988888999999999999999999999999


Q ss_pred             eCCcEEEEEecc
Q 002974          424 VAGKQIKLEASR  435 (861)
Q Consensus       424 I~Gr~IkVe~Ak  435 (861)
                      |.||.|...|-.
T Consensus       515 F~gr~Ita~~~~  526 (549)
T KOG0147|consen  515 FAGRMITAKYLP  526 (549)
T ss_pred             hccceeEEEEee
Confidence            999999998864

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.47  E-value=4.6e-14  Score=146.25  Aligned_cols=150  Identities=23%  Similarity=0.401  Sum_probs=130.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCC--
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP--  355 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~--  355 (861)
                      ..+||++||+.+.+.+|..+|..||.|..+.+   ..||+||+|.+..+|+.|+-.|+++.|.+..+.|.|+......  
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            47999999999999999999999999999987   4579999999999999999999999999988999998753110  


Q ss_pred             ----C----------CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCC
Q 002974          356 ----S----------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR  421 (861)
Q Consensus       356 ----~----------~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG  421 (861)
                          .          ........+.|.++...+.+.+|.+.|.++|.+.....   ..+++||+|...++|.+|+..|++
T Consensus        79 ~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---~~~~~~v~Fs~~~da~ra~~~l~~  155 (216)
T KOG0106|consen   79 RPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---RRNFAFVEFSEQEDAKRALEKLDG  155 (216)
T ss_pred             CCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---hccccceeehhhhhhhhcchhccc
Confidence                0          11234568999999999999999999999999955443   678999999999999999999999


Q ss_pred             CeeCCcEEEEEe
Q 002974          422 SDVAGKQIKLEA  433 (861)
Q Consensus       422 ~~I~Gr~IkVe~  433 (861)
                      ..+.++.|.+..
T Consensus       156 ~~~~~~~l~~~~  167 (216)
T KOG0106|consen  156 KKLNGRRISVEK  167 (216)
T ss_pred             hhhcCceeeecc
Confidence            999999999933

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.47  E-value=3e-13  Score=133.11  Aligned_cols=81  Identities=23%  Similarity=0.439  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ...+++|||+|||++++|++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+++.|.|+.|+|.+
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            456889999999999999999999999999999985     578899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002974          349 SIPKDN  354 (861)
Q Consensus       349 a~~k~~  354 (861)
                      +.++..
T Consensus       111 a~~~~~  116 (144)
T PLN03134        111 ANDRPS  116 (144)
T ss_pred             CCcCCC
Confidence            976544

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.43  E-value=4.9e-13  Score=131.61  Aligned_cols=78  Identities=18%  Similarity=0.366  Sum_probs=72.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+||++.+++++|+++|++||+|++|++     +++++|||||+|.+.++|++|++.||+..|.|++|+|+++.
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            4578999999999999999999999999999876     45679999999999999999999999999999999999998


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ++.
T Consensus       113 ~~~  115 (144)
T PLN03134        113 DRP  115 (144)
T ss_pred             cCC
Confidence            764

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.39  E-value=7.4e-12  Score=135.20  Aligned_cols=165  Identities=16%  Similarity=0.241  Sum_probs=135.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE--------Ee----CCCcccEEEEEeCCHHHHHHHHHHcCccccCc
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI--------YT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR  341 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~sv--------ki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G  341 (861)
                      ..-+..|||.|||.++|.+++.++|++||-|..-        ++    .|+-||=|.+.|-..++++-|++.|++..++|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            3447779999999999999999999999987553        22    58889999999999999999999999999999


Q ss_pred             ceeeeeecCCCCC-----------------------------C-----CCcccCCcceEEecccC----CCc-------H
Q 002974          342 RKLDIHYSIPKDN-----------------------------P-----SEKDANQGTLVVFNLDS----SVS-------T  376 (861)
Q Consensus       342 r~L~V~~a~~k~~-----------------------------~-----~~k~~~~~tLfVgNLp~----svT-------e  376 (861)
                      ++|+|+.|+-+..                             .     ..+....++|.+.|+=.    ..+       +
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            9999988742100                             0     01123357899999821    222       4


Q ss_pred             HHHHHHhcccCcEEEEEeC-CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          377 EELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       377 edLrelFskfGeI~sVrit-gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ++|++-+.+||.|..|.+. .++.|.+-|.|.+.++|..||+.|+|+.+.||+|.......+.
T Consensus       291 edl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKT  353 (382)
T ss_pred             HHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcc
Confidence            7788889999999998874 5678999999999999999999999999999999998876554

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.37  E-value=2.9e-12  Score=131.44  Aligned_cols=151  Identities=21%  Similarity=0.314  Sum_probs=118.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE--eCCC----cccEEEEEeCCHHHHHHHHHHcCccccC---cceee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY--TACK----HRGFVMISYYDIRAARNAMKALQNKPLR---RRKLD  345 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk--itgk----srGyAFVeF~d~e~A~kALkaLnG~~L~---Gr~L~  345 (861)
                      ..-|||||.+||.++...||..||..|--.+.+.  .+.+    .+.+|||.|.+..+|..|+.+|||..+.   +..|+
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            3479999999999999999999999986555543  3333    3479999999999999999999999886   77888


Q ss_pred             eeecCCCCCCCC----------------------c---------------------------c-----------------
Q 002974          346 IHYSIPKDNPSE----------------------K---------------------------D-----------------  359 (861)
Q Consensus       346 V~~a~~k~~~~~----------------------k---------------------------~-----------------  359 (861)
                      |++++......+                      .                           .                 
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            887753110000                      0                           0                 


Q ss_pred             ----------------cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCC-CCccEEEEEECCHHHHHHHHHHhCCC
Q 002974          360 ----------------ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-HKHNHKFIEFYDIRAAETALRTLNRS  422 (861)
Q Consensus       360 ----------------~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritg-ksKGfAFVeF~d~eaA~kAL~~LNG~  422 (861)
                                      ....||||.||..+++|++|+++|+.|--....++.. .....|||+|++.+.|..|+..|.|.
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                            0024899999999999999999999997655555432 23457999999999999999999988


Q ss_pred             eeC
Q 002974          423 DVA  425 (861)
Q Consensus       423 ~I~  425 (861)
                      .|.
T Consensus       272 ~~s  274 (284)
T KOG1457|consen  272 LLS  274 (284)
T ss_pred             eec
Confidence            763

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.36  E-value=1.1e-12  Score=143.68  Aligned_cols=165  Identities=20%  Similarity=0.296  Sum_probs=132.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccc--cCcceeeeeec
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP--LRRRKLDIHYS  349 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~--L~Gr~L~V~~a  349 (861)
                      ....+++.|.+||||++++|+||..++.+||+|..+.. .+.+..|||+|.|.++|..-+.......  ++|++|.|+|+
T Consensus        23 ~~~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~-lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~s  101 (492)
T KOG1190|consen   23 SMAEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLM-LKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYS  101 (492)
T ss_pred             cccCCcceeEeccCCccccHHHHHHhcccccceeeeee-eccchhhhhhhcchhhhhheeecccccCccccCcceeehhh
Confidence            34568999999999999999999999999999999986 4455599999999999988555444433  67899999887


Q ss_pred             CCCCCCC---------------------------C-------cccC--CcceEEecccCCCcHHHHHHHhcccCcEEEEE
Q 002974          350 IPKDNPS---------------------------E-------KDAN--QGTLVVFNLDSSVSTEELHQIFGIYGEIREIR  393 (861)
Q Consensus       350 ~~k~~~~---------------------------~-------k~~~--~~tLfVgNLp~svTeedLrelFskfGeI~sVr  393 (861)
                      ..+.-..                           .       .+..  --+++|.|+-+.++-|-|.++|++||.|..|.
T Consensus       102 n~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIi  181 (492)
T KOG1190|consen  102 NHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKII  181 (492)
T ss_pred             hHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEE
Confidence            4321000                           0       0000  11578889999999999999999999999987


Q ss_pred             eCCCCccE-EEEEECCHHHHHHHHHHhCCCeeCC--cEEEEEeccCC
Q 002974          394 DTQHKHNH-KFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPG  437 (861)
Q Consensus       394 itgksKGf-AFVeF~d~eaA~kAL~~LNG~~I~G--r~IkVe~Akpk  437 (861)
                      ...+..+| |+|+|.|.+.|..|..+|+|+.|..  +.|++.+++-.
T Consensus       182 TF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt  228 (492)
T KOG1190|consen  182 TFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLT  228 (492)
T ss_pred             EEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcc
Confidence            77777887 9999999999999999999998863  78999888754

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.36  E-value=5.3e-12  Score=136.42  Aligned_cols=237  Identities=19%  Similarity=0.306  Sum_probs=168.8

Q ss_pred             hcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc---ccccCcchhhhccCCCcCC---CccCCCCCCCc
Q 002974          193 IGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM---ELEGDDRLFAVQKNSDFVG---GVSNQGVSAGS  265 (861)
Q Consensus       193 IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm---Ele~d~~~s~~~s~s~~~g---g~~~~~~~ng~  265 (861)
                      +|.+.-+- +|.+..-++-||..+..+..=|    .+...+-|+   |.|-.+.  +-.+...+++   +..|-+...-.
T Consensus       118 VGSIsfEl~EDtiR~AF~PFGPIKSInMSWD----p~T~kHKgFAFVEYEvPEa--AqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  118 VGSISFELREDTIRRAFDPFGPIKSINMSWD----PATGKHKGFAFVEYEVPEA--AQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             eeeeEEEechHHHHhhccCCCCcceeecccc----cccccccceEEEEEeCcHH--HHHHHHHhccccccCccccccCCC
Confidence            67766655 8999999999999998887765    366667776   4443321  1222333443   22221111111


Q ss_pred             ccCC-------CCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHH
Q 002974          266 VVGE-------HPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKA  333 (861)
Q Consensus       266 ~~Ge-------~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALka  333 (861)
                      .-++       ...+.+.-.+|||..+.++.+|+||+..|+.||+|..|++     ...+|||+||+|.+..+...|+..
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            1111       1123455789999999999999999999999999999985     578999999999999999999999


Q ss_pred             cCccccCcceeeeeecCCCCC-----------------------------------------------------------
Q 002974          334 LQNKPLRRRKLDIHYSIPKDN-----------------------------------------------------------  354 (861)
Q Consensus       334 LnG~~L~Gr~L~V~~a~~k~~-----------------------------------------------------------  354 (861)
                      ||-..|.|+-|+|..+....+                                                           
T Consensus       272 MNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~  351 (544)
T KOG0124|consen  272 MNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGT  351 (544)
T ss_pred             cchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCC
Confidence            999999999888854321000                                                           


Q ss_pred             ---------------------C----------------------------CCc---------------------------
Q 002974          355 ---------------------P----------------------------SEK---------------------------  358 (861)
Q Consensus       355 ---------------------~----------------------------~~k---------------------------  358 (861)
                                           +                            .++                           
T Consensus       352 l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~s  431 (544)
T KOG0124|consen  352 LPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSS  431 (544)
T ss_pred             ccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCcc
Confidence                                 0                            000                           


Q ss_pred             -----------ccCCcceEEecc--cCCCc---HHHHHHHhcccCcEEEEEeCCCCcc---------EEEEEECCHHHHH
Q 002974          359 -----------DANQGTLVVFNL--DSSVS---TEELHQIFGIYGEIREIRDTQHKHN---------HKFIEFYDIRAAE  413 (861)
Q Consensus       359 -----------~~~~~tLfVgNL--p~svT---eedLrelFskfGeI~sVritgksKG---------fAFVeF~d~eaA~  413 (861)
                                 ....+.|.++|+  |.+++   +.+|++.+++||.|.+|-+...+.+         --||+|....++.
T Consensus       432 ARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~  511 (544)
T KOG0124|consen  432 ARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETH  511 (544)
T ss_pred             HHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHH
Confidence                       001346777887  55555   4789999999999999877543332         3699999999999


Q ss_pred             HHHHHhCCCeeCCcEEEEEecc
Q 002974          414 TALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       414 kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      +|+++|+|+.|+|+++..+...
T Consensus       512 rak~ALdGRfFgGr~VvAE~YD  533 (544)
T KOG0124|consen  512 RAKQALDGRFFGGRKVVAEVYD  533 (544)
T ss_pred             HHHHhhccceecCceeehhhhh
Confidence            9999999999999999876554

>PF00076 RRM_1: RNA recognition motif

Probab=99.34  E-value=3.5e-12  Score=107.29  Aligned_cols=66  Identities=30%  Similarity=0.616  Sum_probs=62.2

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          280 LFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       280 LfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      |||+|||.++++++|+++|++||.|..+++    .+..++||||+|.+.++|++|++.|+|..+.|++|+
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            799999999999999999999999999875    467899999999999999999999999999999885

(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 ....

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.32  E-value=1.9e-11  Score=134.06  Aligned_cols=160  Identities=23%  Similarity=0.325  Sum_probs=136.7

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCC
Q 002974          277 SRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP  355 (861)
Q Consensus       277 srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~  355 (861)
                      +..|.|.||.. .||.+-|..+|.-||+|..|++-.+.+--|.|+|.|...|+-|+..|+|..+.|++|+|.+++...-.
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            68899999964 58999999999999999999986566689999999999999999999999999999999998754211


Q ss_pred             ------CC--------------------cc-----cCCcceEEecccCCCcHHHHHHHhcccCcE-EEEEeCCCCccEEE
Q 002974          356 ------SE--------------------KD-----ANQGTLVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQHKHNHKF  403 (861)
Q Consensus       356 ------~~--------------------k~-----~~~~tLfVgNLp~svTeedLrelFskfGeI-~sVritgksKGfAF  403 (861)
                            .+                    +.     ....+|...|+|.++++|+|+.+|..-|-. +-.+..++.+.+|+
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                    00     124589999999999999999999998755 55666777889999


Q ss_pred             EEECCHHHHHHHHHHhCCCeeCC-cEEEEEeccC
Q 002974          404 IEFYDIRAAETALRTLNRSDVAG-KQIKLEASRP  436 (861)
Q Consensus       404 VeF~d~eaA~kAL~~LNG~~I~G-r~IkVe~Akp  436 (861)
                      +++.+.|+|..|+-.++...+++ ..|+|.+++.
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

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.31  E-value=2.9e-11  Score=133.34  Aligned_cols=160  Identities=21%  Similarity=0.376  Sum_probs=132.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhh-cCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFE-QFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFs-qfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      -.|.+||.|||+++.-.+|++||. +.|+|..|.+    .+|.||||.|+|+++|.+++|++.||...+.||+|.|+-..
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            356799999999999999999997 6899999984    79999999999999999999999999999999999985321


Q ss_pred             CC---------------------------------------------CCCCC--c-------------------------
Q 002974          351 PK---------------------------------------------DNPSE--K-------------------------  358 (861)
Q Consensus       351 ~k---------------------------------------------~~~~~--k-------------------------  358 (861)
                      ..                                             .+.+.  .                         
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                                             00000  0                         


Q ss_pred             ---------ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          359 ---------DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       359 ---------~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                               .....++||.||.+.+..+.|++.|.-.|+|+.|..    .+.++|||.|+|..+-+|..||..|++.-+.
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                     001358999999999999999999999999988753    4678999999999999999999999987777


Q ss_pred             CcEEEEEecc
Q 002974          426 GKQIKLEASR  435 (861)
Q Consensus       426 Gr~IkVe~Ak  435 (861)
                      .++..+....
T Consensus       283 ~~~~~~Rl~~  292 (608)
T KOG4212|consen  283 DRRMTVRLDR  292 (608)
T ss_pred             cccceeeccc
Confidence            7777766543

>PF00076 RRM_1: RNA recognition motif

Probab=99.31  E-value=7.7e-12  Score=105.19  Aligned_cols=66  Identities=35%  Similarity=0.548  Sum_probs=61.5

Q ss_pred             eEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       365 LfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      |||+|||..+++++|+++|++||.|..+.+.    +..+++|||+|.+.++|++|++.|+|..+.|++|+
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            7999999999999999999999999988763    45689999999999999999999999999999986

(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=99.31  E-value=1.5e-11  Score=125.56  Aligned_cols=118  Identities=29%  Similarity=0.459  Sum_probs=102.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      .++|||+|||.++++++|+++|.+||.|..+.+     +++++|||||+|.+.++|..|++.+++..|.|+.|.|.+...
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            699999999999999999999999999988764     589999999999999999999999999999999999999542


Q ss_pred             ----CCCCC----------------CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe
Q 002974          352 ----KDNPS----------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD  394 (861)
Q Consensus       352 ----k~~~~----------------~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri  394 (861)
                          +....                ........+++.+++..++..++...|..+|.+..+.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  257 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASL  257 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeec
Confidence                22211                01123568999999999999999999999999977665

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=8.4e-12  Score=124.26  Aligned_cols=79  Identities=23%  Similarity=0.488  Sum_probs=74.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      -.++|||+||+..+++.||..+|..||.|..|++.....|||||+|+++.+|+.|+..|+|+.|.|..|+|+.+.-+..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            4789999999999999999999999999999999999999999999999999999999999999999999999875433

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.24  E-value=6.9e-11  Score=132.67  Aligned_cols=160  Identities=16%  Similarity=0.259  Sum_probs=127.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE---eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svk---itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...-|-+++||+++|++||.++|+.|+ |+.+.   .+++..|-|||+|.+.+++++|++ ++...+..|-|.|--+..+
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            355677899999999999999999998 44444   468999999999999999999997 7888888898988666544


Q ss_pred             CCC-------CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEE-EEe----CCCCccEEEEEECCHHHHHHHHHHhC
Q 002974          353 DNP-------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRD----TQHKHNHKFIEFYDIRAAETALRTLN  420 (861)
Q Consensus       353 ~~~-------~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~s-Vri----tgksKGfAFVeF~d~eaA~kAL~~LN  420 (861)
                      +..       .....+...|-+++||+.||++||.++|+..-.|.. |.+    -+++.|-|||+|++.+.|++||. -|
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       111245678999999999999999999998654444 322    34567899999999999999999 47


Q ss_pred             CCeeCCcEEEEEeccCCc
Q 002974          421 RSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       421 G~~I~Gr~IkVe~Akpk~  438 (861)
                      ...|.-|-|.|-.+...+
T Consensus       166 re~iGhRYIEvF~Ss~~e  183 (510)
T KOG4211|consen  166 RENIGHRYIEVFRSSRAE  183 (510)
T ss_pred             HHhhccceEEeehhHHHH
Confidence            778888999997765443

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.22  E-value=4.8e-12  Score=126.63  Aligned_cols=161  Identities=20%  Similarity=0.266  Sum_probs=121.7

Q ss_pred             HHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc---ccccCcchhhhccCCCcCCCccCCCCCCCcc
Q 002974          191 QTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM---ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSV  266 (861)
Q Consensus       191 q~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm---Ele~d~~~s~~~s~s~~~gg~~~~~~~ng~~  266 (861)
                      -++|||++.. +++|++++-+.+.+-....++|.    +.....|+   |+.+.+..+.+.++..+-...+..  .....
T Consensus        12 iyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDr----v~~~~qGygF~Ef~~eedadYAikiln~VkLYgrp--Irv~k   85 (203)
T KOG0131|consen   12 LYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDR----VTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRP--IRVNK   85 (203)
T ss_pred             EEEecCCHHHHHHHHHHHHHhcCceeeeecchhh----hcccccceeEEEEechhhhHHHHHHHHHHHhcCce--eEEEe
Confidence            4699999988 99999999999999999998884    44555555   554444333333322222222222  22222


Q ss_pred             cCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE------eCCCcccEEEEEeCCHHHHHHHHHHcCccccC
Q 002974          267 VGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY------TACKHRGFVMISYYDIRAARNAMKALQNKPLR  340 (861)
Q Consensus       267 ~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk------itgksrGyAFVeF~d~e~A~kALkaLnG~~L~  340 (861)
                      ++.......-..+|||+||.+.++|..|.++|+.||.|...-      .+++++|||||.|.+.+++++|++.++|+.+.
T Consensus        86 as~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~  165 (203)
T KOG0131|consen   86 ASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLC  165 (203)
T ss_pred             cccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhc
Confidence            333344555679999999999999999999999999876631      47899999999999999999999999999999


Q ss_pred             cceeeeeecCCCCCCCC
Q 002974          341 RRKLDIHYSIPKDNPSE  357 (861)
Q Consensus       341 Gr~L~V~~a~~k~~~~~  357 (861)
                      .+++.|.|+..++...+
T Consensus       166 nr~itv~ya~k~~~kg~  182 (203)
T KOG0131|consen  166 NRPITVSYAFKKDTKGE  182 (203)
T ss_pred             CCceEEEEEEecCCCcc
Confidence            99999999987766543

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.20  E-value=2e-11  Score=116.16  Aligned_cols=78  Identities=26%  Similarity=0.458  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .+.++||||+||+..++|++|.+||++||+|+.|.+     +....|||||+|.+.++|..|++.++|+.|..+.|+|.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            456999999999999999999999999999999974     677889999999999999999999999999999999988


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      ...
T Consensus       113 D~G  115 (153)
T KOG0121|consen  113 DAG  115 (153)
T ss_pred             ccc
Confidence            743

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.19  E-value=7.2e-11  Score=126.94  Aligned_cols=82  Identities=22%  Similarity=0.412  Sum_probs=75.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .....++|+|.|||+...|-||+.+|++||+|.+|.|   ...+|||+||+|++.++|++|.++|+|..+.||+|.|+.+
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            3445789999999999999999999999999999985   5779999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      ..+-.
T Consensus       172 TarV~  176 (376)
T KOG0125|consen  172 TARVH  176 (376)
T ss_pred             chhhc
Confidence            87643

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.18  E-value=3e-11  Score=120.37  Aligned_cols=78  Identities=32%  Similarity=0.491  Sum_probs=72.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+||+..+++.||..+|.+||.|..|-+.-...|||||+|+|+.+|+.|+..|+|+.|.|..|+|+++.-..
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            367999999999999999999999999999988777889999999999999999999999999999999999987554

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.16  E-value=1.5e-10  Score=132.62  Aligned_cols=165  Identities=17%  Similarity=0.329  Sum_probs=130.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .....+.+||++||..+++.+++++...||.++....     ++.++||||.+|.++.....|+..|||+.+.+++|.|+
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            3455789999999999999999999999999887762     57899999999999999999999999999999999999


Q ss_pred             ecCCCCCCCCcc--------------------cCCcceEEeccc--CCC-cH-------HHHHHHhcccCcEEEEEeCCC
Q 002974          348 YSIPKDNPSEKD--------------------ANQGTLVVFNLD--SSV-ST-------EELHQIFGIYGEIREIRDTQH  397 (861)
Q Consensus       348 ~a~~k~~~~~k~--------------------~~~~tLfVgNLp--~sv-Te-------edLrelFskfGeI~sVritgk  397 (861)
                      .+..........                    .....|...|+=  .++ ++       |+++..+++||.|..|.+...
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            887643321111                    112233333331  111 11       567788899999999986321


Q ss_pred             --------CccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          398 --------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       398 --------sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                              ..|..||+|.+.++|++|.++|+|..++||.|...|....
T Consensus       445 ~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  445 YPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             CCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence                    2567999999999999999999999999999999988643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.15  E-value=1.3e-10  Score=123.55  Aligned_cols=76  Identities=18%  Similarity=0.291  Sum_probs=69.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      .++|||+|||+.++|++|+++|+.||+|.+|++  .+..+|||||+|.+.++|+.|+. |+|..|.|+.|.|.++....
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCC
Confidence            689999999999999999999999999999996  33468999999999999999995 99999999999999986543

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.14  E-value=1.5e-10  Score=106.70  Aligned_cols=81  Identities=30%  Similarity=0.488  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      +....+.|||+|||.++|.++..++|.+||.|+.|++  +...+|-|||.|++..+|.+|++.|.|..+.++.|.|.|..
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            4556899999999999999999999999999999996  67889999999999999999999999999999999999987


Q ss_pred             CCC
Q 002974          351 PKD  353 (861)
Q Consensus       351 ~k~  353 (861)
                      +.+
T Consensus        94 ~~~   96 (124)
T KOG0114|consen   94 PED   96 (124)
T ss_pred             HHH
Confidence            643

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.14  E-value=1.5e-10  Score=98.70  Aligned_cols=66  Identities=23%  Similarity=0.560  Sum_probs=59.0

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          280 LFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       280 LfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      |||+|||+++++++|+++|+.||.|..+++    .+..+++|||+|.+.++|++|++.+++..++|++|+
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            799999999999999999999999999985    245689999999999999999999999999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=1.2e-10  Score=125.16  Aligned_cols=98  Identities=15%  Similarity=0.270  Sum_probs=79.4

Q ss_pred             ccccCcceeeeeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe---CCCCccEEEEEECCHHHH
Q 002974          336 NKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD---TQHKHNHKFIEFYDIRAA  412 (861)
Q Consensus       336 G~~L~Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri---tgksKGfAFVeF~d~eaA  412 (861)
                      +-...|..+.+......    ......++|+|.|||+...|-||+.+|.+||+|.+|.|   ...+||||||+|++.++|
T Consensus        74 ~~~t~g~~~~~~~st~s----~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~da  149 (376)
T KOG0125|consen   74 GAPTDGQPIQTQPSTNS----SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADA  149 (376)
T ss_pred             CCCCCCCccccCCCCcC----CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhH
Confidence            33444555554433221    22234578999999999999999999999999999987   345799999999999999


Q ss_pred             HHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          413 ETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       413 ~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ++|-++|||..|.||+|.|..+..+
T Consensus       150 dRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  150 DRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHHHHhhcceeeceEEEEeccchh
Confidence            9999999999999999999998765

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.12  E-value=1.9e-10  Score=122.40  Aligned_cols=75  Identities=19%  Similarity=0.346  Sum_probs=68.7

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCC--CCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVritg--ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      .++|||+||++.+++++|+++|+.||+|++|++..  ..+|||||+|.+.++|+.||. |+|..|.|+.|+|.++..-
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            46899999999999999999999999999998743  357999999999999999996 9999999999999998743

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.11  E-value=8.1e-10  Score=120.30  Aligned_cols=167  Identities=21%  Similarity=0.325  Sum_probs=135.9

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHH--cCccccCcceeeeee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA--LQNKPLRRRKLDIHY  348 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALka--LnG~~L~Gr~L~V~~  348 (861)
                      +-...++-.|.|++|-..++|.||.+..+.||.|..+.. ...+..|.|+|+|++.|++|+..  -+...+.|+.--++|
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 56677999999999999999853  344557788888888


Q ss_pred             cCCCCCC---CCcccCCcceEEecc--cCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          349 SIPKDNP---SEKDANQGTLVVFNL--DSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       349 a~~k~~~---~~k~~~~~tLfVgNL--p~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      +..+.-.   .+....+..|.+.=|  -+.+|-+.|..++...|+|.+|.+..+..--|.|||++.+.|++|..+|||.+
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            8554322   122233445555544  46789999999999999999999876644469999999999999999999999


Q ss_pred             eC-C-cEEEEEeccCCc
Q 002974          424 VA-G-KQIKLEASRPGG  438 (861)
Q Consensus       424 I~-G-r~IkVe~Akpk~  438 (861)
                      |+ | ++|+|++|+|..
T Consensus       184 IYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  184 IYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             ccccceeEEEEecCcce
Confidence            86 3 899999999975

>PLN03213 repressor of silencing 3; Provisional

Probab=99.10  E-value=1.2e-10  Score=129.92  Aligned_cols=78  Identities=14%  Similarity=0.240  Sum_probs=69.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCH--HHHHHHHHHcCccccCcceeeeeecCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDI--RAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-tgksrGyAFVeF~d~--e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ....+||||||++.+++++|+.+|..||.|..|.+ ....||||||+|.+.  .++++||..|||..+.||.|+|+.|++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            34689999999999999999999999999999985 222399999999987  789999999999999999999998876


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      .
T Consensus        88 ~   88 (759)
T PLN03213         88 H   88 (759)
T ss_pred             H
Confidence            4

>PLN03213 repressor of silencing 3; Provisional

Probab=99.09  E-value=4.4e-10  Score=125.51  Aligned_cols=84  Identities=20%  Similarity=0.277  Sum_probs=73.2

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-CCCccEEEEEECCH--HHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDI--RAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-gksKGfAFVeF~d~--eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ....+||||||++.+++++|+..|+.||.|..|.+. ...||||||+|.+.  .++.+||..|||..+.|+.|+|..|++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            345789999999999999999999999999998763 12389999999977  789999999999999999999999998


Q ss_pred             Cchhhhc
Q 002974          437 GGARRFM  443 (861)
Q Consensus       437 k~~rrl~  443 (861)
                      .=..|+.
T Consensus        88 ~YLeRLk   94 (759)
T PLN03213         88 HYLARLK   94 (759)
T ss_pred             HHHHHHH
Confidence            7544433

>smart00362 RRM_2 RNA recognition motif

Probab=99.09  E-value=4.3e-10  Score=92.90  Aligned_cols=69  Identities=30%  Similarity=0.571  Sum_probs=63.1

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeCCC---CccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVritgk---sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      +|||+|||..+++++|+++|.+||.|..+++...   .+++|||+|.+.++|++|++.+++..+.|++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            5899999999999999999999999999876433   47999999999999999999999999999999873

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.08  E-value=3.5e-10  Score=96.36  Aligned_cols=66  Identities=26%  Similarity=0.538  Sum_probs=58.8

Q ss_pred             eEEecccCCCcHHHHHHHhcccCcEEEEEeCC----CCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       365 LfVgNLp~svTeedLrelFskfGeI~sVritg----ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      |||+|||+.+++++|+++|+.||.|..+++..    ..+++|||+|.+.++|.+|++.+++..+.|++|+
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            79999999999999999999999999988643    3479999999999999999999999999999985

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 ....

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.08  E-value=5.6e-10  Score=103.01  Aligned_cols=81  Identities=28%  Similarity=0.422  Sum_probs=75.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      -.+.|||.|||+++|.|+..++|.+||.|..|++  +..-+|-|||.|++..+|++|++.|+|..+.++.+.|-+..+..
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            4578999999999999999999999999999997  55668999999999999999999999999999999999999877


Q ss_pred             hhh
Q 002974          439 ARR  441 (861)
Q Consensus       439 ~rr  441 (861)
                      +.+
T Consensus        97 ~~~   99 (124)
T KOG0114|consen   97 AFK   99 (124)
T ss_pred             HHH
Confidence            655

>smart00362 RRM_2 RNA recognition motif

Probab=99.07  E-value=5.2e-10  Score=92.38  Aligned_cols=69  Identities=33%  Similarity=0.605  Sum_probs=63.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC---CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTA---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svkit---gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      +|||+|||..+++++|+++|.+||.|..+++.   +.++|+|||+|.+.++|++|++.+++..+.|++|.|+
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            58999999999999999999999999998863   3457999999999999999999999999999998873

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.05  E-value=2.7e-10  Score=120.96  Aligned_cols=106  Identities=24%  Similarity=0.293  Sum_probs=91.6

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchhhh
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRF  442 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~rrl  442 (861)
                      .+|||+|||..+++.+|+.+|++||+|.+|.|+   |+||||..+|..+|+.||+.|||..|.|..|.|+.++.|.... 
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv---KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk~s-   78 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV---KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSKAS-   78 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee---cccceEEeecccccHHHHhhcccceecceEEEEEeccccCCCc-
Confidence            369999999999999999999999999999986   6899999999999999999999999999999999999884322 


Q ss_pred             chhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEeCCCC
Q 002974          443 MVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTCMDNG  482 (861)
Q Consensus       443 ~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~~enG  482 (861)
                                ..++ .|+.+..+..+|    .+||.|..|...++
T Consensus        79 ----------tkl~vgNis~tctn~ElRa~fe~ygpviecdivkd  113 (346)
T KOG0109|consen   79 ----------TKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD  113 (346)
T ss_pred             ----------cccccCCCCccccCHHHhhhhcccCCceeeeeecc
Confidence                      1223 678888887777    89998888875544

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.05  E-value=2.5e-10  Score=116.32  Aligned_cols=80  Identities=25%  Similarity=0.500  Sum_probs=75.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      +.+.....+|.|-||...++.++|+.+|++||.|-+|+|     |..++|||||.|.+..+|+.|+++|+|.+|.|+.|+
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            456667889999999999999999999999999999986     789999999999999999999999999999999999


Q ss_pred             eeecC
Q 002974          346 IHYSI  350 (861)
Q Consensus       346 V~~a~  350 (861)
                      |++|.
T Consensus        87 Vq~ar   91 (256)
T KOG4207|consen   87 VQMAR   91 (256)
T ss_pred             ehhhh
Confidence            99885

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.05  E-value=4.4e-10  Score=117.10  Aligned_cols=77  Identities=23%  Similarity=0.380  Sum_probs=72.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...+|-|.||+.++++++|+++|.+||.|..|.+     ++.+||||||.|++.++|++||+.|||.-++.-.|+|+|++
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            4568999999999999999999999999999854     78899999999999999999999999999999999999999


Q ss_pred             CC
Q 002974          436 PG  437 (861)
Q Consensus       436 pk  437 (861)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            86

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.04  E-value=5.8e-10  Score=116.24  Aligned_cols=79  Identities=23%  Similarity=0.447  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      -.++++|-|.||+.+++|.+|++||..||.|..|++     |+.+||||||.|.+.++|++||+.|+|.-+..--|+|.|
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            347899999999999999999999999999999984     899999999999999999999999999999999999999


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9885

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.03  E-value=2.9e-10  Score=118.04  Aligned_cols=80  Identities=25%  Similarity=0.329  Sum_probs=69.8

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      .|...++|||++|++.+..|+|++.|++||+|++..+     ++++|||+||+|+|.++|.+|++. -.-.|+||+..|.
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            3455689999999999999999999999999999654     788999999999999999999994 3347899999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      +|--+.
T Consensus        87 lA~lg~   92 (247)
T KOG0149|consen   87 LASLGG   92 (247)
T ss_pred             hhhhcC
Confidence            887644

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.03  E-value=7e-10  Score=118.23  Aligned_cols=79  Identities=27%  Similarity=0.457  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...|-+||||+-|+.+++|..|+..|+.||+|+.|.     ++++++|||||+|++..+...|.+..+|+.|.|+.|.|.
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            347899999999999999999999999999999987     489999999999999999999999999999999999998


Q ss_pred             ecCC
Q 002974          348 YSIP  351 (861)
Q Consensus       348 ~a~~  351 (861)
                      +...
T Consensus       177 vERg  180 (335)
T KOG0113|consen  177 VERG  180 (335)
T ss_pred             eccc
Confidence            8754

>PF13893 RRM_5: RNA recognition motif

Probab=99.01  E-value=1.2e-09  Score=89.87  Aligned_cols=56  Identities=27%  Similarity=0.569  Sum_probs=51.5

Q ss_pred             HHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          379 LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       379 LrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      |+++|++||+|+.|.+..+.+++|||+|.+.++|++|++.|||..+.|++|+|+||
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            68999999999999986655799999999999999999999999999999999986

(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 ....

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.00  E-value=6e-10  Score=106.24  Aligned_cols=75  Identities=25%  Similarity=0.402  Sum_probs=68.6

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...+|||+||...++||+|.++|+++|+|+.|-+     +....|||||+|...++|+.|++-++|..+..+.|++.|.-
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            4679999999999999999999999999999854     44567999999999999999999999999999999999854

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.99  E-value=7.6e-10  Score=114.94  Aligned_cols=78  Identities=24%  Similarity=0.408  Sum_probs=68.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .+..-++||||+|++.+..++|++.|++||+|++..+     ++++|||+||.|.|.++|.+|++ --+-.|+||+-.++
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~-dp~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACK-DPNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhc-CCCCcccccccccc
Confidence            4455789999999999999999999999999998763     79999999999999999999997 34466899998888


Q ss_pred             ecCC
Q 002974          348 YSIP  351 (861)
Q Consensus       348 ~a~~  351 (861)
                      .+.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            7754

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

Probab=98.97  E-value=5.9e-10  Score=126.92  Aligned_cols=161  Identities=24%  Similarity=0.356  Sum_probs=128.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      ..+.++|+|-|||..|++++|+.+|+.||+|+.|+.+...+|.+||+|.|+++|++|+++|++..+.|+.|+........
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~~  151 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARRA  151 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccccc
Confidence            56799999999999999999999999999999999999999999999999999999999999999999998832221110


Q ss_pred             CC------------------CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHH
Q 002974          354 NP------------------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA  415 (861)
Q Consensus       354 ~~------------------~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kA  415 (861)
                      ..                  ....-....+++- |++..+..-++.+|+.+|.+.. +.++..+.--|++|.+..++..+
T Consensus       152 ~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~~~~~~hq~~~~~~~~~s~a~~  229 (549)
T KOG4660|consen  152 MGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RETPLLNHQRFVEFADNRSYAFS  229 (549)
T ss_pred             chhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-ccccchhhhhhhhhccccchhhc
Confidence            00                  0001113344444 9998888888899999999988 87777777889999999999777


Q ss_pred             HHHhCCCeeCCcEEEEEeccCC
Q 002974          416 LRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       416 L~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      +... |..+.+....+.++.+.
T Consensus       230 ~~~~-G~~~s~~~~v~t~S~~~  250 (549)
T KOG4660|consen  230 EPRG-GFLISNSSGVITFSGPG  250 (549)
T ss_pred             ccCC-ceecCCCCceEEecCCC
Confidence            6644 66667777666666663

>smart00360 RRM RNA recognition motif

Probab=98.97  E-value=1.9e-09  Score=88.57  Aligned_cols=66  Identities=32%  Similarity=0.598  Sum_probs=60.3

Q ss_pred             EcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          282 VRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       282 VgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      |+|||..+++++|+++|++||.|..+++     +++++|||||+|.+.++|.+|++.+++..+.|+.|.|+
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            6899999999999999999999999885     35568999999999999999999999999999998873

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.96  E-value=2.4e-09  Score=112.62  Aligned_cols=75  Identities=15%  Similarity=0.181  Sum_probs=68.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ...+|||+||++.+|+++|+++|+.||+|..|++  .++.++||||+|+++++|+.|+ .|+|..|.++.|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            3579999999999999999999999999999986  4567789999999999999999 5999999999999987653

>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=98.96  E-value=3.6e-09  Score=87.84  Aligned_cols=70  Identities=33%  Similarity=0.594  Sum_probs=64.1

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeCCC----CccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH----KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVritgk----sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      +|+|+|||..+++++|+++|+.||.|..+.+...    .+++|||+|.+.++|..|++.+++..+.|++|.|.+
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            5899999999999999999999999999886433    379999999999999999999999999999999864

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).

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.94  E-value=7.8e-10  Score=112.74  Aligned_cols=77  Identities=27%  Similarity=0.511  Sum_probs=71.5

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      .-.+|-|-||.+-++.++|+.+|++||.|-+|.|     +.+++|||||.|.+..+|+.|+++|+|..+.|+.|+|++|+
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            3468999999999999999999999999999876     67789999999999999999999999999999999999887


Q ss_pred             CC
Q 002974          436 PG  437 (861)
Q Consensus       436 pk  437 (861)
                      =.
T Consensus        92 yg   93 (256)
T KOG4207|consen   92 YG   93 (256)
T ss_pred             cC
Confidence            54

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.94  E-value=3.3e-09  Score=88.02  Aligned_cols=70  Identities=33%  Similarity=0.656  Sum_probs=63.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCC----CcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svkitg----ksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      +|+|+|||..+++++|+++|+.||.|..+.+..    ..+|+|||+|.+.++|+.|++.+++..+.|+.+.|.+
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            589999999999999999999999999988632    3489999999999999999999999999999998864

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

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.93  E-value=2.9e-09  Score=112.09  Aligned_cols=74  Identities=19%  Similarity=0.245  Sum_probs=67.6

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeC--CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVrit--gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ..+|||+||++.+|+++|+++|+.||+|.+|++.  ++.++||||+|+++++|+.|+. |+|..|.+++|.|..+..
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            4689999999999999999999999999999874  3456899999999999999996 999999999999998764

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.93  E-value=3.4e-09  Score=113.11  Aligned_cols=92  Identities=25%  Similarity=0.395  Sum_probs=79.6

Q ss_pred             CCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          350 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       350 ~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      .|..++......-+||||+-|+++++|.+|+..|++||.|+.|++     +++++|||||+|+++.+..+|.+..+|..|
T Consensus        89 dP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~I  168 (335)
T KOG0113|consen   89 DPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKI  168 (335)
T ss_pred             CCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCcee
Confidence            344444444566789999999999999999999999999999864     789999999999999999999999999999


Q ss_pred             CCcEEEEEeccCCchhh
Q 002974          425 AGKQIKLEASRPGGARR  441 (861)
Q Consensus       425 ~Gr~IkVe~Akpk~~rr  441 (861)
                      +|+.|.|.+-..+..+.
T Consensus       169 dgrri~VDvERgRTvkg  185 (335)
T KOG0113|consen  169 DGRRILVDVERGRTVKG  185 (335)
T ss_pred             cCcEEEEEecccccccc
Confidence            99999999887665433

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.93  E-value=1.6e-08  Score=112.02  Aligned_cols=70  Identities=20%  Similarity=0.265  Sum_probs=64.2

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ++|+|+|||.++|++.|++-|..||.|..+.+  .++++|  .|.|.++++|++|+..|+|..+.||.|+|.+.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            58999999999999999999999999999887  455554  99999999999999999999999999999874

>PF13893 RRM_5: RNA recognition motif

Probab=98.91  E-value=3.1e-09  Score=87.45  Aligned_cols=56  Identities=29%  Similarity=0.632  Sum_probs=50.8

Q ss_pred             HHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          294 LKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       294 L~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      |+++|++||+|..+.+..+.+++|||+|.+.++|++|++.|||..+.|++|+|.|+
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            68999999999999974444799999999999999999999999999999999986

(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 ....

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.90  E-value=4.4e-09  Score=107.40  Aligned_cols=75  Identities=29%  Similarity=0.568  Sum_probs=70.1

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ..+|||+||+..+++++|+++|.+||.|..|.+     ++..+|||||+|.+.++|..|++.+++..|.|++|+|.++.+
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            589999999999999999999999999988764     467899999999999999999999999999999999999764

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.90  E-value=1.8e-09  Score=108.57  Aligned_cols=78  Identities=32%  Similarity=0.451  Sum_probs=70.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC--CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit--gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      +.++|||+|||.++-+.+|.++|.+||.|.+|.+.  .....||||+|++..+|+.||..-+|..+.|++|+|+++....
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr   84 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGR   84 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCC
Confidence            56799999999999999999999999999998763  3335799999999999999999999999999999999998653

>smart00360 RRM RNA recognition motif

Probab=98.90  E-value=3.9e-09  Score=86.68  Aligned_cols=66  Identities=33%  Similarity=0.570  Sum_probs=59.6

Q ss_pred             EecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          367 VFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       367 VgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      |+|||..+++++|+++|++||.|..+.+.     +..+++|||+|.+.++|.+|++.+++..+.|++|+|+
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            57999999999999999999999998763     3347899999999999999999999999999999873

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.89  E-value=1.2e-09  Score=112.10  Aligned_cols=80  Identities=29%  Similarity=0.520  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...|+||||+|..+|+|.-|...|-.||+|..|.+     +.++||||||+|.-.++|.+||..||+..|.||.|+|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34799999999999999999999999999999985     6899999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .|..-
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            88644

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.88  E-value=1.1e-09  Score=112.45  Aligned_cols=81  Identities=27%  Similarity=0.505  Sum_probs=74.7

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||++|..++++.-|...|-+||.|+.|.+     ..+.||||||+|.-.|+|.+||..||+.++.||.|+|.+|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            4689999999999999999999999999999975     46779999999999999999999999999999999999999


Q ss_pred             CCchhh
Q 002974          436 PGGARR  441 (861)
Q Consensus       436 pk~~rr  441 (861)
                      |...+.
T Consensus        89 P~kike   94 (298)
T KOG0111|consen   89 PEKIKE   94 (298)
T ss_pred             CccccC
Confidence            976443

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.82  E-value=6.5e-10  Score=111.48  Aligned_cols=76  Identities=20%  Similarity=0.406  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .++.-|||||||.+.||.||..+|++||+|+.|.+     |++++||||+.|+|.++..-|+..|||..|.||.|+|.-.
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            45889999999999999999999999999999874     8999999999999999999999999999999999999754


Q ss_pred             C
Q 002974          350 I  350 (861)
Q Consensus       350 ~  350 (861)
                      .
T Consensus       113 ~  113 (219)
T KOG0126|consen  113 S  113 (219)
T ss_pred             c
Confidence            3

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.81  E-value=6.3e-09  Score=118.62  Aligned_cols=77  Identities=25%  Similarity=0.450  Sum_probs=73.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      +.|||||||++++|++|..+|+..|.|.++++     +++.|||||++|.+.++|.+|++.|||..+.||+|+|.|+...
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            89999999999999999999999999999984     8999999999999999999999999999999999999999765


Q ss_pred             CC
Q 002974          353 DN  354 (861)
Q Consensus       353 ~~  354 (861)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.80  E-value=2.6e-09  Score=126.64  Aligned_cols=160  Identities=20%  Similarity=0.344  Sum_probs=140.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC----CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA----CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkit----gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      +...++|||++||+..+++.+|+..|..+|.|..|.+.    +....||||.|.+...+-.|+..+.+..|..-.+++.+
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            45679999999999999999999999999999999863    23345999999999999999999999998877777777


Q ss_pred             cCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCC--
Q 002974          349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG--  426 (861)
Q Consensus       349 a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G--  426 (861)
                      ..++      ....+.++|++|...+....|.+.|..||.|..|.+ .+..-||+|.|++...|++|+..|-|..|+|  
T Consensus       448 G~~k------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy-~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~  520 (975)
T KOG0112|consen  448 GQPK------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY-RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPP  520 (975)
T ss_pred             cccc------cccceeeccCCCCCCChHHHHHHHhhccCcceeeec-ccCCcceeeecccCccchhhHHHHhcCcCCCCC
Confidence            7552      345678999999999999999999999999999885 3566799999999999999999999999986  


Q ss_pred             cEEEEEeccCCch
Q 002974          427 KQIKLEASRPGGA  439 (861)
Q Consensus       427 r~IkVe~Akpk~~  439 (861)
                      ++|+|.++.+-..
T Consensus       521 ~r~rvdla~~~~~  533 (975)
T KOG0112|consen  521 RRLRVDLASPPGA  533 (975)
T ss_pred             cccccccccCCCC
Confidence            8899999987653

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.80  E-value=8.7e-09  Score=99.16  Aligned_cols=82  Identities=17%  Similarity=0.433  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .....-.|||.++...++|++|.+.|..||+|+.+.+     ++-.||||+|+|++.++|++|+.++||..|.|++|.|.
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            4445789999999999999999999999999999974     68889999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 002974          348 YSIPKDN  354 (861)
Q Consensus       348 ~a~~k~~  354 (861)
                      |+..+..
T Consensus       148 w~Fv~gp  154 (170)
T KOG0130|consen  148 WCFVKGP  154 (170)
T ss_pred             EEEecCC
Confidence            9975543

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.77  E-value=1.2e-08  Score=116.28  Aligned_cols=79  Identities=27%  Similarity=0.368  Sum_probs=74.1

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ..+||+|+|+++++++|..+|+..|.|.++++     +++.|||||++|.+.++|+.|++.|||.++.|++|+|.|+...
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            78999999999999999999999999999875     7888999999999999999999999999999999999999877


Q ss_pred             chhh
Q 002974          438 GARR  441 (861)
Q Consensus       438 ~~rr  441 (861)
                      ..+.
T Consensus        99 ~~~~  102 (435)
T KOG0108|consen   99 KNAE  102 (435)
T ss_pred             chhH
Confidence            6554

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.76  E-value=9.7e-09  Score=98.84  Aligned_cols=81  Identities=21%  Similarity=0.407  Sum_probs=73.0

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      +......|||.++....++++|.+.|..||+|+.|.+     ++-.||||+|+|++.++|++|+.+|||..+.|..|.|.
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            3445678999999999999999999999999999875     55668999999999999999999999999999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      |+--++
T Consensus       148 w~Fv~g  153 (170)
T KOG0130|consen  148 WCFVKG  153 (170)
T ss_pred             EEEecC
Confidence            986554

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.76  E-value=1.5e-09  Score=108.99  Aligned_cols=77  Identities=21%  Similarity=0.349  Sum_probs=71.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...-|||+|||+.+|+.||.-.|++||+|+.|.+     +++++||||+.|+|.++...|+..|||..|.||.|+|....
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            4568999999999999999999999999999864     88999999999999999999999999999999999998754


Q ss_pred             CC
Q 002974          436 PG  437 (861)
Q Consensus       436 pk  437 (861)
                      ..
T Consensus       114 ~Y  115 (219)
T KOG0126|consen  114 NY  115 (219)
T ss_pred             cc
Confidence            43

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.76  E-value=1.6e-07  Score=102.82  Aligned_cols=165  Identities=21%  Similarity=0.355  Sum_probs=135.0

Q ss_pred             CCCCCcEEEEcCCC--CCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccC--cceeeeee
Q 002974          273 GEHPSRTLFVRNIN--SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR--RRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP--~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~--Gr~L~V~~  348 (861)
                      ...+...|.+.=|.  ..+|-+-|..+...+|+|..|.+-.+.--.|+|+|++.+.|++|..+|||..|.  ...|+|+|
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            34556777766554  568899999999999999999886665568999999999999999999998875  57899999


Q ss_pred             cCCCCCC------C-------------C-------------------------------------------------cc-
Q 002974          349 SIPKDNP------S-------------E-------------------------------------------------KD-  359 (861)
Q Consensus       349 a~~k~~~------~-------------~-------------------------------------------------k~-  359 (861)
                      ++|..-.      +             +                                                 ++ 
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            9764210      0             0                                                 00 


Q ss_pred             ---------cCCcceEEecccCC-CcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          360 ---------ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       360 ---------~~~~tLfVgNLp~s-vTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                               .....+.|-+|+.. ++-+.|-.+|..||.|+.|+....+.|-|.|++.|..+.++|+..||+..+-|.+|
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                     00236788899764 56688999999999999999887788999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 002974          430 KLEASRPG  437 (861)
Q Consensus       430 kVe~Akpk  437 (861)
                      .|.+++..
T Consensus       356 ~v~~SkQ~  363 (494)
T KOG1456|consen  356 NVCVSKQN  363 (494)
T ss_pred             EEeecccc
Confidence            99998754

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.75  E-value=1.6e-08  Score=118.52  Aligned_cols=77  Identities=32%  Similarity=0.547  Sum_probs=73.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      ++|||||.|+.+++|.||..+|+.||+|.+|.+ ..++|||||.+....+|.+|+.+|.+..+.++.|+|.|+..+.-
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~l-i~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~  497 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIIL-IPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGP  497 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEee-ccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCc
Confidence            899999999999999999999999999999998 67899999999999999999999999999999999999986544

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.73  E-value=1.9e-08  Score=115.54  Aligned_cols=166  Identities=18%  Similarity=0.332  Sum_probs=136.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcC-----------C-CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQF-----------G-DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR  340 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqf-----------G-~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~  340 (861)
                      .....+.+||+++|+.++++.+..+|..-           | .|..+.+ +..++||||+|.+.++|..|+. +++..+.
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-NLEKNFAFIEFRSISEATEAMA-LDGIIFE  248 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee-cccccceeEEecCCCchhhhhc-ccchhhC
Confidence            34568999999999999999999988743           3 3777777 6788999999999999999995 9999999


Q ss_pred             cceeeeeecCCCCCC-------------------CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CC
Q 002974          341 RRKLDIHYSIPKDNP-------------------SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQ  396 (861)
Q Consensus       341 Gr~L~V~~a~~k~~~-------------------~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tg  396 (861)
                      |+.+++.........                   ........++||++||..+++++++++...||.++..+.     ++
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            998887543221110                   011123568999999999999999999999999987543     46


Q ss_pred             CCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchh
Q 002974          397 HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGAR  440 (861)
Q Consensus       397 ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~r  440 (861)
                      .+|||||.+|.+......|+..|||..+++++|.|..|......
T Consensus       329 ~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~  372 (500)
T KOG0120|consen  329 NSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASN  372 (500)
T ss_pred             cccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchh
Confidence            78999999999999999999999999999999999998776533

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.73  E-value=9.5e-08  Score=108.51  Aligned_cols=142  Identities=19%  Similarity=0.314  Sum_probs=106.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-------CCCccc---EEEEEeCCHHHHHHHHHHcCccccCcce
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-------ACKHRG---FVMISYYDIRAARNAMKALQNKPLRRRK  343 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-------tgksrG---yAFVeF~d~e~A~kALkaLnG~~L~Gr~  343 (861)
                      ..-++.||||+||++++|++|...|..||.+.--.-       ....+|   |+|+.|+++...+.-+.+..-   ...+
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~  332 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGN  332 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccc
Confidence            456999999999999999999999999998765432       123556   999999999998887765322   2222


Q ss_pred             eeeeecCCCCC-------------------CCCcccCCcceEEecccCCCcHHHHHHHhc-ccCcEEEEEeCC-----CC
Q 002974          344 LDIHYSIPKDN-------------------PSEKDANQGTLVVFNLDSSVSTEELHQIFG-IYGEIREIRDTQ-----HK  398 (861)
Q Consensus       344 L~V~~a~~k~~-------------------~~~k~~~~~tLfVgNLp~svTeedLrelFs-kfGeI~sVritg-----ks  398 (861)
                      +.+..+.+...                   ....-...+|||||+||.-++.++|..+|. -||.|..+-|..     -.
T Consensus       333 ~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYP  412 (520)
T KOG0129|consen  333 YYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYP  412 (520)
T ss_pred             eEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCC
Confidence            22222221111                   111223468999999999999999999999 599999987632     35


Q ss_pred             ccEEEEEECCHHHHHHHHHH
Q 002974          399 HNHKFIEFYDIRAAETALRT  418 (861)
Q Consensus       399 KGfAFVeF~d~eaA~kAL~~  418 (861)
                      ||-|=|.|.+..+-.+||.+
T Consensus       413 kGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  413 KGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCcceeeecccHHHHHHHhh
Confidence            78999999999999999983

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.70  E-value=2.4e-08  Score=105.20  Aligned_cols=97  Identities=18%  Similarity=0.335  Sum_probs=82.1

Q ss_pred             cceeeeeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHH
Q 002974          341 RRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETAL  416 (861)
Q Consensus       341 Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL  416 (861)
                      .|.|.|+.+.....    ...+++|||+-|...-.|||++.+|..||.|++|.+    .+.+||+|||+|.+..+|..||
T Consensus         2 nrpiqvkpadsesr----g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI   77 (371)
T KOG0146|consen    2 NRPIQVKPADSESR----GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAI   77 (371)
T ss_pred             CCCccccccccccC----CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHH
Confidence            46777776654322    235789999999999999999999999999999976    5678999999999999999999


Q ss_pred             HHhCCCe-eCC--cEEEEEeccCCchhh
Q 002974          417 RTLNRSD-VAG--KQIKLEASRPGGARR  441 (861)
Q Consensus       417 ~~LNG~~-I~G--r~IkVe~Akpk~~rr  441 (861)
                      ..|+|.. +-|  ..|.|+++....+|.
T Consensus        78 ~aLHgSqTmpGASSSLVVK~ADTdkER~  105 (371)
T KOG0146|consen   78 NALHGSQTMPGASSSLVVKFADTDKERT  105 (371)
T ss_pred             HHhcccccCCCCccceEEEeccchHHHH
Confidence            9999984 444  789999999887776

>smart00361 RRM_1 RNA recognition motif

Probab=98.63  E-value=8.2e-08  Score=82.98  Aligned_cols=57  Identities=28%  Similarity=0.474  Sum_probs=50.5

Q ss_pred             HHHHHHHhc----ccCcEEEEE-e-----C--CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          376 TEELHQIFG----IYGEIREIR-D-----T--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       376 eedLrelFs----kfGeI~sVr-i-----t--gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      +++|+++|+    +||.|.+|. +     +  ++++|||||+|.+.++|.+|++.|||+.+.|+.|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578888888    999999884 2     2  5679999999999999999999999999999999873

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.59  E-value=1.3e-08  Score=104.76  Aligned_cols=129  Identities=23%  Similarity=0.298  Sum_probs=106.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ....+||||+|+-..|+|+-|.++|-+.|+|..|.+    ..+.| ||||.|+++-...-|++.+||..+.++.++|.+-
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            345799999999999999999999999999999986    34455 9999999999999999999999999888887544


Q ss_pred             CCCCCCCCcccCCcceEEec----ccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhC
Q 002974          350 IPKDNPSEKDANQGTLVVFN----LDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLN  420 (861)
Q Consensus       350 ~~k~~~~~k~~~~~tLfVgN----Lp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LN  420 (861)
                                       .|+    |...++++.+.+.|+.-|.|..+++    .++.+.++|+.+....+.-.|+....
T Consensus        85 -----------------~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~  146 (267)
T KOG4454|consen   85 -----------------CGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQ  146 (267)
T ss_pred             -----------------cCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhc
Confidence                             344    5677899999999999999988875    34567788888876666666665433

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.57  E-value=1.1e-07  Score=98.86  Aligned_cols=76  Identities=29%  Similarity=0.542  Sum_probs=71.2

Q ss_pred             cceEEecccCCCcHHHHHH----HhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          363 GTLVVFNLDSSVSTEELHQ----IFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLre----lFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .||||.||+..+..++|++    +|++||+|..|..  +.+.+|-|||.|.+.++|-.|++.|+|..+.|+.++|.||+.
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s   89 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKS   89 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccC
Confidence            3999999999999999988    9999999999875  667899999999999999999999999999999999999998


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      +.
T Consensus        90 ~s   91 (221)
T KOG4206|consen   90 DS   91 (221)
T ss_pred             cc
Confidence            75

>smart00361 RRM_1 RNA recognition motif

Probab=98.56  E-value=1.5e-07  Score=81.43  Aligned_cols=56  Identities=23%  Similarity=0.402  Sum_probs=50.5

Q ss_pred             HHHHHHHhh----cCCCEEEEE---e---C--CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          291 DSELKALFE----QFGDIRTIY---T---A--CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       291 EedL~elFs----qfG~I~svk---i---t--gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      +++|+++|.    +||.|..+.   +   +  +.++|||||+|.+.++|.+|++.|||..+.||.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678899998    999999884   2   2  678999999999999999999999999999999976

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.56  E-value=1.9e-07  Score=101.73  Aligned_cols=83  Identities=23%  Similarity=0.467  Sum_probs=72.9

Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHH-cCccccCcceeeee
Q 002974          269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA-LQNKPLRRRKLDIH  347 (861)
Q Consensus       269 e~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALka-LnG~~L~Gr~L~V~  347 (861)
                      ..+..+...++|||++|...++|.+|++.|.+||+|+.+.+ -..+++|||+|.+.++|+.|.+. ++...|.|++|.|.
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            45566778999999999999999999999999999999997 45667999999999999998875 46566899999999


Q ss_pred             ecCCC
Q 002974          348 YSIPK  352 (861)
Q Consensus       348 ~a~~k  352 (861)
                      |..++
T Consensus       299 Wg~~~  303 (377)
T KOG0153|consen  299 WGRPK  303 (377)
T ss_pred             eCCCc
Confidence            99883

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.54  E-value=1.2e-07  Score=111.22  Aligned_cols=79  Identities=29%  Similarity=0.386  Sum_probs=74.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchhh
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR  441 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~rr  441 (861)
                      .+||||+.|+..+++.||+.+|+.||+|.+|.+. ..+++|||++....+|.+|+.+|+...+.++.|+|.|+..++.+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeec-cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            6899999999999999999999999999999976 478999999999999999999999999999999999999988665

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.49  E-value=8.1e-08  Score=100.90  Aligned_cols=162  Identities=19%  Similarity=0.228  Sum_probs=122.0

Q ss_pred             CcEEEEcCCCCCCcHHH-H--HHHhhcCCCEEEEE----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          277 SRTLFVRNINSNVEDSE-L--KALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       277 srtLfVgNLP~~vTEed-L--~elFsqfG~I~svk----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      --..+++++-..+..+- |  ...|+.|-.+...+    ..+..++++|+.|....+-.++-..-+++.+.-+++++.-.
T Consensus        96 vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~g  175 (290)
T KOG0226|consen   96 VFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAG  175 (290)
T ss_pred             cccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccc
Confidence            34456666666665544 3  55666665544433    24677899999999888888887777778887777766555


Q ss_pred             CCCCCC--CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEE---E--EeCCCCccEEEEEECCHHHHHHHHHHhCCC
Q 002974          350 IPKDNP--SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---I--RDTQHKHNHKFIEFYDIRAAETALRTLNRS  422 (861)
Q Consensus       350 ~~k~~~--~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~s---V--ritgksKGfAFVeF~d~eaA~kAL~~LNG~  422 (861)
                      ..-.++  .+.+.++-+||++.|..+++++.|.+.|.+|-.-..   |  +-+++++||+||.|.+..++..|+++|+|+
T Consensus       176 tswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gk  255 (290)
T KOG0226|consen  176 TSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGK  255 (290)
T ss_pred             cccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccc
Confidence            443333  245567889999999999999999999999854322   2  238899999999999999999999999999


Q ss_pred             eeCCcEEEEEeccCCc
Q 002974          423 DVAGKQIKLEASRPGG  438 (861)
Q Consensus       423 ~I~Gr~IkVe~Akpk~  438 (861)
                      .++.+.|++..+.-+.
T Consensus       256 yVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  256 YVGSRPIKLRKSEWKE  271 (290)
T ss_pred             ccccchhHhhhhhHHh
Confidence            9999999997765544

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.48  E-value=2.8e-07  Score=100.47  Aligned_cols=79  Identities=29%  Similarity=0.405  Sum_probs=69.8

Q ss_pred             CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCC-CeeCCcEEEEEecc
Q 002974          357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR-SDVAGKQIKLEASR  435 (861)
Q Consensus       357 ~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG-~~I~Gr~IkVe~Ak  435 (861)
                      .++..-++|||++|...+++.+|++.|.+||+|+.|++.. .+++|||+|.+.++|+.|.+++-. ..|+|++|+|.|..
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 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP-RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec-ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            3456678999999999999999999999999999999764 567999999999999998876544 47899999999999


Q ss_pred             C
Q 002974          436 P  436 (861)
Q Consensus       436 p  436 (861)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            8

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.47  E-value=3.5e-07  Score=100.64  Aligned_cols=201  Identities=15%  Similarity=0.202  Sum_probs=122.5

Q ss_pred             HHHHHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCccccccCcchhhhcc--CCCcCCCccCCCCCCC
Q 002974          188 IEAQTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQK--NSDFVGGVSNQGVSAG  264 (861)
Q Consensus       188 ~eaq~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGmEle~d~~~s~~~s--~s~~~gg~~~~~~~ng  264 (861)
                      .....||.|..+. +|-|..-+..++.+..+....|..- -..-..|.++++.+...+....  ...+++..-.......
T Consensus         6 ~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t-~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    6 SGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPST-GRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCC-CCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            3345588888877 7777766666766665555554321 1111223345554442221111  2223321111111111


Q ss_pred             cccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCcccc
Q 002974          265 SVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPL  339 (861)
Q Consensus       265 ~~~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L  339 (861)
                      ..............+|||+.||.++++++|++.|++||.|..+-+     +.+.+||+||.|.+.+++++++. ...+.|
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~  163 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDF  163 (311)
T ss_pred             cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeee
Confidence            111111222235779999999999999999999999998877753     67899999999999999999995 778889


Q ss_pred             CcceeeeeecCCCCCCCCcccC-CcceEEecccCCCcHHHHHHHhcccCcEE
Q 002974          340 RRRKLDIHYSIPKDNPSEKDAN-QGTLVVFNLDSSVSTEELHQIFGIYGEIR  390 (861)
Q Consensus       340 ~Gr~L~V~~a~~k~~~~~k~~~-~~tLfVgNLp~svTeedLrelFskfGeI~  390 (861)
                      .++++.|..|.+++........ .......|+....+.-.|..+|.-|+.+.
T Consensus       164 ~gk~vevkrA~pk~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~~  215 (311)
T KOG4205|consen  164 NGKKVEVKRAIPKEVMQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPVG  215 (311)
T ss_pred             cCceeeEeeccchhhccccccccccccccccccccccccccchhccccCccc
Confidence            9999999999998764322111 11222224444444455666666666544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.46  E-value=1.8e-07  Score=102.09  Aligned_cols=163  Identities=20%  Similarity=0.282  Sum_probs=131.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...+++|++++...+.+.+...++..+|.+..+..     ...++|+++|.|...+.+..|+.......+.++.+.....
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            45899999999999999999999999998777653     5678999999999999999999754445666665555444


Q ss_pred             CCCCCCCC------cccCCcceE-EecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHH
Q 002974          350 IPKDNPSE------KDANQGTLV-VFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALR  417 (861)
Q Consensus       350 ~~k~~~~~------k~~~~~tLf-VgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~  417 (861)
                      ........      ......++| |++|+.++++++|+..|..+|.|..+++     .+..++||||+|.+...+..|+.
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~  245 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALN  245 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhh
Confidence            33321110      111233455 9999999999999999999999999986     45678999999999999999999


Q ss_pred             HhCCCeeCCcEEEEEeccCCc
Q 002974          418 TLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       418 ~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      . ....+.++.+.+....+..
T Consensus       246 ~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  246 D-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             c-ccCcccCcccccccCCCCc
Confidence            7 8889999999999988765

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.36  E-value=7.9e-07  Score=97.75  Aligned_cols=160  Identities=12%  Similarity=0.189  Sum_probs=117.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcC-----C--CEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQF-----G--DIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqf-----G--~I~svki-tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      --.|-.++||+++++.|+.++|.+-     |  .|.-|+. +++..|-|||.|..+++|+.|+. .+...+..|-|.+-.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIElFR  239 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIELFR  239 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHHHH
Confidence            4456668999999999999999632     2  2344443 78899999999999999999996 455555555444422


Q ss_pred             cCCC-----------------CC-------C---CCcccCCcceEEecccCCCcHHHHHHHhcccCc-EEE--EEe----
Q 002974          349 SIPK-----------------DN-------P---SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE-IRE--IRD----  394 (861)
Q Consensus       349 a~~k-----------------~~-------~---~~k~~~~~tLfVgNLp~svTeedLrelFskfGe-I~s--Vri----  394 (861)
                      +...                 ..       +   ........+|.+++||+..+.|+|.++|..|-. |..  |.+    
T Consensus       240 STaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~  319 (508)
T KOG1365|consen  240 STAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG  319 (508)
T ss_pred             HhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC
Confidence            2100                 00       0   011223678999999999999999999998864 222  332    


Q ss_pred             CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          395 TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       395 tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      .++..|-|||+|.+.+.|.+|....+.+..+.|-|.|-.+.-.
T Consensus       320 qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~e  362 (508)
T KOG1365|consen  320 QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVE  362 (508)
T ss_pred             CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHH
Confidence            4667789999999999999999998888888999998776543

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.34  E-value=6.1e-08  Score=114.97  Aligned_cols=141  Identities=13%  Similarity=0.213  Sum_probs=122.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +..+++||+||+..+.+++|...|..+|.+..+++     .++-||+|||.|..+++|.+|+....++.+.         
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g---------  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG---------  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh---------
Confidence            45678999999999999999999999998877753     6888999999999999999999754443332         


Q ss_pred             CCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          350 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       350 ~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                                  ...++|.|+|+..|.++|+.+|+++|.+++.++    .++.+|.|+|.|.+..+|.+++...+...+.
T Consensus       736 ------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~r  803 (881)
T KOG0128|consen  736 ------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKR  803 (881)
T ss_pred             ------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhh
Confidence                        346999999999999999999999999999764    4678999999999999999999988888888


Q ss_pred             CcEEEEEeccC
Q 002974          426 GKQIKLEASRP  436 (861)
Q Consensus       426 Gr~IkVe~Akp  436 (861)
                      -+.+.|..+.|
T Consensus       804 E~~~~v~vsnp  814 (881)
T KOG0128|consen  804 ENNGEVQVSNP  814 (881)
T ss_pred             hcCccccccCC
Confidence            88888877766

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.27  E-value=2.2e-06  Score=88.12  Aligned_cols=80  Identities=19%  Similarity=0.358  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcC-CCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQF-GDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqf-G~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ......-+||+.+|.-+.+.++..+|.++ |.|+.+++     ||.+||||||+|++.+.|.-|-+.||+..+.++.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            44567789999999999999999999998 77777764     8999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 002974          347 HYSIPK  352 (861)
Q Consensus       347 ~~a~~k  352 (861)
                      ++-.+.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            987654

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.26  E-value=9.8e-07  Score=96.20  Aligned_cols=78  Identities=21%  Similarity=0.427  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..|.+.|||-.|.+-++++||.-+|+.||.|.+|.+     ++.+.-||||+|++.+++++|.-.|++..|..+.|.|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            457899999999999999999999999999999974     788888999999999999999999999999999999999


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      +..
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            864

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.13  E-value=3e-06  Score=92.50  Aligned_cols=80  Identities=23%  Similarity=0.345  Sum_probs=72.4

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      .+...|||.-|.+-+++++|.-+|+.||+|.+|.+     ++.+-.||||+|.+.+++++|.-+|++..|..++|.|.++
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            45678999999999999999999999999999876     4556679999999999999999999999999999999999


Q ss_pred             cCCch
Q 002974          435 RPGGA  439 (861)
Q Consensus       435 kpk~~  439 (861)
                      +.-..
T Consensus       317 QSVsk  321 (479)
T KOG0415|consen  317 QSVSK  321 (479)
T ss_pred             hhhhh
Confidence            87553

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.09  E-value=6.1e-06  Score=94.22  Aligned_cols=78  Identities=18%  Similarity=0.333  Sum_probs=70.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..-.++|||.+|...+...+|++||++||+|+-.++     +...+.|+||++.+.++|.+||..|+.+.|.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            445899999999999999999999999999998884     344677999999999999999999999999999999988


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      ++.
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            753

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.07  E-value=8.1e-06  Score=95.56  Aligned_cols=79  Identities=20%  Similarity=0.405  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--------CCCcccEEEEEeCCHHHHHHHHHHcCccccCccee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  344 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L  344 (861)
                      ++...++|||+||++.++++.|...|..||+|..+++        ....+.|+||.|-+..+|++|++.|+|+.+.+..+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            4556889999999999999999999999999999985        34567799999999999999999999999999999


Q ss_pred             eeeecCC
Q 002974          345 DIHYSIP  351 (861)
Q Consensus       345 ~V~~a~~  351 (861)
                      ++.|+++
T Consensus       250 K~gWgk~  256 (877)
T KOG0151|consen  250 KLGWGKA  256 (877)
T ss_pred             eeccccc
Confidence            9999853

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.04  E-value=5.9e-07  Score=99.65  Aligned_cols=149  Identities=17%  Similarity=0.335  Sum_probs=123.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcC--CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccc-cCcceeeeeecCCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQF--GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP-LRRRKLDIHYSIPKDN  354 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqf--G~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~-L~Gr~L~V~~a~~k~~  354 (861)
                      ..||++||.+.++.++|..+|...  +--..+   -...|||||.+.+...|.+|++.++|+. +.|+.+.|..+.++..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f---l~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq   78 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF---LVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce---eeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            468999999999999999999854  111111   1246899999999999999999999975 8899999999988766


Q ss_pred             CCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCC--ccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK--HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       355 ~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgks--KGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ++      +++-|.|+|+...++.|..+...||.++.|..+...  .-..-|+|...+.+..||..|+|..+....++|.
T Consensus        79 rs------rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~  152 (584)
T KOG2193|consen   79 RS------RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVG  152 (584)
T ss_pred             Hh------hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcc
Confidence            53      459999999999999999999999999988653222  2234578889999999999999999999999998


Q ss_pred             ecc
Q 002974          433 ASR  435 (861)
Q Consensus       433 ~Ak  435 (861)
                      |--
T Consensus       153 YiP  155 (584)
T KOG2193|consen  153 YIP  155 (584)
T ss_pred             cCc
Confidence            753

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.02  E-value=1.4e-05  Score=82.39  Aligned_cols=78  Identities=19%  Similarity=0.272  Sum_probs=71.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhccc-CcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIY-GEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskf-GeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ...+.+||..+|.-+.+.++..+|.+| |.|..+++     +|.+||||||+|++.+.|+-|-+.||+..+.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            446789999999999999999999998 77887765     789999999999999999999999999999999999999


Q ss_pred             ccCC
Q 002974          434 SRPG  437 (861)
Q Consensus       434 Akpk  437 (861)
                      -.|.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            8877

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.01  E-value=8.7e-06  Score=93.01  Aligned_cols=76  Identities=20%  Similarity=0.366  Sum_probs=68.6

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||.+|...+-..+|+.+|++||+|+-.++     .+..++|+||++.+.++|.+||..|+.+++.|+.|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            468999999999999999999999999988775     334578999999999999999999999999999999999865


Q ss_pred             C
Q 002974          437 G  437 (861)
Q Consensus       437 k  437 (861)
                      .
T Consensus       485 E  485 (940)
T KOG4661|consen  485 E  485 (940)
T ss_pred             C
Confidence            3

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.96  E-value=4.1e-06  Score=86.69  Aligned_cols=76  Identities=21%  Similarity=0.203  Sum_probs=67.7

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ..+||||+|+...++++-|.++|-+-|.|..|.+.    .+.| ||||.|.++....-|++.+||..+.++.|+|.+-.-
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            46799999999999999999999999999999873    2334 999999999999999999999999999999887654


Q ss_pred             C
Q 002974          437 G  437 (861)
Q Consensus       437 k  437 (861)
                      .
T Consensus        87 ~   87 (267)
T KOG4454|consen   87 N   87 (267)
T ss_pred             C
Confidence            3

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.91  E-value=1.4e-05  Score=93.70  Aligned_cols=78  Identities=28%  Similarity=0.399  Sum_probs=71.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC--------CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT--------QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit--------gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      +...++|||+||++.++++.|...|+.||.|..|++.        ...+.++||-|-+..+|++|++.|+|..+.++.++
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            5667899999999999999999999999999999862        23467999999999999999999999999999999


Q ss_pred             EEeccC
Q 002974          431 LEASRP  436 (861)
Q Consensus       431 Ve~Akp  436 (861)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999964

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.88  E-value=8.6e-06  Score=85.28  Aligned_cols=71  Identities=24%  Similarity=0.433  Sum_probs=66.3

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ..+||++||+.+.+.+|..+|..||.|..|.+   ..+|+||+|.|..+|..|+..||+++|.|.++.|++++.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m---k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM---KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee---ecccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            36899999999999999999999999999886   468999999999999999999999999998899999885

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.85  E-value=3.5e-05  Score=82.24  Aligned_cols=79  Identities=27%  Similarity=0.384  Sum_probs=70.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .+.-..+|+|.|||..|+++||+++|.+||.+..+-+    .+.+.|.|=|.|...++|.+|++.++|..+.|+.+++..
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            3344678999999999999999999999998887764    688999999999999999999999999999999999887


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      ..+
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.85  E-value=2.2e-05  Score=89.67  Aligned_cols=77  Identities=26%  Similarity=0.417  Sum_probs=64.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .....+|||+|||.++++++|++.|.+||.|+...+     .++...||||+|++.++++.|+.+- -..|.+++|.|+-
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Vee  363 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEE  363 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEe
Confidence            344666999999999999999999999999998875     2344489999999999999999754 6778899999975


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      -.+
T Consensus       364 k~~  366 (419)
T KOG0116|consen  364 KRP  366 (419)
T ss_pred             ccc
Confidence            443

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.84  E-value=2.5e-05  Score=91.28  Aligned_cols=167  Identities=14%  Similarity=0.072  Sum_probs=121.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhc-CC---CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQ-FG---DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsq-fG---~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      +.-..+.+.+-++.++.+.++.|++++|.. +-   .|....+.....|-++|+|....++++|++ -+......|.+.|
T Consensus       305 pqvv~d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~  383 (944)
T KOG4307|consen  305 PQVVSDKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQT  383 (944)
T ss_pred             CcccchhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceee
Confidence            334445666777899999999999999973 22   233333555568999999999999999986 5666666777777


Q ss_pred             eecCCCCC------------C--------------CC---------cccCCcceEEecccCCCcHHHHHHHhcccCcEEE
Q 002974          347 HYSIPKDN------------P--------------SE---------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE  391 (861)
Q Consensus       347 ~~a~~k~~------------~--------------~~---------k~~~~~tLfVgNLp~svTeedLrelFskfGeI~s  391 (861)
                      ..+.....            .              .+         .......|||..||..+++.++.++|+..-.|++
T Consensus       384 ~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved  463 (944)
T KOG4307|consen  384 GPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVED  463 (944)
T ss_pred             cCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhh
Confidence            44321100            0              00         0112458999999999999999999998777766


Q ss_pred             -EEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          392 -IRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       392 -Vri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                       |.+    +++.++.|||.|..++++.+|...-+...++.+.|+|.-...+.
T Consensus       464 ~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~  515 (944)
T KOG4307|consen  464 FIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYA  515 (944)
T ss_pred             eeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhHH
Confidence             665    34456789999999999999998666677778999998654433

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.83  E-value=4.5e-05  Score=79.40  Aligned_cols=78  Identities=21%  Similarity=0.292  Sum_probs=66.1

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEE--EEeCCCC----ccEEEEEECCHHHHHHHHHHhCCCeeC---CcEEEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--IRDTQHK----HNHKFIEFYDIRAAETALRTLNRSDVA---GKQIKL  431 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~s--Vritgks----KGfAFVeF~d~eaA~kAL~~LNG~~I~---Gr~IkV  431 (861)
                      .-+||||.+||.++...+|+.+|..|---+.  ++.+.+.    +-+|||.|.+...|.+|+.+|||..++   +..|++
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            4689999999999999999999999754444  3444443    368999999999999999999999986   789999


Q ss_pred             EeccCCc
Q 002974          432 EASRPGG  438 (861)
Q Consensus       432 e~Akpk~  438 (861)
                      ++++...
T Consensus       113 ElAKSNt  119 (284)
T KOG1457|consen  113 ELAKSNT  119 (284)
T ss_pred             eehhcCc
Confidence            9998765

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.81  E-value=2.9e-05  Score=88.69  Aligned_cols=75  Identities=25%  Similarity=0.452  Sum_probs=64.6

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe---C--CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD---T--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri---t--gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      .+|||+|||.+++.++|+++|+.||.|+...+   .  ++...||||+|++.++++.||++ +-..|++++|.|+-.++.
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            45999999999999999999999999998654   1  23348999999999999999995 577899999999987765


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            4

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.73  E-value=6.1e-05  Score=82.61  Aligned_cols=74  Identities=15%  Similarity=0.342  Sum_probs=66.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEE--------EEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~s--------Vri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                      ++.|||.|||.++|.+++.++|++||.|..        |++    .++-||=|++.|--.++...|++.|++..+.|++|
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            567999999999999999999999999876        343    45668889999999999999999999999999999


Q ss_pred             EEEecc
Q 002974          430 KLEASR  435 (861)
Q Consensus       430 kVe~Ak  435 (861)
                      +|+.|+
T Consensus       214 rVerAk  219 (382)
T KOG1548|consen  214 RVERAK  219 (382)
T ss_pred             EEehhh
Confidence            999874

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.73  E-value=8.8e-05  Score=79.25  Aligned_cols=78  Identities=21%  Similarity=0.330  Sum_probs=70.2

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ...+|+|.||++.|+++||+++|..||.++.+-+    .+.+.|.|-|.|...++|++|++.+++..+.|+.+++....+
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            4578999999999999999999999998888755    566789999999999999999999999999999999988776


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            54

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.68  E-value=0.00012  Score=80.96  Aligned_cols=155  Identities=16%  Similarity=0.230  Sum_probs=113.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhc-----CCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQ-----FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsq-----fG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ++..+-.++||+..++.+|..+|+-     -|.+......+...|.|.|.|.|.+.-+.|++ -+...+.+|.|.|-.+.
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka~  137 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKAT  137 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeeccC
Confidence            3555667899999999999999973     34444444568888999999999999999997 66677778888775544


Q ss_pred             CCCC------------CCCcccCCcceEEecccCCCcHHHHHHHhccc-----C--cEEEEEe-CCCCccEEEEEECCHH
Q 002974          351 PKDN------------PSEKDANQGTLVVFNLDSSVSTEELHQIFGIY-----G--EIREIRD-TQHKHNHKFIEFYDIR  410 (861)
Q Consensus       351 ~k~~------------~~~k~~~~~tLfVgNLp~svTeedLrelFskf-----G--eI~sVri-tgksKGfAFVeF~d~e  410 (861)
                      ..+-            +--...++-.|.+++||+++++.|+.++|..-     |  .|..|+- .++..|-|||.|..++
T Consensus       138 ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee  217 (508)
T KOG1365|consen  138 GEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEE  217 (508)
T ss_pred             chhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHH
Confidence            3211            01122345577889999999999999999732     2  2333443 5677899999999999


Q ss_pred             HHHHHHHHhCCCeeCCcEEEEE
Q 002974          411 AAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       411 aA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      +|+.||.+ |...|+-|-|.+-
T Consensus       218 ~aq~aL~k-hrq~iGqRYIElF  238 (508)
T KOG1365|consen  218 DAQFALRK-HRQNIGQRYIELF  238 (508)
T ss_pred             HHHHHHHH-HHHHHhHHHHHHH
Confidence            99999984 5556655655553

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

Probab=97.62  E-value=0.00021  Score=66.37  Aligned_cols=74  Identities=20%  Similarity=0.352  Sum_probs=60.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcC--CCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccC----cceeee
Q 002974          278 RTLFVRNINSNVEDSELKALFEQF--GDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLR----RRKLDI  346 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqf--G~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~----Gr~L~V  346 (861)
                      +||.|+|||...|.++|.+++...  |...-+++     ++.+.|||||.|.+++.|.+..+.++|+.+.    .+.+.|
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            689999999999999999988754  44444442     5778999999999999999999999998875    456677


Q ss_pred             eecCC
Q 002974          347 HYSIP  351 (861)
Q Consensus       347 ~~a~~  351 (861)
                      .||.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77753

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=97.62  E-value=2.5e-05  Score=86.56  Aligned_cols=157  Identities=18%  Similarity=0.179  Sum_probs=117.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC--------CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTA--------CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkit--------gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ..|.|.||.+.++.++++.||...|+|..+++-        ......|||.|.|...+..|- .|.++++-++.|.|-.+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence            489999999999999999999999999998741        234568999999999988887 58888887877766432


Q ss_pred             CCCCC-------------------CC---------C-c-----------------------ccCCcceEEecccCCCcHH
Q 002974          350 IPKDN-------------------PS---------E-K-----------------------DANQGTLVVFNLDSSVSTE  377 (861)
Q Consensus       350 ~~k~~-------------------~~---------~-k-----------------------~~~~~tLfVgNLp~svTee  377 (861)
                      .....                   +.         . +                       ..-.++++|.+|+..+...
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            11000                   00         0 0                       0013689999999999999


Q ss_pred             HHHHHhcccCcEEEEEeC-CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          378 ELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       378 dLrelFskfGeI~sVrit-gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ++.+.|..+|+|...++. +...-+|-|+|........|++ ++|.++.-....+..-+|
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            999999999999887753 3345678899999999999998 677777643333333333

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.62  E-value=6.3e-05  Score=80.07  Aligned_cols=79  Identities=16%  Similarity=0.295  Sum_probs=70.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.+.+||+|+...++.+++...|+.||.|..+.     ..+.+||||||+|.+.+.+++|++ |++..|.|+.+.|
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            4566789999999999999999999999999997554     356689999999999999999998 9999999999999


Q ss_pred             eecCC
Q 002974          347 HYSIP  351 (861)
Q Consensus       347 ~~a~~  351 (861)
                      .+...
T Consensus       175 t~~r~  179 (231)
T KOG4209|consen  175 TLKRT  179 (231)
T ss_pred             eeeee
Confidence            87654

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.62  E-value=7.2e-05  Score=79.63  Aligned_cols=79  Identities=23%  Similarity=0.376  Sum_probs=70.0

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      +......+||+|+...++.+++...|+.||.|..|.+     .++.|||+||+|.+.+.++.|+. |++..|.|+.|.|.
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            3456778999999999999999999999999975543     45679999999999999999999 99999999999999


Q ss_pred             eccCC
Q 002974          433 ASRPG  437 (861)
Q Consensus       433 ~Akpk  437 (861)
                      +.+-.
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            88754

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.54  E-value=0.00013  Score=83.19  Aligned_cols=104  Identities=15%  Similarity=0.162  Sum_probs=80.5

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEE---EEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~s---VritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      .-|-+++||+++|++||+++|+.++ |+.   .+.+++..|-|||+|.+.+++++|++ .+...+..|-|.|-.+...+.
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e~   88 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAEA   88 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCccc
Confidence            4577889999999999999999986 344   34468889999999999999999999 688889999999999988775


Q ss_pred             hhhchhhhhhh-cccc-CC-CCCCCCCCcccc
Q 002974          440 RRFMVQSEQEQ-DDLN-LC-QIPFDDLSSGQM  468 (861)
Q Consensus       440 rrl~qq~eq~q-~E~~-vg-kNLp~s~tee~L  468 (861)
                      ...++...-.. .... |- +.||.+++++++
T Consensus        89 d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI  120 (510)
T KOG4211|consen   89 DWVMRPGGPNSSANDGVVRLRGLPFSCTEEDI  120 (510)
T ss_pred             cccccCCCCCCCCCCceEEecCCCccCcHHHH
Confidence            55333311111 1111 22 889999999988

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.47  E-value=0.00012  Score=77.72  Aligned_cols=76  Identities=20%  Similarity=0.319  Sum_probs=66.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCE-----EEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDI-----RTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I-----~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...-+||.|.|..+++++-|...|.+|-..     ..-+-+++++||+||.|.++.++..|++.|+|+.++.|.|++.-+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            446789999999999999999999988643     333357999999999999999999999999999999999988655


Q ss_pred             C
Q 002974          350 I  350 (861)
Q Consensus       350 ~  350 (861)
                      .
T Consensus       268 ~  268 (290)
T KOG0226|consen  268 E  268 (290)
T ss_pred             h
Confidence            4

>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=97.45  E-value=0.00046  Score=62.35  Aligned_cols=69  Identities=20%  Similarity=0.388  Sum_probs=49.1

Q ss_pred             cEEEEcCCCCCCcHHH----HHHHhhcCC-CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          278 RTLFVRNINSNVEDSE----LKALFEQFG-DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       278 rtLfVgNLP~~vTEed----L~elFsqfG-~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ..|||.|||.+.+...    |+.|+..|| +|..|     ..+.|+|.|.+.+.|++|.+.|+|..+.|++|.|.|...
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            4699999999998765    556777886 67766     357999999999999999999999999999999999843

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.40  E-value=0.00065  Score=61.42  Aligned_cols=69  Identities=23%  Similarity=0.307  Sum_probs=48.6

Q ss_pred             cceEEecccCCCcHHH----HHHHhcccC-cEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          363 GTLVVFNLDSSVSTEE----LHQIFGIYG-EIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       363 ~tLfVgNLp~svTeed----LrelFskfG-eI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ..|+|.|||.+.+...    |++++..+| +|.+|.     .+-|+|.|.+.+.|.+|.+.|+|..+.|.+|.|.+...
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            4699999999887654    667777875 676663     47899999999999999999999999999999999843

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.27  E-value=5.7e-05  Score=90.50  Aligned_cols=186  Identities=15%  Similarity=0.135  Sum_probs=135.9

Q ss_pred             CCcEEEEcCCCCCCcHH-HHHHHhhcCCCEEEEEeCC----Ccc-cEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          276 PSRTLFVRNINSNVEDS-ELKALFEQFGDIRTIYTAC----KHR-GFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEe-dL~elFsqfG~I~svkitg----ksr-GyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ..+...+.|+.+...+. ..+..|..+|.|..|+...    .+. .++++.+....+++.|.. ..+.-+.++.+.|..+
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~a  648 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLA  648 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCC
Confidence            35677888888887776 5778999999999998632    222 388999999999999985 7888899999998888


Q ss_pred             CCCCCCCCcc------cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHH
Q 002974          350 IPKDNPSEKD------ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRT  418 (861)
Q Consensus       350 ~~k~~~~~k~------~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~  418 (861)
                      .++.......      ....++||.||+..+.+++|...|..+|.+..+++     .++-+|+|||+|...+.|.+|+..
T Consensus       649 d~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f  728 (881)
T KOG0128|consen  649 DAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF  728 (881)
T ss_pred             CchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhh
Confidence            7665332221      12348999999999999999999999998887654     456689999999999999999995


Q ss_pred             hCCCeeCCcEEEEEeccCCchhhhchhhhhhhccccCCCCCCCCCCcccc----CCcccEEEEe---CCCCCccee
Q 002974          419 LNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQM----VSSGVITSTC---MDNGSIQVL  487 (861)
Q Consensus       419 LNG~~I~Gr~IkVe~Akpk~~rrl~qq~eq~q~E~~vgkNLp~s~tee~L----s~fG~I~Sv~---~enG~srGF  487 (861)
                      ..+..++...+.|                         +++|..-|.+.+    ..+|++++.+   .-.|+.+|.
T Consensus       729 ~d~~~~gK~~v~i-------------------------~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~  779 (881)
T KOG0128|consen  729 RDSCFFGKISVAI-------------------------SGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGK  779 (881)
T ss_pred             hhhhhhhhhhhhe-------------------------eCCCCCCchHHHHhhccccCCccccchhhhhccccccc
Confidence            5444444222222                         334444444444    5666666665   445666665

>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=97.12  E-value=0.00069  Score=63.79  Aligned_cols=77  Identities=22%  Similarity=0.388  Sum_probs=48.6

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCC-----eeCCcEEEEEeccCCc
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS-----DVAGKQIKLEASRPGG  438 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~-----~I~Gr~IkVe~Akpk~  438 (861)
                      .|.|.+++..++.++|++.|+.||.|..|... .....|+|.|.+.++|++|+..+...     .|.+..+.++.-.-..
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~-~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLeGee   81 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS-RGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLEGEE   81 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---HHH
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEec-CCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECCCHH
Confidence            47889999999999999999999999999864 34558999999999999999877544     6677777777655444


Q ss_pred             hhh
Q 002974          439 ARR  441 (861)
Q Consensus       439 ~rr  441 (861)
                      +..
T Consensus        82 E~~   84 (105)
T PF08777_consen   82 EEE   84 (105)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>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=96.68  E-value=0.0043  Score=58.48  Aligned_cols=59  Identities=17%  Similarity=0.282  Sum_probs=39.4

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCcc
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK  337 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~  337 (861)
                      +.|+|.+++..++-++|+++|++||.|..|.+. +...-|||.|.+.++|++|++.+.-.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~-~G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS-RGDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE---TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEec-CCCCEEEEEECCcchHHHHHHHHHhc
Confidence            578999999999999999999999999999873 34448999999999999999876543

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.66  E-value=0.0029  Score=67.46  Aligned_cols=90  Identities=23%  Similarity=0.323  Sum_probs=75.8

Q ss_pred             HHHHHHHHHcCccccCcceeeeeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEE----EeCCCCcc
Q 002974          325 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI----RDTQHKHN  400 (861)
Q Consensus       325 e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sV----ritgksKG  400 (861)
                      .-|..|...|++....++.|+|.|+..           ..|||.||..-++.+.|.+.|+.||+|...    ...++..+
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            357788888999999999999999963           469999999999999999999999998762    23455667


Q ss_pred             EEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          401 HKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       401 fAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                      -++|+|...-.|.+|++.+...-+.
T Consensus        74 eg~v~~~~k~~a~~a~rr~~~~g~~   98 (275)
T KOG0115|consen   74 EGIVEFAKKPNARKAARRCREGGFG   98 (275)
T ss_pred             cchhhhhcchhHHHHHHHhccCccc
Confidence            8999999999999999987554443

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.63  E-value=0.0028  Score=71.49  Aligned_cols=77  Identities=29%  Similarity=0.380  Sum_probs=60.7

Q ss_pred             CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCC------------------CccEEEEEECCHHHHHHHHH
Q 002974          356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH------------------KHNHKFIEFYDIRAAETALR  417 (861)
Q Consensus       356 ~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgk------------------sKGfAFVeF~d~eaA~kAL~  417 (861)
                      .+++...++|.+.|||.+-.-+.|.+||+.+|.|+.|++..-                  .+-+|+|+|...++|.+|.+
T Consensus       225 ~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e  304 (484)
T KOG1855|consen  225 DEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARE  304 (484)
T ss_pred             cccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHH
Confidence            345567899999999999888999999999999999986211                  14579999999999999999


Q ss_pred             HhCCCeeCCcEEEEE
Q 002974          418 TLNRSDVAGKQIKLE  432 (861)
Q Consensus       418 ~LNG~~I~Gr~IkVe  432 (861)
                      .|+...-.-.-++|.
T Consensus       305 ~~~~e~~wr~glkvk  319 (484)
T KOG1855|consen  305 LLNPEQNWRMGLKVK  319 (484)
T ss_pred             hhchhhhhhhcchhh
Confidence            876554443334443

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.60  E-value=0.003  Score=69.31  Aligned_cols=78  Identities=26%  Similarity=0.374  Sum_probs=64.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHH------HHHhhcCCCEEEEEeCCCc------cc--EEEEEeCCHHHHHHHHHHcCccccC
Q 002974          275 HPSRTLFVRNINSNVEDSEL------KALFEQFGDIRTIYTACKH------RG--FVMISYYDIRAARNAMKALQNKPLR  340 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL------~elFsqfG~I~svkitgks------rG--yAFVeF~d~e~A~kALkaLnG~~L~  340 (861)
                      ....-+||-+||+.+..++.      .++|.+||.|..|.+..+.      .+  -+||.|.+.++|.+||.+.+|..+.
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            34667899999999887773      2799999999998763322      22  2499999999999999999999999


Q ss_pred             cceeeeeecCCC
Q 002974          341 RRKLDIHYSIPK  352 (861)
Q Consensus       341 Gr~L~V~~a~~k  352 (861)
                      ||.|+..|...|
T Consensus       192 Gr~lkatYGTTK  203 (480)
T COG5175         192 GRVLKATYGTTK  203 (480)
T ss_pred             CceEeeecCchH
Confidence            999999988765

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.52  E-value=0.0047  Score=67.80  Aligned_cols=76  Identities=22%  Similarity=0.430  Sum_probs=62.2

Q ss_pred             CcceEEecccCCCcHHHH------HHHhcccCcEEEEEeCCCC------ccE--EEEEECCHHHHHHHHHHhCCCeeCCc
Q 002974          362 QGTLVVFNLDSSVSTEEL------HQIFGIYGEIREIRDTQHK------HNH--KFIEFYDIRAAETALRTLNRSDVAGK  427 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedL------relFskfGeI~sVritgks------KGf--AFVeF~d~eaA~kAL~~LNG~~I~Gr  427 (861)
                      ..-+||-+|++.+-.|++      .++|.+||+|..|.+..+.      .+.  .||+|.+.++|.+||.+.+|..++||
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            456899999998877762      4789999999998763221      122  49999999999999999999999999


Q ss_pred             EEEEEeccCC
Q 002974          428 QIKLEASRPG  437 (861)
Q Consensus       428 ~IkVe~Akpk  437 (861)
                      .|+..|...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999987654

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.46  E-value=0.2  Score=55.78  Aligned_cols=73  Identities=11%  Similarity=0.120  Sum_probs=60.7

Q ss_pred             cceEEecccCCCcHHHHHHHhcccC--cEEEEE-----eCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYG--EIREIR-----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfG--eI~sVr-----itgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      -++||+||-+.+|++||.+....-|  .+.+++     ..+++||||+|...+..+.++-++.|-.++|.|..-.|..+.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            4799999999999999999988766  334443     367899999999999999999999999999999766665444

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.42  E-value=0.0069  Score=50.25  Aligned_cols=52  Identities=23%  Similarity=0.374  Sum_probs=43.4

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHH
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL  416 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL  416 (861)
                      +.|-|.+.+....+ .++..|..||+|..+.+. ..+...+|+|.+..+|++||
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            46888999877664 455688899999999875 56789999999999999995

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.41  E-value=0.0071  Score=50.14  Aligned_cols=53  Identities=21%  Similarity=0.435  Sum_probs=43.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHH
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAM  331 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kAL  331 (861)
                      ++.|-|.+.+++..+. +.+.|.+||+|..+.++ ....+.||+|.+..+|++|+
T Consensus         1 ~~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~-~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP-ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC-CCCcEEEEEECCHHHHHhhC
Confidence            3578888888776654 45589999999999984 56779999999999999995

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.37  E-value=0.003  Score=70.09  Aligned_cols=79  Identities=20%  Similarity=0.300  Sum_probs=69.9

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEE-------------eCCCCccEEEEEECCHHHHHHHHHHhCCCeeCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-------------DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG  426 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVr-------------itgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G  426 (861)
                      ....+|||-+|+..+++++|.++|.++|.|+.=+             .+.+.|+-|.|.|.|..+|++|+.-++++.+.|
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3456899999999999999999999999987622             366778999999999999999999999999999


Q ss_pred             cEEEEEeccCCc
Q 002974          427 KQIKLEASRPGG  438 (861)
Q Consensus       427 r~IkVe~Akpk~  438 (861)
                      .+|+|.++..+.
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999998887654

>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=96.36  E-value=0.0096  Score=55.81  Aligned_cols=74  Identities=20%  Similarity=0.300  Sum_probs=54.1

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEE------------eCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCc-
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR------------DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGK-  427 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVr------------itgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr-  427 (861)
                      ..+.|.|.+.|+.. -..|.+.|++||+|.+..            -.....+...|+|.++.+|.+||+ -||..+.|. 
T Consensus         5 ~~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            34678999999884 456778999999998875            123456789999999999999999 699999985 


Q ss_pred             EEEEEeccC
Q 002974          428 QIKLEASRP  436 (861)
Q Consensus       428 ~IkVe~Akp  436 (861)
                      .+-|.++++
T Consensus        83 mvGV~~~~~   91 (100)
T PF05172_consen   83 MVGVKPCDP   91 (100)
T ss_dssp             EEEEEE-HH
T ss_pred             EEEEEEcHH
Confidence            556777743

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.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.12  E-value=0.0062  Score=67.70  Aligned_cols=80  Identities=20%  Similarity=0.274  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-------------eCCCcccEEEEEeCCHHHHHHHHHHcCccccC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-------------TACKHRGFVMISYYDIRAARNAMKALQNKPLR  340 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-------------itgksrGyAFVeF~d~e~A~kALkaLnG~~L~  340 (861)
                      .....+|||-+||..+++.+|.+.|.+||.|..-+             .|.+.|+-|.|.|.|...|+.|+..++++.+.
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            45678999999999999999999999999886543             26789999999999999999999999999999


Q ss_pred             cceeeeeecCCCC
Q 002974          341 RRKLDIHYSIPKD  353 (861)
Q Consensus       341 Gr~L~V~~a~~k~  353 (861)
                      +..|+|..+..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998886543

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.11  E-value=0.0051  Score=69.50  Aligned_cols=74  Identities=28%  Similarity=0.486  Sum_probs=59.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCC-------------------cccEEEEEeCCHHHHHHHHHH
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-------------------HRGFVMISYYDIRAARNAMKA  333 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgk-------------------srGyAFVeF~d~e~A~kALka  333 (861)
                      .+-++++|.+-|||.+-.-+-|.++|..||.|..|++ ++                   .+-+|+|+|...+.|.+|.+.
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRI-ckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRI-CKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeee-cCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            3458999999999999999999999999999999986 11                   255899999999999999997


Q ss_pred             cCccccCcceeeee
Q 002974          334 LQNKPLRRRKLDIH  347 (861)
Q Consensus       334 LnG~~L~Gr~L~V~  347 (861)
                      |+...-+..-|+|.
T Consensus       306 ~~~e~~wr~glkvk  319 (484)
T KOG1855|consen  306 LNPEQNWRMGLKVK  319 (484)
T ss_pred             hchhhhhhhcchhh
Confidence            76554444444443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=95.80  E-value=0.0074  Score=66.39  Aligned_cols=78  Identities=22%  Similarity=0.440  Sum_probs=69.2

Q ss_pred             CCcEEE-EcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          276 PSRTLF-VRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       276 ~srtLf-VgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +..++| |++|+.++++++|+..|..+|.|..+++     ++..+|||||.|.....+..|+.. +...+.++.+.+.+.
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            455555 9999999999999999999999999985     678999999999999999999987 888899999999988


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .+...
T Consensus       262 ~~~~~  266 (285)
T KOG4210|consen  262 EPRPK  266 (285)
T ss_pred             CCCcc
Confidence            76544

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.73  E-value=0.035  Score=67.81  Aligned_cols=80  Identities=25%  Similarity=0.375  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCc--ceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~G--r~L~V~~a~  350 (861)
                      ...+.+.+||++|.+.+....|...|..||.|+.|.+ ....-||||.|++...|+.|+..|.|..|.+  +.|+|.|+.
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            5567999999999999999999999999999999987 4455699999999999999999999999984  779998886


Q ss_pred             CCC
Q 002974          351 PKD  353 (861)
Q Consensus       351 ~k~  353 (861)
                      +..
T Consensus       530 ~~~  532 (975)
T KOG0112|consen  530 PPG  532 (975)
T ss_pred             CCC
Confidence            543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=95.70  E-value=0.024  Score=67.35  Aligned_cols=71  Identities=20%  Similarity=0.280  Sum_probs=61.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCE----EEEE-eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDI----RTIY-TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I----~svk-itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      +.|-+.|+|++++.+||.++|..|-.+    ..-+ ..++..|-|.|.|++.++|.+|...|+++.|..|++++..
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            378899999999999999999999643    2222 3688899999999999999999999999999999988753

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.58  E-value=0.0062  Score=65.05  Aligned_cols=68  Identities=22%  Similarity=0.393  Sum_probs=58.6

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCC---------------ccE--EEEEECCHHHHHHHHHHhCCCe
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK---------------HNH--KFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgks---------------KGf--AFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      ..+.||+++||+.+...-|+++|+.||+|-.|.+.+..               +.|  |.|+|.+...|.++...||+..
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            45789999999999999999999999999998763211               112  8999999999999999999999


Q ss_pred             eCCcE
Q 002974          424 VAGKQ  428 (861)
Q Consensus       424 I~Gr~  428 (861)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99865

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.51  E-value=0.009  Score=63.84  Aligned_cols=68  Identities=18%  Similarity=0.404  Sum_probs=59.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC-------------CCccc----EEEEEeCCHHHHHHHHHHcCccc
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-------------CKHRG----FVMISYYDIRAARNAMKALQNKP  338 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkit-------------gksrG----yAFVeF~d~e~A~kALkaLnG~~  338 (861)
                      ....||+++||+.+.-.-|+++|.+||.|-.|++.             +.++.    -|+|+|.+...|.++...||+..
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            57789999999999999999999999999999852             11221    38999999999999999999999


Q ss_pred             cCcce
Q 002974          339 LRRRK  343 (861)
Q Consensus       339 L~Gr~  343 (861)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99876

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.20  E-value=0.038  Score=64.46  Aligned_cols=76  Identities=17%  Similarity=0.227  Sum_probs=60.2

Q ss_pred             cCCcceEEecccCCC------cHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeC-CcE
Q 002974          360 ANQGTLVVFNLDSSV------STEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA-GKQ  428 (861)
Q Consensus       360 ~~~~tLfVgNLp~sv------TeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~-Gr~  428 (861)
                      .....|+|.|+|.--      -..-|.++|+++|+|..+.+    .+..+||.|++|.+..+|+.|++.|||+.|. .++
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            345688999998522      23457789999999988654    4567999999999999999999999999886 577


Q ss_pred             EEEEecc
Q 002974          429 IKLEASR  435 (861)
Q Consensus       429 IkVe~Ak  435 (861)
                      ..|...+
T Consensus       136 f~v~~f~  142 (698)
T KOG2314|consen  136 FFVRLFK  142 (698)
T ss_pred             EEeehhh
Confidence            7776543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.19  E-value=0.0089  Score=63.93  Aligned_cols=61  Identities=30%  Similarity=0.402  Sum_probs=50.0

Q ss_pred             HHHHHHhc-ccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          377 EELHQIFG-IYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       377 edLrelFs-kfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ++|...|+ +||+|+++++-    ..-.|-++|.|...++|++|++.||+..+.|++|..++..-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            45555556 89999998642    234677999999999999999999999999999999887543

>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=94.83  E-value=0.059  Score=50.58  Aligned_cols=73  Identities=12%  Similarity=0.178  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE------------eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcc-
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY------------TACKHRGFVMISYYDIRAARNAMKALQNKPLRRR-  342 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svk------------itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr-  342 (861)
                      ..+.|.|=+.|+. ....+.+.|++||+|.+..            .......+..|+|.++.+|++||+ .||+.+.|. 
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            3566888888877 6677888999999999886            113455699999999999999996 899999875 


Q ss_pred             eeeeeecC
Q 002974          343 KLDIHYSI  350 (861)
Q Consensus       343 ~L~V~~a~  350 (861)
                      .+-|.+..
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            45566663

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=94.73  E-value=0.042  Score=64.15  Aligned_cols=72  Identities=21%  Similarity=0.389  Sum_probs=57.1

Q ss_pred             CcEEEEcCCCCCCc------HHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccC-cceee
Q 002974          277 SRTLFVRNINSNVE------DSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLD  345 (861)
Q Consensus       277 srtLfVgNLP~~vT------EedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~-Gr~L~  345 (861)
                      ...|+|-|+|---.      ..-|.++|+++|+|..+++    .++.+||.|++|.+.++|+.|++.|||+.|. ...+.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            45677888874321      2346689999999999885    4779999999999999999999999999876 56666


Q ss_pred             eee
Q 002974          346 IHY  348 (861)
Q Consensus       346 V~~  348 (861)
                      |..
T Consensus       138 v~~  140 (698)
T KOG2314|consen  138 VRL  140 (698)
T ss_pred             eeh
Confidence            643

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.54  E-value=0.12  Score=51.69  Aligned_cols=76  Identities=29%  Similarity=0.370  Sum_probs=53.8

Q ss_pred             cCCcceEEecccC-----CCcH----HHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          360 ANQGTLVVFNLDS-----SVST----EELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       360 ~~~~tLfVgNLp~-----svTe----edLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      ....||.|.=+.+     ..-+    .+|.+.|..||+|.=||..+   +.-+|+|.+-+.|.+|+. ++|..+.|+.|+
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l~  100 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTLK  100 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEEE
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEEE
Confidence            4566777775551     1222    46888899999998888764   468999999999999999 999999999999


Q ss_pred             EEeccCCch
Q 002974          431 LEASRPGGA  439 (861)
Q Consensus       431 Ve~Akpk~~  439 (861)
                      |+...|.-.
T Consensus       101 i~LKtpdW~  109 (146)
T PF08952_consen  101 IRLKTPDWL  109 (146)
T ss_dssp             EEE------
T ss_pred             EEeCCccHH
Confidence            999887653

; PDB: 1UFW_A 2DNR_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=94.45  E-value=0.025  Score=63.95  Aligned_cols=78  Identities=27%  Similarity=0.362  Sum_probs=62.7

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCC-eeCCcEEEEEeccCCchhh
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS-DVAGKQIKLEASRPGGARR  441 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~-~I~Gr~IkVe~Akpk~~rr  441 (861)
                      .++|++||.+.++..+|..+|... +|-.-...--..||+||.+.|...|.+|++.++|+ ++.|+++.|+.+.++..|.
T Consensus         2 nklyignL~p~~~psdl~svfg~a-k~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrs   80 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDA-KIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRS   80 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccc-cCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHh
Confidence            469999999999999999999764 11000111124689999999999999999999998 7889999999998887555

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=94.15  E-value=0.041  Score=60.93  Aligned_cols=71  Identities=15%  Similarity=0.276  Sum_probs=59.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFG--DIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG--~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .-.+|||||-+.+|++||.+....-|  .+.+++     ..+.+||||+|...+..+.++.++.|-.+.|.|+.-.|-
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            56799999999999999999887666  344443     478999999999999999999999999999988876553

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.00  E-value=0.11  Score=56.76  Aligned_cols=61  Identities=18%  Similarity=0.227  Sum_probs=50.4

Q ss_pred             HHHHHHHhcccCcEEEEEeCC---CC---ccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          376 TEELHQIFGIYGEIREIRDTQ---HK---HNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       376 eedLrelFskfGeI~sVritg---ks---KGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ++++++.+.+||.|..|.+..   ..   .--.||+|...++|.+|+-.|||+.|+||.++..+..-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            477899999999999876521   11   12379999999999999999999999999999888764

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=93.93  E-value=0.042  Score=64.45  Aligned_cols=79  Identities=22%  Similarity=0.329  Sum_probs=66.2

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhh-cCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccC---cceeee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFE-QFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR---RRKLDI  346 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFs-qfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~---Gr~L~V  346 (861)
                      |.....++.|||.||=.-.|.-+|+.|+. .+|.|...++ .+-|-.|||.|.+.++|.+.+.+|+|..+-   .+.|.+
T Consensus       438 PsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm-DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM-DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH-HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            34566799999999999999999999999 6778888776 456778999999999999999999997653   566777


Q ss_pred             eecC
Q 002974          347 HYSI  350 (861)
Q Consensus       347 ~~a~  350 (861)
                      .|..
T Consensus       517 df~~  520 (718)
T KOG2416|consen  517 DFVR  520 (718)
T ss_pred             eecc
Confidence            6654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=93.79  E-value=0.13  Score=59.91  Aligned_cols=62  Identities=23%  Similarity=0.315  Sum_probs=55.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhh-cCCCEEEEEeC-----CCcccEEEEEeCCHHHHHHHHHH
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFE-QFGDIRTIYTA-----CKHRGFVMISYYDIRAARNAMKA  333 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFs-qfG~I~svkit-----gksrGyAFVeF~d~e~A~kALka  333 (861)
                      ..-++.+|||||.||.-++.++|..+|+ -||.|..+-++     +-.+|-|-|.|.+-.+-.+||.+
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            3567899999999999999999999999 89999988752     45889999999999999999973

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=93.14  E-value=0.091  Score=59.19  Aligned_cols=73  Identities=19%  Similarity=0.383  Sum_probs=61.3

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCC--------CccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--------KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgk--------sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +.|-|.||.++++.++++.+|.-.|+|.++++++.        ....|||.|.|...+..|.. |....+-++.|.|-++
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            47999999999999999999999999999987552        23479999999999999877 7778777777777665


Q ss_pred             cC
Q 002974          435 RP  436 (861)
Q Consensus       435 kp  436 (861)
                      -.
T Consensus        87 ~~   88 (479)
T KOG4676|consen   87 GD   88 (479)
T ss_pred             CC
Confidence            43

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=92.79  E-value=0.27  Score=49.10  Aligned_cols=73  Identities=23%  Similarity=0.383  Sum_probs=52.2

Q ss_pred             CCcEEEEcCCC-----C-CCcH---HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          276 PSRTLFVRNIN-----S-NVED---SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       276 ~srtLfVgNLP-----~-~vTE---edL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      +..||.|.=+.     . ..++   .+|.+.|.+||++.-++...   +.-+|.|.+-+.|.+|+. ++|..+.|+.|+|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~---~~mwVTF~dg~sALaals-~dg~~v~g~~l~i  101 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG---DTMWVTFRDGQSALAALS-LDGIQVNGRTLKI  101 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET---TCEEEEESSCHHHHHHHH-GCCSEETTEEEEE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC---CeEEEEECccHHHHHHHc-cCCcEECCEEEEE
Confidence            45666666554     1 2222   36778899999999888632   578999999999999996 9999999999999


Q ss_pred             eecCCC
Q 002974          347 HYSIPK  352 (861)
Q Consensus       347 ~~a~~k  352 (861)
                      +.-.+.
T Consensus       102 ~LKtpd  107 (146)
T PF08952_consen  102 RLKTPD  107 (146)
T ss_dssp             EE----
T ss_pred             EeCCcc
Confidence            876553

; PDB: 1UFW_A 2DNR_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=92.73  E-value=0.17  Score=59.18  Aligned_cols=79  Identities=22%  Similarity=0.238  Sum_probs=60.9

Q ss_pred             ccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhh--cCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCc--cccCc
Q 002974          266 VVGEHPYGEHPSRTLFVRNINSNVEDSELKALFE--QFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRR  341 (861)
Q Consensus       266 ~~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFs--qfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG--~~L~G  341 (861)
                      ..|++....+..|.|.++-||..+-+++++.||+  .|-++.+|...  ...-.||.|++..||++|.+.|..  +.|.|
T Consensus       164 ekgekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa--~N~nWyITfesd~DAQqAykylreevk~fqg  241 (684)
T KOG2591|consen  164 EKGEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFA--HNDNWYITFESDTDAQQAYKYLREEVKTFQG  241 (684)
T ss_pred             cCccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeee--ecCceEEEeecchhHHHHHHHHHHHHHhhcC
Confidence            3445555666788899999999999999999998  48888888762  233479999999999999988754  34666


Q ss_pred             ceeee
Q 002974          342 RKLDI  346 (861)
Q Consensus       342 r~L~V  346 (861)
                      ++|..
T Consensus       242 KpImA  246 (684)
T KOG2591|consen  242 KPIMA  246 (684)
T ss_pred             cchhh
Confidence            66543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=92.73  E-value=0.052  Score=58.23  Aligned_cols=58  Identities=19%  Similarity=0.300  Sum_probs=47.5

Q ss_pred             HHHHHhh-cCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          293 ELKALFE-QFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       293 dL~elFs-qfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      +|...|+ +||+|+.+.+    ...-+|-+||.|...++|++|+..||+..+.|++|...+..
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3444444 8999999875    22356789999999999999999999999999999988764

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=91.67  E-value=0.19  Score=57.89  Aligned_cols=63  Identities=22%  Similarity=0.281  Sum_probs=54.3

Q ss_pred             cHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          375 STEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       375 TeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      +-++|...|.+||+|..|.+.. +--.|.|+|.+..+|-+|-. .++..|+++.|+|.|-.+...
T Consensus       386 t~a~ln~hfA~fG~i~n~qv~~-~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~~  448 (526)
T KOG2135|consen  386 TIADLNPHFAQFGEIENIQVDY-SSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSPV  448 (526)
T ss_pred             hHhhhhhhhhhcCccccccccC-chhhheeeeeccccccchhc-cccceecCceeEEEEecCCcc
Confidence            4588999999999999998643 35679999999999988877 699999999999999998663

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=91.51  E-value=0.75  Score=42.02  Aligned_cols=56  Identities=16%  Similarity=0.315  Sum_probs=43.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCc
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN  336 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG  336 (861)
                      ....||. .|..+...||.++|+.||.|.--.++   -.-|||...+.+.|..|+..+..
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~---dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN---DTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEEEC---TTEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc---CCcEEEEeecHHHHHHHHHHhcc
Confidence            3456666 99999999999999999999888873   34799999999999999987753

; 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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.40  E-value=0.7  Score=46.09  Aligned_cols=76  Identities=21%  Similarity=0.322  Sum_probs=58.2

Q ss_pred             cccCCcceEEecccCCCc-HHH---HHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          358 KDANQGTLVVFNLDSSVS-TEE---LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svT-eed---LrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ++..-.+|.|+=|..++. .+|   +.+..+.||+|.+|...|  +.-|.|.|+|..+|-+|+.++.. ...|..+++.|
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            345567888886665542 234   455567899999998765  56799999999999999998766 66788888888


Q ss_pred             ccC
Q 002974          434 SRP  436 (861)
Q Consensus       434 Akp  436 (861)
                      -.+
T Consensus       159 qqr  161 (166)
T PF15023_consen  159 QQR  161 (166)
T ss_pred             ccc
Confidence            654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=91.12  E-value=0.21  Score=58.85  Aligned_cols=79  Identities=15%  Similarity=0.250  Sum_probs=66.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcc-cCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCee---CCcEEEEEec
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGI-YGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV---AGKQIKLEAS  434 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFsk-fGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I---~Gr~IkVe~A  434 (861)
                      ......|+|.||-.-.|.-+|+.++.+ .|.|++. ++.+-|..|||.|.+.++|.+.+.+|||...   +++.|.+.|.
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            344678999999999999999999995 5666665 5556788999999999999999999999854   4689999988


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      ....
T Consensus       520 ~~de  523 (718)
T KOG2416|consen  520 RADE  523 (718)
T ss_pred             chhH
Confidence            7554

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=90.31  E-value=1  Score=45.01  Aligned_cols=76  Identities=22%  Similarity=0.333  Sum_probs=59.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcH-HHH---HHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          272 YGEHPSRTLFVRNINSNVED-SEL---KALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTE-edL---~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ..+.+-.||.|+=|..++.. +||   ..-++.||+|.+|...|  +--|.|.|.|..+|-+|+.+++. ...|..+++.
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            35678899999877766642 444   45567899999998744  45799999999999999999886 5667888887


Q ss_pred             ecC
Q 002974          348 YSI  350 (861)
Q Consensus       348 ~a~  350 (861)
                      |-.
T Consensus       158 Wqq  160 (166)
T PF15023_consen  158 WQQ  160 (166)
T ss_pred             ccc
Confidence            754

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=88.89  E-value=1.7  Score=47.96  Aligned_cols=75  Identities=19%  Similarity=0.223  Sum_probs=60.2

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCC-cEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG-KQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G-r~IkVe~Akpk~  438 (861)
                      .+.-|.|.++++.-. .-|..+|.+||+|.+.. .+....+-+|.|.++-+|.+||. -||+.|+| ..|=|..+..+.
T Consensus       196 ~D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv-~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDks  271 (350)
T KOG4285|consen  196 ADTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHV-TPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDKS  271 (350)
T ss_pred             ccceEEEeccCccch-hHHHHHHHhhCeeeeee-cCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCHH
Confidence            367788889987544 45677999999998876 34667799999999999999999 59999988 466777776654

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=88.33  E-value=0.92  Score=49.77  Aligned_cols=74  Identities=16%  Similarity=0.348  Sum_probs=55.0

Q ss_pred             CcEEEEcCC--CCCCc---HHHHHHHhhcCCCEEEEEe---CC---CcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          277 SRTLFVRNI--NSNVE---DSELKALFEQFGDIRTIYT---AC---KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       277 srtLfVgNL--P~~vT---EedL~elFsqfG~I~svki---tg---ksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      .+.|.++|+  +-.++   +.++++-.++||.|..|.+   .+   ...--.||+|...++|.+|+-.|||..+.||.+.
T Consensus       281 tkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~  360 (378)
T KOG1996|consen  281 TKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVS  360 (378)
T ss_pred             hHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeee
Confidence            444555555  23444   3467788899999998874   11   1122579999999999999999999999999988


Q ss_pred             eeecC
Q 002974          346 IHYSI  350 (861)
Q Consensus       346 V~~a~  350 (861)
                      ..|..
T Consensus       361 A~Fyn  365 (378)
T KOG1996|consen  361 ACFYN  365 (378)
T ss_pred             heecc
Confidence            77664

>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=85.84  E-value=0.77  Score=47.26  Aligned_cols=77  Identities=8%  Similarity=0.081  Sum_probs=49.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhc-CCCE---EEEE--e-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcc
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQ-FGDI---RTIY--T-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR  342 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsq-fG~I---~svk--i-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr  342 (861)
                      +.....|.|++||+..|++++.+.+.. +++-   ..+.  .     ....-.-|||.|.+.+++....+.++|..+.+.
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            345679999999999999999997776 6665   3332  1     111223699999999999999999999876532


Q ss_pred             -----eeeeeecC
Q 002974          343 -----KLDIHYSI  350 (861)
Q Consensus       343 -----~L~V~~a~  350 (861)
                           ...|.+|.
T Consensus        84 kg~~~~~~VE~Ap   96 (176)
T PF03467_consen   84 KGNEYPAVVEFAP   96 (176)
T ss_dssp             TS-EEEEEEEE-S
T ss_pred             CCCCcceeEEEcc
Confidence                 33455553

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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=85.11  E-value=2.6  Score=36.47  Aligned_cols=54  Identities=24%  Similarity=0.318  Sum_probs=40.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhccc----CcEEEEEeCCCCccEEEEEECCHHHHHHHHHHh
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIY----GEIREIRDTQHKHNHKFIEFYDIRAAETALRTL  419 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskf----GeI~sVritgksKGfAFVeF~d~eaA~kAL~~L  419 (861)
                      ..+|+|.+++ +++.++|+.+|..|    +. ..|.....  .-|=|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWIdD--tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWIDD--TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEecC--CcEEEEECCHHHHHHHHHcC
Confidence            3579999995 48889999999998    42 33443222  23789999999999999865

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=84.24  E-value=4  Score=37.45  Aligned_cols=53  Identities=17%  Similarity=0.288  Sum_probs=39.0

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhC
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN  420 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LN  420 (861)
                      ..+|+ .|..+...||.++|+.||.|.--=+.   -.-|||...+.+.|..|+..+.
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~---dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN---DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEEEEEEC---TTEEEEEECCCHHHHHHHHHHT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEEEEEEc---CCcEEEEeecHHHHHHHHHHhc
Confidence            44555 99999999999999999987433222   2369999999999999999875

; 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.

>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=83.87  E-value=1.6  Score=45.41  Aligned_cols=62  Identities=16%  Similarity=0.273  Sum_probs=46.1

Q ss_pred             cHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcC--ccccCcceeeeeecCCC
Q 002974          290 EDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ--NKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       290 TEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLn--G~~L~Gr~L~V~~a~~k  352 (861)
                      ..+.|+++|..|+.+..+.. -++-+-..|.|.+.++|.+|...|+  +..+.|..++|-|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~-L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSP-LKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEE-ETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEE-cCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            34789999999998877764 3566678999999999999999999  89999999999988543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=83.70  E-value=2  Score=44.62  Aligned_cols=63  Identities=17%  Similarity=0.292  Sum_probs=45.5

Q ss_pred             cHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhC--CCeeCCcEEEEEeccCCc
Q 002974          375 STEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN--RSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       375 TeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LN--G~~I~Gr~IkVe~Akpk~  438 (861)
                      ..+.|+++|..|+.+....... +=+=..|.|.+.++|.+|...|+  +..+.|..++|.++....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~-sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK-SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET-TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcC-CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            3578999999999988876543 33348899999999999999999  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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=83.64  E-value=4.7  Score=34.91  Aligned_cols=54  Identities=20%  Similarity=0.425  Sum_probs=41.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcC----CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHc
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQF----GDIRTIYTACKHRGFVMISYYDIRAARNAMKAL  334 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqf----G~I~svkitgksrGyAFVeF~d~e~A~kALkaL  334 (861)
                      ...|+|+++. +.+.++|+.+|..|    ++..-=.+...   -|=|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt---ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT---SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC---cEEEEECCHHHHHHHHHcC
Confidence            4579999996 68889999999999    54333234222   4668999999999999765

>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=82.82  E-value=1.8  Score=44.63  Aligned_cols=75  Identities=9%  Similarity=0.078  Sum_probs=49.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcc-cCcE---EEEE--eCC---C--CccEEEEEECCHHHHHHHHHHhCCCeeCC---
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGI-YGEI---REIR--DTQ---H--KHNHKFIEFYDIRAAETALRTLNRSDVAG---  426 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFsk-fGeI---~sVr--itg---k--sKGfAFVeF~d~eaA~kAL~~LNG~~I~G---  426 (861)
                      ...+|.|++||+.+|++++.+.++. ++..   ..+.  ...   +  .-.-|||.|.+.+++..-...++|..+-.   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3468999999999999999998887 7765   3333  110   1  12349999999999999999999987642   


Q ss_pred             --cEEEEEecc
Q 002974          427 --KQIKLEASR  435 (861)
Q Consensus       427 --r~IkVe~Ak  435 (861)
                        .+..|++|-
T Consensus        86 ~~~~~~VE~Ap   96 (176)
T PF03467_consen   86 NEYPAVVEFAP   96 (176)
T ss_dssp             -EEEEEEEE-S
T ss_pred             CCcceeEEEcc
Confidence              455666664

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.

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=82.74  E-value=1.6  Score=42.72  Aligned_cols=100  Identities=18%  Similarity=0.154  Sum_probs=70.1

Q ss_pred             HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCCCCccc--CCcceEEec
Q 002974          292 SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDA--NQGTLVVFN  369 (861)
Q Consensus       292 edL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~~~k~~--~~~tLfVgN  369 (861)
                      ..|.++....|.+.-..+   ..++..++|.+.++++++++ .....+.+..+.++.-.+.....+...  ..--|-|.|
T Consensus        36 ~~l~~~W~~~~~~~i~~l---~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~vWVri~g  111 (153)
T PF14111_consen   36 QELAKIWKLKGGVKIRDL---GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNPSEVKFEHIPVWVRIYG  111 (153)
T ss_pred             HHHHHHhCCCCcEEEEEe---CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhcccccccccceeccchhhhhcc
Confidence            344444444555544444   56899999999999999986 444557788888876665544333222  233466779


Q ss_pred             ccCC-CcHHHHHHHhcccCcEEEEEeC
Q 002974          370 LDSS-VSTEELHQIFGIYGEIREIRDT  395 (861)
Q Consensus       370 Lp~s-vTeedLrelFskfGeI~sVrit  395 (861)
                      ||.. .+++-|+++-+.+|++.++...
T Consensus       112 lP~~~~~~~~~~~i~~~iG~~i~vD~~  138 (153)
T PF14111_consen  112 LPLHLWSEEILKAIGSKIGEPIEVDEN  138 (153)
T ss_pred             CCHHHhhhHHHHHHHHhcCCeEEEEcC
Confidence            9986 6888899999999999999864

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=82.39  E-value=0.69  Score=53.56  Aligned_cols=78  Identities=17%  Similarity=0.246  Sum_probs=65.5

Q ss_pred             CCCCCcEEEEcCCCCCCc-HHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          273 GEHPSRTLFVRNINSNVE-DSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vT-EedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      -..+.+.|-+.-+|.... -++|...|.+||.|..|.+.- +---|.|+|.+..+|-+|.+ ..+..|++|.|+|.|-.+
T Consensus       368 ~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~-~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  368 AVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDY-SSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccC-chhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            355688888888888775 588999999999999999833 34579999999999988874 899999999999999876


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      .
T Consensus       446 s  446 (526)
T KOG2135|consen  446 S  446 (526)
T ss_pred             C
Confidence            3

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=82.14  E-value=0.75  Score=51.33  Aligned_cols=76  Identities=18%  Similarity=0.258  Sum_probs=60.5

Q ss_pred             CcEEEEcCCCCCCcHHHHH---HHhhcCCCEEEEEeCCCc------c--cEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          277 SRTLFVRNINSNVEDSELK---ALFEQFGDIRTIYTACKH------R--GFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~---elFsqfG~I~svkitgks------r--GyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      .+-+||-+|+..+.++++.   +.|.+||.|..|.+.+..      .  --+||.|...++|..||..-+|..+.|+.|+
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            4567888888887666554   489999999999763321      1  1489999999999999999999999999988


Q ss_pred             eeecCCC
Q 002974          346 IHYSIPK  352 (861)
Q Consensus       346 V~~a~~k  352 (861)
                      ..+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            8877654

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=81.08  E-value=0.68  Score=51.65  Aligned_cols=79  Identities=16%  Similarity=0.295  Sum_probs=62.0

Q ss_pred             CcceEEecccCCCcHHHHH---HHhcccCcEEEEEeCCCC--------ccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          362 QGTLVVFNLDSSVSTEELH---QIFGIYGEIREIRDTQHK--------HNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLr---elFskfGeI~sVritgks--------KGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      ..-+||-+|+..+.++.+.   +.|.+||.|..|......        ..-++|+|...++|..||...+|..+.|+.|+
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            4567888888877665544   478999999998764322        11389999999999999999999999999999


Q ss_pred             EEeccCCchh
Q 002974          431 LEASRPGGAR  440 (861)
Q Consensus       431 Ve~Akpk~~r  440 (861)
                      ..+...+-..
T Consensus       157 a~~gttkycs  166 (327)
T KOG2068|consen  157 ASLGTTKYCS  166 (327)
T ss_pred             HhhCCCcchh
Confidence            8888776533

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=80.57  E-value=1  Score=55.28  Aligned_cols=75  Identities=16%  Similarity=0.232  Sum_probs=63.9

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEEeccCCc
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEASRPGG  438 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I--~Gr~IkVe~Akpk~  438 (861)
                      -+.++.|.+-..+-.-|..+|++||+|.++... +.-..|.|+|...+.|..|+.+|+|+++  .|-+.+|.+++.-.
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtl-r~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTL-RDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheec-ccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            456777778888889999999999999998742 3456899999999999999999999976  48899999998654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	861
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-06
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		5e-06
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		5e-06
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		1e-05
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		1e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		1e-05
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		1e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-05
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		4e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-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
1a9n_B	96	Crystal Structure Of The Spliceosomal U2b''-U2a' Pr		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		1e-04
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		1e-04
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		2e-04
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		2e-04
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		2e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
1drz_A	97	U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOM		3e-04
3cul_A	98	Aminoacyl-Trna Synthetase Ribozyme Length = 98		3e-04
1cx0_A	95	Hepatitis Delta Virus Ribozyme Length = 95		4e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-04

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/151 (28%), Positives = 68/151 (45%), Gaps = 14/151 (9%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
           L V  +  ++ D EL ALF   G I T      Y      G+  + +     ++ A+K L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--- 391
               +R ++L + Y+ P    S KD N   L V NL  +++ ++L  IFG YG I +   
Sbjct: 66  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 392 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 420
           +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 = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/141 (26%), Positives = 63/141 (44%), Gaps = 15/141 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           LFV N+  ++ + E++ LFE++G    ++   K +GF  I       A  A   L N PL
Sbjct: 25  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 340 RRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE----IRDT 395
           R ++L + ++           +  +L V NL   VS E L + F ++G++      + D 
Sbjct: 84  RGKQLRVRFA----------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDR 133
Query: 396 QHKHNHKFIEFYDIRAAETAL 416
                   +EF    AA  AL
Sbjct: 134 GRPSGKGIVEFSGKPAARKAL 154

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 43/151 (28%), Positives = 67/151 (44%), Gaps = 14/151 (9%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
           L V  +  +  D EL ALF   G I T      Y      G+  + +     ++ A+K L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--- 391
               +R ++L + Y+ P    S KD N   L V NL  +++ ++L  IFG YG I +   
Sbjct: 77  NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 392 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 420
           +RD  T       F+ +     A+ A+  LN
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F QFG I  I  +   K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           NA++++Q  P   + + I Y+
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 48/169 (28%), Positives = 72/169 (42%), Gaps = 17/169 (10%)
Query: 273 GEHPSRT--LFVRNINSNVEDSELK-ALFEQFG-------DIRTIYTACKHRGFVMISYY 322
           G  P+    LFV N+N N    ELK  + + F        D+R   T    R F    Y 
Sbjct: 1   GTEPTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYV 53
Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQI 382
           D  +A +  KAL+   L+    +I    PK   S+K+ +  TL+  NL   V+ +EL ++
Sbjct: 54  DFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEV 113
Query: 383 FGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
           F    EIR +          +IEF     AE        +++ G+ I L
Sbjct: 114 FEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F QFG I  I  +   K RG   + + ++ +A N
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 330 AMKALQNKPLRRRKLDIHYS 349
           A++++Q  P   + + I Y+
Sbjct: 68  ALRSMQGFPFYDKPMRIQYA 87

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/160 (28%), Positives = 72/160 (45%), Gaps = 15/160 (9%)
Query: 280 LFVRNINSNVEDSELK-ALFEQFG-------DIRTIYTACKHRGFVMISYYDIRAARNAM 331
           LF+ N+N N   +ELK A+ E F        D+RT      +R F    Y D  +A +  
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 332 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE 391
           KAL+   L+    +I    PK   S+K     TL+  NL  +++ +EL ++F    EIR 
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 392 IRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
           +          +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 = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F QFG I  I  +   K RG   + + ++ +A N
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 330 AMKALQNKPLRRRKLDIHYS 349
           A++++Q  P   + + I Y+
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 86

>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: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAET 414
           +++G L V  L    + + L Q+F  YG+I E+     R+TQ      F+ F +I  A+ 
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 415 ALRTLNRSDVAGKQIKLE 432
           A+  +N   V G+QI+++
Sbjct: 70  AMMAMNGKSVDGRQIRVD 87

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A N
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 330 AMKALQNKPLRRRKLDIHYS 349
           A++++Q  P   + + I Y+
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 86

>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 = 4e-05,   Method: Composition-based stats.
 Identities = 45/161 (27%), Positives = 72/161 (44%), Gaps = 22/161 (13%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRAARNA 330
           L V  +  N+   E ++LF   G+I +    CK           G+  ++Y D + A  A
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIES----CKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI- 389
           +  L    L+ + + + Y+ P  + S +DAN   L V  L  +++ +EL Q+F  YG I 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPS-SASIRDAN---LYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 390 --REIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
             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 = 5e-04,   Method: Composition-based stats.
 Identities = 32/107 (29%), Positives = 49/107 (45%), Gaps = 17/107 (15%)
Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
           ++  L+V  L  +++ EE   +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 416 LRTLNRSDVAGKQIKLEASRPGGAR------------RFMVQSEQEQ 450
           + 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 = 47.0 bits (110), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 45/155 (29%), Positives = 67/155 (43%), Gaps = 22/155 (14%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRAARNA 330
           L V  +  N+   E K+LF   GDI +    CK           G+  ++Y D   A  A
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIES----CKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIR 390
           +  L    L+ + + + Y+ P  + S +DAN   L V  L  ++S +E+ Q+F  YG I 
Sbjct: 63  INTLNGLKLQTKTIKVSYARPS-SASIRDAN---LYVSGLPKTMSQKEMEQLFSQYGRII 118
Query: 391 EIR-----DTQHKHNHKFIEFYDIRAAETALRTLN 420
             R      T       FI F     AE A++ LN
Sbjct: 119 TSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 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: 275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR------GFVMISYYDIRAAR 328
           +P  +L+V +++ +V ++ L   F   G I +I   C+        G+  +++     A 
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 388
            A+  +    ++ + + I +S  + +PS + +  G + + NLD S+  + L+  F  +G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 389 I---REIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           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: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           NA++++Q  P   + + I Y+
Sbjct: 67  NALRSMQGFPFYDKPMRIQYA 87

>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 = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    ALF QFG +  I      K RG   + + ++ ++ N
Sbjct: 5   PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTN 64
Query: 330 AMKALQNKPLRRRKLDIHYS 349
           A++ LQ  P   + + I Y+
Sbjct: 65  ALRQLQGFPFYGKPMRIQYA 84

>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 = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/169 (21%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
           ++V +I   + +  ++  F  FG I++I         KH+GF  + Y    AA+ A++ +
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 335 QNKPLRRRKLDIHY--SIPKDNP-----SEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 387
            +  L  R + +    +I +  P     +E+      + V ++   +S +++  +F  +G
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 388 EIRE---IRD-TQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
           +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: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           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: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           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 = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 4   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 63
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           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 = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           NA++++Q  P   + + I Y+
Sbjct: 66  NALRSMQGFPFYDKPMRIQYA 86

>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: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 3   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 62
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           NA++++Q  P   + + I Y+
Sbjct: 63  NALRSMQGFPFYDKPMRIQYA 83

>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 = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           NA++++Q  P   + + I Y+
Sbjct: 61  NALRSMQGFPFYDKPMRIQYA 81

>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 = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
            P+ T+++ N+N  ++  ELK    A+F +FG I  I  +   K RG   + + ++ +A 
Sbjct: 2   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 61
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
           NA++++Q  P   + + I Y+
Sbjct: 62  NALRSMQGFPFYDKPMRIQYA 82

>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: 275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR------GFVMISYYDIRAAR 328
           +P  +L+V +++ +V ++ L   F   G I +I   C+        G+  +++     A 
Sbjct: 8   YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 66
Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 388
            A+  +    ++ + + I +S  + +PS + +  G + + NLD S+  + L+  F  +G 
Sbjct: 67  RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124
Query: 389 I---REIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           I   + + D      + F+ F    AAE A+  +N
Sbjct: 125 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/141 (26%), Positives = 59/141 (41%), Gaps = 15/141 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           LFV N+ +++ + + K LFE++G+   ++   + RGF  I       A  A   L    L
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 340 RRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE----IRDT 395
           + R L I ++           +   L V NL   VS E L Q F  +G + +    + D 
Sbjct: 84  KSRPLRIRFA----------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR 133
Query: 396 QHKHNHKFIEFYDIRAAETAL 416
                  F+EF     A  AL
Sbjct: 134 GRATGKGFVEFAAKPPARKAL 154

>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC Ribozyme Complex Length = 97

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A N
Sbjct: 7   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 66
Query: 330 AMKALQNKPLRRRKLDIHYS 349
           A+++ Q  P   +   I Y+
Sbjct: 67  ALRSXQGFPFYDKPXRIQYA 86

>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme Length = 98

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A N
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 67
Query: 330 AMKALQNKPLRRRKLDIHYS 349
           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 = 4e-04,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A N
Sbjct: 5   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 64
Query: 330 AMKALQNKPLRRRKLDIHYS 349
           A+++ Q  P   +   I Y+
Sbjct: 65  ALRSXQGFPFYDKPXRIQYA 84

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 38/169 (22%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
           ++V +I   + +  ++  F  FG I++I         KH+GF  + Y    AA+ A++ +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 335 QNKPLRRRKL------DIHYSIP-KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 387
            +  L  R +      +I  + P  D  +E+      + V ++   +S +++  +F  +G
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 388 EIREI---RD-TQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
           +I+     RD T  KH  + FIE+   ++++ A+ ++N  D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	861
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-30
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-27
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-27
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-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	4e-24
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-23
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-22
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-22
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-22
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-05
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-21
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-20
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-20
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-07
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-20
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-20
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-20
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-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,	2e-17
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-04
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-14
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	9e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-14
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-14
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-14
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	7e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	7e-10
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-10
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-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	1e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-08
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	2e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-09
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-08
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-11
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-11
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	9e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-10
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-10
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	9e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-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	4e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-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	6e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-09
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-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	6e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-08
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-09
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-09
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-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,	4e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-06
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-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	6e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-06
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	7e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-08
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	9e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-08
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-04
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-04
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	8e-08
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	4e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-08
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	6e-08
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	9e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	9e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-05
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-05
2div_A	99	TRNA selenocysteine associated protein; structural	4e-07
2div_A	99	TRNA selenocysteine associated protein; structural	1e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-07
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	6e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	9e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-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	3e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	6e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	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,	4e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-04

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score =  117 bits (294), Expect = 4e-30
 Identities = 30/196 (15%), Positives = 59/196 (30%), Gaps = 39/196 (19%)

Query: 276 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
            S  L V  ++ S +    +  +F  +G++  +       G  M+   D  A   A+  L
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 335 QNKPLRRRKLDIHYS------------IPKDNPSEKDANQG------------------- 363
            N  +  +K+++  S            +   + S KD ++                    
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 364 --TLVVFNLDSSVSTEELHQIFGIYG-----EIREIRDTQHKHNHKFIEFYDIRAAETAL 416
              L  FN    V+ E   +I    G      ++       + +   +E+     A   L
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 417 RTLNRSDVAGKQIKLE 432
             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 = 4e-10
 Identities = 23/107 (21%), Positives = 47/107 (43%), Gaps = 6/107 (5%)

Query: 360 ANQGTLVVFNLDSSVSTEE-LHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRT 418
           A+   L+V+ LD S    + +  +F +YG + +++  + K     +E  D  A + A+  
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 419 LNRSDVAGKQIKLEASR-----PGGARRFMVQSEQEQDDLNLCQIPF 460
           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: 274 EHPSRTLFVRNINSNVEDSELKALFEQFG-----DIRTIYTACKHRGFVMISYYDIRAAR 328
           +HPS  L   N    V +     + ++ G      ++      +     ++ +     A 
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 329 NAMKALQNKPLRRRKLDIHYSI 350
             +  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 (276), Expect = 2e-27
 Identities = 36/195 (18%), Positives = 68/195 (34%), Gaps = 34/195 (17%)

Query: 276 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
            +  L V N+N   V    L  LF  +GD++ +      +   ++   D   A+ AM  L
Sbjct: 33  GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 92

Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQG------------------------------- 363
               L  + + I  S  ++    ++  +                                
Sbjct: 93  NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 152

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 422
           TL + N+  SVS E+L  +F   G + +  +  Q       I+   +  A  AL  L+  
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 212

Query: 423 DVA-GKQIKLEASRP 436
           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 = 57.7 bits (139), Expect = 2e-09
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 1/97 (1%)

Query: 355 PSEKDANQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 413
           P    A    L+V NL+   V+ + L  +FG+YG+++ ++   +K  +  ++  D   A+
Sbjct: 27  PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQ 86

Query: 414 TALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
            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 (272), Expect = 3e-27
 Identities = 36/194 (18%), Positives = 68/194 (35%), Gaps = 34/194 (17%)

Query: 277 SRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           +  L V N+N   V    L  LF  +GD++ +      +   ++   D   A+ AM  L 
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 336 NKPLRRRKLDIHYSIPKDNPSEKDANQG-------------------------------T 364
              L  + + I  S  ++    ++  +                                T
Sbjct: 63  GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEI-REIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           L + N+  SVS E+L  +F   G + +  +  Q       I+   +  A  AL  L+  D
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182

Query: 424 VA-GKQIKLEASRP 436
           +     +++  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 = 5e-09
 Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 361 NQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL 419
               L+V NL+   V+ + L  +FG+YG+++ ++   +K  +  ++  D   A+ A+  L
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHL 61

Query: 420 NRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
           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 = 4e-08
 Identities = 25/105 (23%), Positives = 42/105 (40%), Gaps = 4/105 (3%)

Query: 247 QKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI-R 305
               D+     ++    GS   ++ +   PS TL + NI  +V + +LK LF   G + +
Sbjct: 92  GLTKDYGNSPLHRFKKPGSKNFQNIF--PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK 149

Query: 306 TIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR-RKLDIHYS 349
                 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 =  107 bits (269), Expect = 8e-26
 Identities = 30/185 (16%), Positives = 61/185 (32%), Gaps = 11/185 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
               L V N+  ++   + + L   FG +   +        + +G+    Y    +A  A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVS-TEELHQIFGIYGEI 389
              L  KPL  R L +H++      +    +   L V  L    +  + L +        
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAG-QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 390 REIRDTQHKHNHK----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQ 445
              +    +         +E+     AE A +  +   + G  +++    PG   R M+ 
Sbjct: 213 TFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLA 272

Query: 446 SEQEQ 450
           +    
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 (257), Expect = 2e-24
 Identities = 29/175 (16%), Positives = 66/175 (37%), Gaps = 17/175 (9%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
            R + +R +  +V + E+  L   +  ++  +   K++G   ++  +   A  A+ A   
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-KYKGTAFVTLLNGEQAEAAINAFHQ 79

Query: 337 KPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ 396
             LR R+L +            DA    L V NL  S++ ++  ++   +G +       
Sbjct: 80  SRLRERELSV-------QLQPTDAL---LCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

Query: 397 HKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQS 446
            +   +     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 = 64.2 bits (157), Expect = 3e-11
 Identities = 15/104 (14%), Positives = 44/104 (42%), Gaps = 11/104 (10%)

Query: 334 LQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR 393
           L  + +R+R          ++   +  N+  +++  L   V+ +E+H +   Y  ++   
Sbjct: 3   LDPEEIRKRL---------EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCF 52

Query: 394 DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG 437
             ++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 = 54.2 bits (131), Expect = 5e-08
 Identities = 16/86 (18%), Positives = 25/86 (29%), Gaps = 5/86 (5%)

Query: 274 EHPSRTLFVRNINSNVEDSE-LKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAAR 328
              SR L V  +     D + L               AC    + +GF ++ Y     A 
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAE 240

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDN 354
            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 (257), Expect = 2e-25
 Identities = 33/169 (19%), Positives = 65/169 (38%), Gaps = 7/169 (4%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARN 329
                 LF+ N+N N   +ELK    +      +         +R F  + +        
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 389
           A++ L    +   ++ +     +D+   + A   TL+  NL  +++ +EL ++F    EI
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGRDSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEI 126

Query: 390 REIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG 438
           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 = 59.9 bits (146), Expect = 2e-10
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHNHK---FIEFYDI 409
               +      L + NL+ + S  EL           ++         ++   +++F   
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64

Query: 410 RAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
              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 = 99.2 bits (248), Expect = 4e-24
 Identities = 33/173 (19%), Positives = 64/173 (36%), Gaps = 20/173 (11%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIY-------TACKHRGFVMISYYDIRAARN 329
           +  +FV  +     + +L+ LFEQ+G +  I           + +G   +++Y  +AA  
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 389
           A  AL N  +           P D+          L +  +    +  ++  +F  +G+I
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122

Query: 390 REI---RDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
            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 = 58.8 bits (143), Expect = 4e-10
 Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 12/102 (11%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD-TQHKHNHK---FIEFYDIRAAE 413
           +   + V  +  + S ++L ++F  YG + E   +RD +Q+    K   F+ FY  +AA 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 414 TALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNL 455
            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 =  100 bits (251), Expect = 2e-23
 Identities = 33/175 (18%), Positives = 67/175 (38%), Gaps = 16/175 (9%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT---IYTAC--KHRGFVMISYYDIRAA 327
                 TL++ N   +     ++ L +    +     + +      R F  I       A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 328 RNAMKALQNKPLRRRKLDIHYSIP--KDNPSEKDANQG-TLVVFNLDSSVSTEE-LHQIF 383
           R  ++ L    +    L    S P  K   ++    +G  +++ NL + +  E  L + F
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232

Query: 384 GIYGEIREIR---DTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
             +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 = 95.8 bits (239), Expect = 7e-22
 Identities = 24/187 (12%), Positives = 59/187 (31%), Gaps = 28/187 (14%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARNAMKALQ 335
           T+ V+N+  +   +++   F+  G I  +  A    K+  F  I +     A  A+    
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT- 101

Query: 336 NKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT 395
           +K + + ++ +            +     L + N   S +   +  +      +      
Sbjct: 102 HKVVGQNEIIVS--------HLTECT---LWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150

Query: 396 QHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
                +      +I+      A   +  LN   + G  +  + S P          + ++
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP--------LEKSKR 202

Query: 451 DDLNLCQ 457
            D    +
Sbjct: 203 TDSATLE 209

>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 = 58.5 bits (142), Expect = 3e-09
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 352 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYD 408
            +    ++    T++V NL  S +  ++++ F   G I  +        +     IEF  
Sbjct: 31  ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR 90

Query: 409 IRAAETALRTLNRSDVAGKQIKLE 432
              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 = 97.0 bits (242), Expect = 5e-23
 Identities = 34/185 (18%), Positives = 79/185 (42%), Gaps = 10/185 (5%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAAR 328
            +P  +L+V +++ +V ++ L   F   G I +I         +  G+  +++     A 
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 388
            A+  +    ++ + + I +S     PS + +  G + + NLD S+  + L+  F  +G 
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRD--PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129

Query: 389 IREIR---DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQ 445
           I   +   D      + F+ F    AAE A+  +N   +  +++ +   +    R   + 
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG 189

Query: 446 SEQEQ 450
           +  ++
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 = 65.0 bits (159), Expect = 6e-12
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 6/94 (6%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI---REIRD--TQHKHNHKFIEFYD 408
           NPS       +L V +L   V+   L++ F   G I   R  RD  T+    + ++ F  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 409 IRAAETALRTLNRSDVAGKQIKLE-ASRPGGARR 441
              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 = 95.5 bits (238), Expect = 2e-22
 Identities = 38/202 (18%), Positives = 85/202 (42%), Gaps = 33/202 (16%)

Query: 260 GVSAGSVVGEHPYGEHPS----------RTLFVRNINSNVEDSELKALFEQFGDIRTIYT 309
           G    S+ G    G   +            ++V +I   + +  ++  F  FG I++I  
Sbjct: 1   GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60

Query: 310 AC-----KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK-------DNPSE 357
           +      KH+GF  + Y    AA+ A++ + +  L  R + +             D  +E
Sbjct: 61  SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE 120

Query: 358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHK---FIEFYDI 409
           +      + V ++   +S +++  +F  +G+I+         T     HK   FIE+   
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG---KHKGYGFIEYEKA 177

Query: 410 RAAETALRTLNRSDVAGKQIKL 431
           ++++ 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 = 3e-11
 Identities = 23/130 (17%), Positives = 46/130 (35%), Gaps = 14/130 (10%)

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 388
           + M ++       R                 A    + V ++   +  + + Q F  +G 
Sbjct: 2   SHMASMTGGQQMGRG-------SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGP 54

Query: 389 IRE---IRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRF 442
           I+      D+     HK   F+E+    AA+ AL  +N   + G+ IK+      G  + 
Sbjct: 55  IKSIDMSWDSVTM-KHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP 113

Query: 443 MVQSEQEQDD 452
           ++    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 = 3e-10
 Identities = 20/93 (21%), Positives = 47/93 (50%), Gaps = 5/93 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
               ++V +++ ++ D ++K++FE FG I++   A      KH+G+  I Y   +++++A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
           + ++    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 = 91.1 bits (227), Expect = 3e-22
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 6/85 (7%)

Query: 274 EHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIY--TACKHRGFVMISYYDIRAA 327
             P+ T+++ N+N  ++  ELK    A+F +FG I  I    + K RG   + + ++ +A
Sbjct: 5   TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPK 352
            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 = 3e-11
 Identities = 20/95 (21%), Positives = 47/95 (49%), Gaps = 14/95 (14%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEEL----HQIFGIYGEIREIRDTQHKHNHK-- 402
           ++P+  P+       T+ + NL+  +  +EL    H IF  +G+I +I  ++     +  
Sbjct: 1   AVPETRPNH------TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL-KMRGQ 53

Query: 403 -FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
            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 = 4e-22
 Identities = 43/165 (26%), Positives = 70/165 (42%), Gaps = 14/165 (8%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAM 331
           +  L V  +  ++ D EL ALF   G I T      Y      G+  + +     ++ A+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 332 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE 391
           K L    +R ++L + Y+ P    S KD N   L V NL  +++ ++L  IFG YG I +
Sbjct: 63  KVLNGITVRNKRLKVSYARPG-GESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQ 118

Query: 392 IRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKL 431
               + 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 = 61.4 bits (150), Expect = 4e-11
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 5/87 (5%)

Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAET 414
           A+   L+V  L   ++  EL+ +F   G I     +RD  T + + + F++F     ++ 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 9e-05
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
               L+V N+   + D +L  +F ++G I            + RG   + Y     A+ A
Sbjct: 88  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147

Query: 331 MKALQNKPL 339
           + 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 = 89.6 bits (223), Expect = 7e-21
 Identities = 41/167 (24%), Positives = 69/167 (41%), Gaps = 16/167 (9%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRGFVMISYYDIRAARNA 330
              L V  +  N+   E ++LF   G+I +     +        G+  ++Y D + A  A
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESC-KLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIR 390
           +  L    L+ + + + Y+ P    S +DAN   L V  L  +++ +EL Q+F  YG I 
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSA-SIRDAN---LYVSGLPKTMTQKELEQLFSQYGRII 116

Query: 391 EIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
             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 = 7e-11
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
           ++  L+V  L  +++ EE   +FG  GEI     +RD  T     + F+ + D + AE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 416 LRTLNRSDVAGKQIKLEASRPGGAR 440
           + 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 = 87.7 bits (217), Expect = 1e-20
 Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 6/101 (5%)

Query: 267 VGEHPYGEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIY--TACKHRGFVMIS 320
           +G  P    PS+ + + NIN  V   +L+    AL    GDI  I    +  + G   I 
Sbjct: 19  LGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIV 78

Query: 321 YYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
           +    +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 = 63.8 bits (155), Expect = 2e-12
 Identities = 18/112 (16%), Positives = 39/112 (34%), Gaps = 9/112 (8%)

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEEL----HQIFGIY 386
           MK        R+ +D         P   + +Q  +++ N++  V  E+L    + +    
Sbjct: 1   MKETAAAKFERQHMD--SPDLGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQ 57

Query: 387 GEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 1e-20
 Identities = 26/170 (15%), Positives = 61/170 (35%), Gaps = 22/170 (12%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----------KHRGFVMISYYDIRA 326
           +R L+V NI   + +  +   F     +  +  A           + + F  + +  +  
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 386
              AM A      + + L I                  L +  L + ++ +++ ++   +
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLP----GAHKLFIGGLPNYLNDDQVKELLTSF 118

Query: 387 GEIRE---IRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIK 430
           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 = 1e-07
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 6/85 (7%)

Query: 270 HPYGEHPS-RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYD 323
           H Y   P    LF+  + + + D ++K L   FG ++             +G+    Y D
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 324 IRAARNAMKALQNKPLRRRKLDIHY 348
           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 = 88.5 bits (220), Expect = 3e-20
 Identities = 28/195 (14%), Positives = 66/195 (33%), Gaps = 34/195 (17%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----------KHRGFVMISYYDIR 325
            +R L+V NI   + +  +   F     +  +  A           + + F  + +  + 
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 326 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG----------------TLVVFN 369
               AM A      + + L I              N                   L +  
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

Query: 370 LDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEFYDIRAAETALRTLNRSD 423
           L + ++ +++ ++   +G ++    ++D+      K   F E+ DI   + A+  LN   
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180

Query: 424 VAGKQIKLEASRPGG 438
           +  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 = 86.1 bits (213), Expect = 3e-20
 Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 3/109 (2%)

Query: 257 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF 316
           S+  V  GS +G+      PSR + +R +  +V + E+ +L   FG +  +    K +  
Sbjct: 11  SSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNL-LMLKGKNQ 69

Query: 317 VMISYYDIRAARNAMKALQNKP--LRRRKLDIHYSIPKDNPSEKDANQG 363
             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 = 6e-07
 Identities = 21/112 (18%), Positives = 39/112 (34%), Gaps = 9/112 (8%)

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 386
             +      +  L  R   +  S     PS        + +  L   V+  E+  +   +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR------VIHIRKLPIDVTEGEVISLGLPF 55

Query: 387 GEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNRSDVAGKQIKLEASRP 436
           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 = 84.5 bits (209), Expect = 7e-20
 Identities = 23/103 (22%), Positives = 41/103 (39%), Gaps = 3/103 (2%)

Query: 263 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYY 322
            GS    H     PSR + +R +  +V + E+ +L   FG +  +    K +    I   
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNL-LMLKGKNQAFIEMN 60

Query: 323 DIRAARNAMKALQNKP--LRRRKLDIHYSIPKDNPSEKDANQG 363
              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 = 5e-07
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNR 421
            + +  L   V+  E+  +   +G++  +   + K N  FIE     AA T +   T   
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK-NQAFIEMNTEEAANTMVNYYTSVT 76

Query: 422 SDVAGKQIKLEASRP 436
             + 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 = 1e-19
 Identities = 30/163 (18%), Positives = 66/163 (40%), Gaps = 11/163 (6%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFG---DIRTIYTA-CKHRGFVMISYYDIRAARNAMKA 333
           R L+V N++  + +  LK  F+  G   +I+ +     K+  +  + Y+    A  A++ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 334 LQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR 393
           L  K +    + I+++           +   L V +L+ +V  E L   F  +       
Sbjct: 61  LNGKQIENNIVKINWAFQS--QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 394 -----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
                 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 = 1e-10
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEI---REIRD-TQHKHNHKFIEFYDIRAAETALRTL 419
            L V NLD +++ + L Q F + G I   + + D      N+ F+E++    A  AL+TL
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 420 NRSDVAGKQIKLEASRPGGARR 441
           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 = 44.1 bits (105), Expect = 4e-05
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
            +  LFV ++N NV+D  L+  F+ F    + +          RG+  +S+     A+NA
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145

Query: 331 MKALQNKPLRRRKLDIHYS 349
           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 = 85.9 bits (213), Expect = 9e-19
 Identities = 39/146 (26%), Positives = 57/146 (39%), Gaps = 15/146 (10%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 338
            LFV N+ +++ + + K LFE++G+   ++   + RGF  I       A  A   L    
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDGTI 82

Query: 339 LRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR----D 394
           L+ R L I         +   A    L V NL   VS E L Q F  +G + +      D
Sbjct: 83  LKSRPLRI-------RFATHGAA---LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD 132

Query: 395 TQHKHNHKFIEFYDIRAAETALRTLN 420
                   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 = 62.8 bits (153), Expect = 7e-11
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 8/91 (8%)

Query: 351 PKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIREI---RDTQHKHNHKFIEF 406
               P EK   Q   L V NL + ++ E+  ++F  YGE  E+   RD        FI  
Sbjct: 10  SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----RGFGFIRL 65

Query: 407 YDIRAAETALRTLNRSDVAGKQIKLEASRPG 437
                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 = 52.8 bits (127), Expect = 1e-07
 Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 5/91 (5%)

Query: 275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNA 330
                L V+N++  V +  L+  F QFG +           +  G   + +     AR A
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153

Query: 331 MKALQNK-PLRRRKLDIHYSIPKDNPSEKDA 360
           ++   +   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 = 78.1 bits (193), Expect = 1e-17
 Identities = 20/83 (24%), Positives = 38/83 (45%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA 333
              +RTL  +N++ N+ + ELK +FE   +IR +    K +G   I +     A   ++ 
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 334 LQNKPLRRRKLDIHYSIPKDNPS 356
            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 = 68.8 bits (169), Expect = 2e-14
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 2/91 (2%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 410
           P  +   + A   TL+  NL  +++ +EL ++F    EIR +          +IEF    
Sbjct: 7   PCTSKKVRAAR--TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 411 AAETALRTLNRSDVAGKQIKLEASRPGGARR 441
            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 = 77.8 bits (192), Expect = 2e-17
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC--KHRGFVMISYYDIRAARNAMKA 333
            +R L++RN+   +   E+  +F ++G IR I      + RG   + Y DI  A+NA+  
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66

Query: 334 LQNKPLRRRKLDIHYSIPKDNPSEKD 359
           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 = 67.8 bits (166), Expect = 7e-14
 Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 4/90 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETALRTLN 420
            L + NL   ++ EE++ IFG YG IR+IR        +   ++ + DI  A+ A+  L+
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE-TRGTAYVVYEDIFDAKNAVDHLS 68

Query: 421 RSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
             +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 = 1e-15
 Identities = 29/167 (17%), Positives = 62/167 (37%), Gaps = 25/167 (14%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISYYDIRAA 327
           S  +F+  +N +  +  L+  F ++G +    T           + RGF  +S+    + 
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTV----TDLKIMKDPATGRSRGFGFLSFEKPSSV 58

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 387
              +K      L  + +D   +IP+    ++    G + V  +   V  +E  + F  +G
Sbjct: 59  DEVVKTQHI--LDGKVIDPKRAIPR----DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWG 112

Query: 388 EIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI 429
            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: 275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARN 329
             +  +FV  I  +V   E +  F Q+G I            + RGF  ++Y    A   
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144

Query: 330 AMKALQNKPLRRRKLDIHYSIPK 352
             +  +    + 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 = 2e-15
 Identities = 38/196 (19%), Positives = 71/196 (36%), Gaps = 29/196 (14%)

Query: 269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMI 319
           E P      R LF+  ++    D  L++ FEQ+G +    T C         + RGF  +
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60

Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVF--NLDSSVSTE 377
           +Y  +     AM A +   +  R ++   ++ +++     A+     +F   +       
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 378 ELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQI--- 429
            L   F  YG+I  I     + + K     F+ F D  + +  +       V G      
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 178

Query: 430 ----KLEASRPGGARR 441
               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 = 6e-09
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 6/100 (6%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 322
            + P      + +FV  I  + E+  L+  FEQ+G I  I         K RGF  +++ 
Sbjct: 95  SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
           D  +    +   +   +     ++  ++ K   +   ++Q
Sbjct: 155 DHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSSQ 193

>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 = 40.4 bits (95), Expect = 8e-04
 Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 8/98 (8%)

Query: 350 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK--FI 404
           + K    ++      L +  L    + E L   F  +G + +   +RD   K +    F+
Sbjct: 1   MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 405 EFYDIRAAETALRTLNRSDVAGKQI--KLEASRPGGAR 440
            +  +   + A+       V G+ +  K   SR    R
Sbjct: 61  TYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR 97

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 72.0 bits (177), Expect = 2e-15
 Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 5/90 (5%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAA 327
           G+ P + +    +N NV ++ LK +  ++G++  +         KH G   + +   R A
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPSE 357
           +  +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 = 65.5 bits (160), Expect = 4e-13
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
            +    L+ +V    L  +   YGE+ E+    H    K      + F   R A+  ++ 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           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 = 69.6 bits (171), Expect = 1e-14
 Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           P+  L+V  +  N   + L   F++FG IRTI    K   F  I Y  + AA+ A   ++
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMR 74

Query: 336 NKPLRRRKLDIHYSIPKDNPS 356
             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 = 60.3 bits (147), Expect = 2e-11
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            L V  L  + S   L + F  +G IR I D     +  +I++  + AA+ A   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTI-DHVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 424 VAGKQIKL 431
           + 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 = 2e-14
 Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIR 410
              E D    TL V NL   V+   + Q+F   G  +    I +      + F+EFY+ R
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 411 AAETALRTLNRSDVAGKQIKLEASRPGGARR 441
            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 = 9e-09
 Identities = 16/91 (17%), Positives = 43/91 (47%), Gaps = 3/91 (3%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYTACKHRGFVMISYYDIRAARNA 330
           +   RTL+V N++ +V +  +  LF Q G     + I     +  +  + +Y+ R A  A
Sbjct: 12  DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 71

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
           + 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 = 2e-14
 Identities = 13/79 (16%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
            S  + +R +   V +++L    ++FG I  +      +   ++ + D+  A NA+    
Sbjct: 20  ASPVVHIRGLIDGVVEADLVEALQEFGPISYV-VVMPKKRQALVEFEDVLGACNAVNYAA 78

Query: 336 NKP--LRRRKLDIHYSIPK 352
           +    +      ++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 = 9e-08
 Identities = 17/100 (17%), Positives = 32/100 (32%), Gaps = 9/100 (9%)

Query: 338 PLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH 397
                 ++ +    K   S        + +  L   V   +L +    +G I  +     
Sbjct: 3   HHHHHHMENYDDPHKTPASP------VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

Query: 398 KHNHKFIEFYDIRAAETALR--TLNRSDVAGKQIKLEASR 435
           K     +EF D+  A  A+     N+  +AG    +  S 
Sbjct: 57  K-RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95

>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 = 68.3 bits (167), Expect = 3e-14
 Identities = 17/92 (18%), Positives = 39/92 (42%), Gaps = 5/92 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
            S  + VR +  +V +++L    E+FG I  +      +   ++ + +I +A+  +    
Sbjct: 14  VSPVVHVRGLCESVVEADLVEALEKFGTICYV-MMMPFKRQALVEFENIDSAKECVTFAA 72

Query: 336 NKP--LRRRKLDIHYSIPKD--NPSEKDANQG 363
           + 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 = 49.0 bits (117), Expect = 2e-07
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            + V  L  SV   +L +    +G I  +     K     +EF +I +A+  +       
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK-RQALVEFENIDSAKECVTFAADVP 75

Query: 424 --VAGKQIKLEASR 435
             +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 = 68.5 bits (168), Expect = 3e-14
 Identities = 23/108 (21%), Positives = 48/108 (44%), Gaps = 8/108 (7%)

Query: 255 GVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY------ 308
           G S + +    +   +  GE P++ L+++N++  V + +L +LF +F + +         
Sbjct: 4   GSSGEEIRKIPMFSSYNPGE-PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM 62

Query: 309 TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
           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 = 60.8 bits (148), Expect = 2e-11
 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
            L + NL   V+  +L  +F  + E +           +     FI F +   A  AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 419 LNRSDVAGKQIKLEASRPGGAR 440
           +N   + GK + +E  +    R
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQR 108

>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 = 4e-14
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 415
           S   +    L + NL  +V+ ++L Q+FG             K  + F+++ D   A  A
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLA-GQVLLKSGYAFVDYPDQNWAIRA 60

Query: 416 LRTLN-RSDVAGKQIKLEASRPGGARR 441
           + 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 = 58.0 bits (141), Expect = 1e-10
 Identities = 19/87 (21%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNA 330
             G      L++ N++  V   +L+ LF                G+  + Y D   A  A
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRA 60

Query: 331 MKALQNKP-LRRRKLDIHYSIPKDNPS 356
           ++ L  K  L  + +++ YS+ K   S
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRS 87

>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 = 69.1 bits (169), Expect = 5e-14
 Identities = 15/93 (16%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----------KHRGFVMISYYDIR 325
           P+  ++V+N+  +V++ +LK +F ++ D  +               + +G   I   + +
Sbjct: 44  PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 103

Query: 326 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 358
           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 = 55.2 bits (133), Expect = 4e-09
 Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 18/113 (15%)

Query: 334 LQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI---- 389
           +  + +    +         +    + N   + V NL   V  ++L  IFG Y +     
Sbjct: 25  ISREEMETLSV-------FRSYEPGEPNC-RIYVKNLAKHVQEKDLKYIFGRYVDFSSET 76

Query: 390 -REIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
            R + D +     +     FI   + +AA  AL+  N   + GK + ++ +R 
Sbjct: 77  QRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129

>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 = 68.8 bits (168), Expect = 7e-14
 Identities = 29/143 (20%), Positives = 48/143 (33%), Gaps = 20/143 (13%)

Query: 314 RGFVMISYYDIRAARNAMKALQNKP----LRRRKLDIHYSIPKDNPSEKDANQG------ 363
           +G       D   A    K   N                    +       +        
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPL 72

Query: 364 --TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETALRT 418
              + V NL ++ +  EL + FG YG +R +       N     F+EF D R A  A+R 
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV---ARNPPGFAFVEFEDPRDAADAVRE 129

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           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 = 64.1 bits (156), Expect = 3e-12
 Identities = 19/84 (22%), Positives = 40/84 (47%)

Query: 269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAAR 328
            H         ++V N+ +N   +EL+  F  +G +R+++ A    GF  + + D R A 
Sbjct: 65  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAA 124

Query: 329 NAMKALQNKPLRRRKLDIHYSIPK 352
           +A++ L  + L   ++ +  S  +
Sbjct: 125 DAVRELDGRTLCGCRVRVELSNGE 148

>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 = 67.5 bits (165), Expect = 7e-14
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 327
           G           +  +N+ +    +E++  F +FG +  +          ++ + +   A
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-GITAIVEFLEPLEA 59

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEK 358
           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 = 56.0 bits (135), Expect = 1e-09
 Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            ++  NL +     E+ + F  +G +  +   +       +EF +   A  A R L  S 
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-ITAIVEFLEPLEARKAFRHLAYSK 70

Query: 424 VAGKQIKLE 432
                + LE
Sbjct: 71  FHHVPLYLE 79

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.9 bits (164), Expect = 1e-13
 Identities = 11/81 (13%), Positives = 26/81 (32%), Gaps = 1/81 (1%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 410
                        T  + N+    +  +L  +F  +G I + +    +    FI++    
Sbjct: 16  VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFK-HYPEKGCCFIKYDTHE 74

Query: 411 AAETALRTLNRSDVAGKQIKL 431
            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 = 58.9 bits (143), Expect = 6e-11
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
             T ++ NI     +++L  LF+ FG I         +G   I Y     A   + AL N
Sbjct: 27  VTTAYIGNIPHFATEADLIPLFQNFGFILDFKH-YPEKGCCFIKYDTHEQAAVCIVALAN 85

Query: 337 KPLRRRKL 344
            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 = 66.8 bits (163), Expect = 1e-13
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 3/88 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           PSR L +R +   V ++E+ AL   FG +  I    K +    +      AA   +    
Sbjct: 14  PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYS 72

Query: 336 NKP--LRRRKLDIHYSIPKDNPSEKDAN 361
                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 = 47.5 bits (113), Expect = 7e-07
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNR 421
            L +  L   V+  E+  +   +G++  I   + K N  F+E     AA T +   +   
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK-NQAFLELATEEAAITMVNYYSAVT 75

Query: 422 SDVAGKQIKLEASR 435
             +  + 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 = 67.0 bits (164), Expect = 1e-13
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 353 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 412
           D  ++      T+    + S ++ + + Q F  +G+I EIR    K  + F+ F    +A
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESA 74

Query: 413 ETALRTLNRSDVAGKQIKLEASRPGGARR 441
             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 = 56.2 bits (136), Expect = 7e-10
 Identities = 12/85 (14%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           + T++   I S + D  ++  F  FG I  I      +G+  + +    +A +A+ ++  
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEI-RVFPEKGYSFVRFSTHESAAHAIVSVNG 83

Query: 337 KPLRRRKLDIHYSIPKDNPSEKDAN 361
             +    +  ++     + +   ++
Sbjct: 84  TTIEGHVVKCYWGKESPDMTSGPSS 108

>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 = 2e-13
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 414
             +    +  L V NL   ++ EE+ ++F  YG+  E+   + K    FI       AE 
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEI 66

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 60.0 bits (146), Expect = 2e-11
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
               LFV N+  ++ + E++ LFE++G    ++   K +GF  I       A  A   L 
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKGFGFIRLETRTLAEIAKVELD 72

Query: 336 NKPLRRRKLDIHYSIPKDNPS 356
           N PLR ++L + ++    + +
Sbjct: 73  NMPLRGKQLRVRFACHSASLT 93

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 1/86 (1%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
             + L+VRN+  +  +  ++  F        +    K R +  + + +   A  AMKAL 
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPG-AVERVKKIRDYAFVHFSNREDAVEAMKALN 72

Query: 336 NKPLRRRKLDIHYSIPKDNPSEKDAN 361
            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 = 63.8 bits (156), Expect = 1e-12
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 1/81 (1%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 415
            +  ++   L V NL  S S E + + F        +   +   ++ F+ F +   A  A
Sbjct: 9   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG-AVERVKKIRDYAFVHFSNREDAVEA 67

Query: 416 LRTLNRSDVAGKQIKLEASRP 436
           ++ LN   + G  I++  ++P
Sbjct: 68  MKALNGKVLDGSPIEVTLAKP 88

>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 = 65.4 bits (160), Expect = 4e-13
 Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIEFYDIRAAETA 415
             N   + V NL   + T+++  +F  YG IR+I D +++       F+EF D R AE A
Sbjct: 19  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI-DLKNRRGGPPFAFVEFEDPRDAEDA 77

Query: 416 LRTLNRSDVAGKQIKLEASRPGGARR 441
           +   +  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 = 57.3 bits (139), Expect = 2e-10
 Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 4/93 (4%)

Query: 254 GGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH 313
           G   + G+S G          +    ++V N+  ++   +++ +F ++G IR I    + 
Sbjct: 1   GSSGSSGMSGGG--VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR 58

Query: 314 --RGFVMISYYDIRAARNAMKALQNKPLRRRKL 344
               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 = 65.0 bits (159), Expect = 5e-13
 Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 3/98 (3%)

Query: 257 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF 316
           S+  V  GS +     GE  +  LFVR    +V++SEL  +F  FG ++ +       GF
Sbjct: 11  SSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---ILNGF 67

Query: 317 VMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
             + + +  +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 = 7e-13
 Identities = 19/91 (20%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 410
              +  E + +   L V      V   EL++IFG +G ++E++     +   F+EF +  
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---ILNGFAFVEFEEAE 76

Query: 411 AAETALRTLNRSDVAGKQIKLEASRPGGARR 441
           +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 = 64.2 bits (157), Expect = 9e-13
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 369 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ 428
           NL +     EL + F  YG +R +   ++     F+EF D R AE A+R L+   + G +
Sbjct: 7   NLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66

Query: 429 IKLEASRPGGARR 441
           +++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 = 1e-10
 Identities = 20/80 (25%), Positives = 38/80 (47%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
           ++V N+ +     EL+  F  +G +RT++ A    GF  + + D R A +A++ L  K +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 340 RRRKLDIHYSIPKDNPSEKD 359
              ++ +  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 = 63.5 bits (155), Expect = 2e-12
 Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 7/90 (7%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY------TACKHRGFVMISYYDIRAA 327
           +  +  + VRNI       E++ LF  FG+++T+           HRGF  + +   + A
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71

Query: 328 RNAMKALQN-KPLRRRKLDIHYSIPKDNPS 356
           + 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 = 5e-09
 Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHK--- 402
           S        K      ++V N+    +  E+ ++F  +GE++ +R          H+   
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61

Query: 403 FIEFYDIRAAETALRTL-NRSDVAGKQIKLEASRP 436
           F++F   + A+ A   L + + + G+++ LE +  
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 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 = 63.5 bits (155), Expect = 2e-12
 Identities = 23/100 (23%), Positives = 49/100 (49%), Gaps = 9/100 (9%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIR 410
           + S   A    L V NL ++V+ E L + F  +G++     ++D      + FI F +  
Sbjct: 3   SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD------YAFIHFDERD 56

Query: 411 AAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
            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 = 62.3 bits (152), Expect = 4e-12
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-HRGFVMISYYDIRAARNAMKAL 334
             + LFVRN+ + V +  L+  F QFG +       K  + +  I + +   A  AM+ +
Sbjct: 10  KVKVLFVRNLANTVTEEILEKAFSQFGKL----ERVKKLKDYAFIHFDERDGAVKAMEEM 65

Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
             K L    ++I ++ P D   ++   Q
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQ 93

>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 = 62.7 bits (153), Expect = 2e-12
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 414
            S +D    TL V  L  +++  +L   F  +GEIR I     +    FI+F   +AAE 
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTIT-VVQRQQCAFIQFATRQAAEV 63

Query: 415 AL-RTLNRSDVAGKQIKL 431
           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 = 54.2 bits (131), Expect = 2e-09
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 337
            TL+V  +   + +++L+  F QFG+IRTI T  + +    I +   +AA  A +   NK
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQFATRQAAEVAAEKSFNK 71

>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 = 67.6 bits (164), Expect = 2e-12
 Identities = 24/93 (25%), Positives = 47/93 (50%), Gaps = 6/93 (6%)

Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIR--TIYTACKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F QFG I    +  + K RG   + + ++ +A N
Sbjct: 8   PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
           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 = 5e-08
 Identities = 14/75 (18%), Positives = 26/75 (34%)

Query: 269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAAR 328
           +      P+  LF+ N+     +  L  LF QF   + +           + + +   A 
Sbjct: 199 QPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAG 258

Query: 329 NAMKALQNKPLRRRK 343
            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 = 51.4 bits (122), Expect = 4e-07
 Identities = 33/217 (15%), Positives = 68/217 (31%), Gaps = 15/217 (6%)

Query: 364 TLVVFNLDSSVSTEEL----HQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAET 414
           T+ + NL+  +  +EL    + IF  +G+I +I       + K     F+ F ++ +A  
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 67

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVI 474
           ALR++       K ++++ ++        ++    + D    +       +     +   
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127

Query: 475 TSTCMDNGSIQVLHSATRSPAIALTESHQTSSVPNGLPSLARVGSIGKQFGHYEPNLSLD 534
                  G++Q           A    H     P  +P    +   G   G   P     
Sbjct: 128 GGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPP 187

Query: 535 EMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIAD 571
           +     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 = 2e-05
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            L + NL    +   L  +F  +   +E+R    +H+  F+EF +   A  A   L    
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 424 V-AGKQIKLE 432
           +     +K+ 
Sbjct: 269 ITQNNAMKIS 278

>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 = 64.1 bits (156), Expect = 4e-12
 Identities = 25/117 (21%), Positives = 51/117 (43%), Gaps = 6/117 (5%)

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 389
           A+++     L + + D H+    +   +      TL V NL    + E+++++F   G+I
Sbjct: 8   ALRSDSYVELSQYR-DQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 390 REIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
           ++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 = 58.3 bits (141), Expect = 4e-10
 Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
            S TL+V N++    + ++  LF + GDI+ I            GF  + YY    A NA
Sbjct: 38  KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 97

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           M+ +    L  R +   +      
Sbjct: 98  MRYINGTRLDDRIIRTDWDAGFKE 121

>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 = 4e-12
 Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 5/93 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
            S  LFVRN++    + +L+ LF  +G +  ++        K +GF  +++     A  A
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
              +  +  + 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 = 6e-09
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIR 410
           S   +  G L V NL  + S E+L ++F  YG + E+       T+      F+ F    
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 411 AAETALRTLNRSDVAGKQIKLEASRP 436
            A  A   ++     G+ + +  S  
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTI 87

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 61.9 bits (151), Expect = 5e-12
 Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 1/94 (1%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDTQHKHNHKFIEFY 407
           S      S       TLV+ NL  S + E L ++F     I+           + FIEF 
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFA 61

Query: 408 DIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
               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 = 61.9 bits (151), Expect = 6e-12
 Identities = 16/83 (19%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARNAMKA 333
            S+TL + N++ +  +  L+ +FE+   I+ +      K +G+  I +     A+ A+ +
Sbjct: 14  ESKTLVLSNLSYSATEETLQEVFEKATFIK-VPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 334 LQNKPLRRRKLDIHYSIPKDNPS 356
              + +  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 = 61.6 bits (150), Expect = 1e-11
 Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 4/90 (4%)

Query: 353 DNPSEKDANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRA 411
            N ++  +    + + NL+++ V   ++  IF  YG +           + F+++ + R 
Sbjct: 18  TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS---VHKGYAFVQYSNERH 74

Query: 412 AETALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 55.1 bits (133), Expect = 2e-09
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 276 PSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
            +  +F+ N+N+  V+ S+++ +F ++G +        H+G+  + Y + R AR A+   
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGE 82

Query: 335 QNKPLRRRKLDIHYSIPKDNP 355
             + L  + LDI+ +      
Sbjct: 83  NGRVLAGQTLDINMAGEPKPD 103

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 61.0 bits (148), Expect = 1e-11
 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 2/95 (2%)

Query: 262 SAGSVVGEHP--YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMI 319
           S+GS     P   G   +  ++V N+  +   S+LK    + G +    T    R    +
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
            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 = 5e-10
 Identities = 16/87 (18%), Positives = 29/87 (33%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIR 410
           P   P E       + V NL       +L +     G +      Q      F+ + D  
Sbjct: 8   PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSA 67

Query: 411 AAETALRTLNRSDVAGKQIKLEASRPG 437
           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 = 60.3 bits (147), Expect = 2e-11
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 415
           S    N   + V N+ ++ +++EL  +F   G + E        ++ F+       A+ A
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAA 59

Query: 416 LRTLNRSDVAGKQIKLEASRPGGARR 441
           +  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 = 57.6 bits (140), Expect = 1e-10
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
            +  +FV N+++     EL++LFE+ G +         + +  +       A+ A+  L 
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVIECD---VVKDYAFVHMEKEADAKAAIAQLN 64

Query: 336 NKPLRRRKLDIHYSIPKDNPS 356
            K ++ +++++  S      S
Sbjct: 65  GKEVKGKRINVELSTKGQKKS 85

>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: 367 VFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA 425
           + NL   +VS E+L +IF  YG I +I     K+   FI+F + ++   A+   ++    
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIECESQEMNF 71

Query: 426 GKQIKLEASRPGGARRF 442
           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 = 2e-11
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 276 PSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
           P   LF+ N+   NV   +L  +F  +G I  I        F  I + + ++ R+A++  
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECE 65

Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGT 364
             +    +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 = 61.0 bits (148), Expect = 2e-11
 Identities = 16/96 (16%), Positives = 35/96 (36%), Gaps = 9/96 (9%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGD-------IRTIYTACKHRGFVMISYYDIRAAR 328
            +  LF+  I    +  E+     +  +         +     K+RGF  + Y   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 329 NAMKALQNKPLRR--RKLDIHYSIPKDNPSEKDANQ 362
            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 = 51.7 bits (124), Expect = 3e-08
 Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRDTQHKHNHK---FIEFYDIRAAE 413
               L +  +      EE+ +      E    +        K  ++   F+E+   RAA 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 414 TALRTLNRSDVA--GKQIKLEASRP 436
            A R L    +   G QI ++ + P
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEP 91

>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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHK---FIEFYDIRAAETALR 417
            + +  L  +V+ + + +IF  YG+I+ I    +  H H  K   ++EF +   AE AL+
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 418 TLNRSDVAGKQIKLEASRP 436
            ++   + 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 = 2e-08
 Identities = 10/85 (11%), Positives = 29/85 (34%), Gaps = 6/85 (7%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YTACKHRGFVMISYYDIRAARN 329
               + +  +  NV    +  +F  +G I+ I            +G+  + + +   A  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDN 354
           A+K +    +  +++     +    
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWP 87

>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 = 2e-11
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 369 NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ 428
           NL    + +E+  +F  YG++ E        N+ F+   D  AAE A+R L+   + G  
Sbjct: 15  NLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVN 71

Query: 429 IKLEASRPGGARR 441
           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 = 54.9 bits (133), Expect = 1e-09
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           G      LF+ N+     + E+++LFEQ+G +         + +  +   D  AA +A++
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECD---IIKNYGFVHIEDKTAAEDAIR 60

Query: 333 ALQNKPLRRRKLDIHYSIPKDNPS 356
            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 = 2e-11
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
           PSR +++ +I  +  + ++  L    G +  +         + +G+  I + D+ ++ +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPS 356
           ++ 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 = 51.9 bits (125), Expect = 2e-08
 Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 11/91 (12%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FIEFYDIRAAETALRT 418
           + ++    + E++  +    G +  +       T      K   FIEF D+ ++ +A+R 
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGR---SKGYAFIEFRDLESSASAVRN 63

Query: 419 LNRSDVAGKQIKLEASRPGGARRFMVQSEQE 449
           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 = 60.8 bits (148), Expect = 2e-11
 Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 6/96 (6%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIE 405
           P DN S ++ +  T+    L + +   +L   F   G++R++     R+++      ++E
Sbjct: 14  PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 73

Query: 406 FYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 50.0 bits (120), Expect = 1e-07
 Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAAR 328
           E  +RT+F   + + +   +L+  F   G +R +         + +G   + + +I++  
Sbjct: 22  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 81

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDN 354
            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 = 62.0 bits (150), Expect = 3e-11
 Identities = 23/123 (18%), Positives = 56/123 (45%), Gaps = 4/123 (3%)

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLV-VFNLDSSVST 376
           M  ++   +A+ A++A+ +       L    +      +    +    + V NL   V+ 
Sbjct: 1   MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTL 60

Query: 377 EELHQIFGIYGEI-REIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEA 433
           + LHQIF  +G + + I  T++      +++ D  +A+ A  +L+  ++  A   ++++ 
Sbjct: 61  DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

Query: 434 SRP 436
           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 = 52.8 bits (126), Expect = 4e-08
 Identities = 26/125 (20%), Positives = 47/125 (37%), Gaps = 11/125 (8%)

Query: 262 SAGSVVGEHPYGEHPSRTLF--VRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VM 318
           ++ + V         S  L   V N+   V    L  +F +FG +  I T  K+  F  +
Sbjct: 29  ASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQAL 88

Query: 319 ISYYDIRAARNAMKALQNKPL--RRRKLDIHYSIPKD------NPSEKDANQGTLVVFNL 370
           + Y D  +A++A  +L  + +      L I +S          N   +D  +  L   + 
Sbjct: 89  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS 148

Query: 371 DSSVS 375
             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 = 61.8 bits (150), Expect = 3e-11
 Identities = 17/92 (18%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
               LFV +I+   ++ E++  F  +G+I+ I+          +G+ ++ Y   + A  A
Sbjct: 71  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
            +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 = 54.1 bits (130), Expect = 1e-08
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L V ++      +E+ + F  YGEI+ I     R T     +  +E+   + A  A   
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           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 = 61.4 bits (149), Expect = 4e-11
 Identities = 27/142 (19%), Positives = 54/142 (38%), Gaps = 14/142 (9%)

Query: 314 RGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG---------T 364
           +G       D   A    K   N      +     +      +E   +           +
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS 72

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
           L V NL    S + L ++F  YG + ++     R T+      F+ F+D R AE A+  +
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132

Query: 420 NRSDVAGKQIKLEASRPGGARR 441
           + + + 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 = 56.0 bits (135), Expect = 2e-09
 Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 5/104 (4%)

Query: 257 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----- 311
               V+ GS    H        +L V N+        L+ +FE++G +  +Y        
Sbjct: 50  KTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 109

Query: 312 KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP 355
           + 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 = 59.2 bits (144), Expect = 5e-11
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 415
                   TL V+  D  ++   L   F  +G I ++     + N  F+ +  + +A+ A
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQA 65

Query: 416 LRTLNRSDVAGKQIKLEASRP 436
           +  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 = 51.1 bits (123), Expect = 3e-08
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 337
            TL+V   +  +  + L+  F  FG+I  +      R    ++Y  + +A  A+  L   
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGT 72

Query: 338 PLRRRKLDIHYSIPKDNPSEK 358
            +   +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 = 58.4 bits (142), Expect = 7e-11
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
           V N+  + + +EL   F  YG + E        ++ F+       A  A+R L+ ++  G
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIECD---IVKDYAFVHMERAEDAVEAIRGLDNTEFQG 71

Query: 427 KQIKLEASRPGGARR 441
           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 = 3e-10
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
            S  L V NI+    + EL+A FE++G +         + +  +       A  A++ L 
Sbjct: 9   ASTKLHVGNISPTCTNQELRAKFEEYGPVIECD---IVKDYAFVHMERAEDAVEAIRGLD 65

Query: 336 NKPLRRRKLDIHYSIPKDNPS 356
           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 = 9e-11
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 367 VFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA 425
           + NL   +VS E+L +IF  YG I +I     K+   FI+F + ++   A+   ++    
Sbjct: 27  IGNLPLKNVSKEDLFRIFSPYGHIMQIN---IKNAFGFIQFDNPQSVRDAIEXESQEMNF 83

Query: 426 GKQIKLEASRPG 437
           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: 268 GEHPYGEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRA 326
           G  P G H    LF+ N+   NV   +L  +F  +G I  I        F  I + + ++
Sbjct: 13  GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQS 69

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPK 352
            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 = 58.0 bits (141), Expect = 1e-10
 Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 8/97 (8%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH--------RGFVMISYYDI 324
           G   S  LF++N+N +  +  LK +F + G I++   + K          GF  + Y   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 325 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
             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 = 3e-10
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FIEFYDIRA 411
           +    L + NL+ S + E L  +F   G I+       ++           F+E+     
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 412 AETALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 58.9 bits (142), Expect = 1e-10
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 351 PKDNPSEKDANQGTLV-VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDI 409
           P +       N+  L+ + N    ++ + L+ +    G+++ I   +       +EF  +
Sbjct: 13  PGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESV 72

Query: 410 RAAETALRTLNRSDVAGKQIKLE 432
             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 = 9e-08
 Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 274 EHPSRTLF--VRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAM 331
              ++ L   ++N    +    L  +    G ++ I    ++    M+ +  +  A+ A 
Sbjct: 20  SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAK 79

Query: 332 KALQNKPL--RRRKLDIHYSIPKD 353
            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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
           TL V NL    S + L ++F  YG + ++       T+      F+ F+D R A+ A   
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           ++ +++ 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: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 322
           G          TL V N+        L+ +FE++G +  +Y          RGF  + ++
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63

Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPK 352
           D R A++A  A+    L  R+L +  +   
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>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 = 58.2 bits (141), Expect = 2e-10
 Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
               LFV  ++    + ++   F ++G+I+ I+          +G+ ++ Y   + A+ A
Sbjct: 21  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
           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 = 52.4 bits (126), Expect = 2e-08
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L V  +    + E++H  F  YGEI+ I     R T +   +  +E+   + A+ A+  
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           LN  D+ G+ I ++     G  +
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPK 106

>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 = 56.6 bits (137), Expect = 3e-10
 Identities = 12/77 (15%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           G   S  + V+N+  +    E+  L + +  ++  Y   +++    ++  +   A+NA++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-RNKRTAFVTLLNGEQAQNAIQ 58

Query: 333 ALQNKPLRRRKLDIHYS 349
                  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 = 3e-10
 Identities = 12/75 (16%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
               ++V NL    + +E+H +   Y  ++     ++K    F+   +   A+ A++  +
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK-RTAFVTLLNGEQAQNAIQMFH 61

Query: 421 RSDVAGKQIKLEASR 435
           +    GK + ++   
Sbjct: 62  QYSFRGKDLIVQLQP 76

>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 = 56.9 bits (138), Expect = 3e-10
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVMISYYDIRAARNAMK 332
           PS+TLFV+ ++ +  +  LK  F+     R +    T    +GF  + +     A+ A +
Sbjct: 14  PSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETG-SSKGFGFVDFNSEEDAKAAKE 72

Query: 333 ALQNKPLRRRKLDIHYSIPKDNPS 356
           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 = 52.6 bits (127), Expect = 1e-08
 Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEF 406
           S     P+ +     TL V  L    + E L + F      R +  R+T       F++F
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDF 61

Query: 407 YDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
                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 = 56.8 bits (138), Expect = 4e-10
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 11/92 (11%)

Query: 353 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FI 404
              S     +  L V  L   V  + LH  F  +G+I +I      +T+    H+   F+
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE---KHRGFAFV 59

Query: 405 EFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 56.5 bits (137), Expect = 5e-10
 Identities = 24/87 (27%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNA 330
             R L+V  +   V+D  L A F  FGDI  I     Y   KHRGF  + +     A  A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSE 357
           +  +    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 = 56.9 bits (138), Expect = 4e-10
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 5/98 (5%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIR 325
           P  +   R++FV NI     + +LK +F + G + +          K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 326 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
            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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
           ++ V N+    + E+L  IF   G +   R    +   K     F E+ D   A +A+R 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           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 = 56.6 bits (137), Expect = 6e-10
 Identities = 19/105 (18%), Positives = 42/105 (40%), Gaps = 11/105 (10%)

Query: 265 SVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMI 319
           S     P      +T+F+RN++ + E+  L  + +QFGD++ +           +G    
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

Query: 320 SYYDIRAARNAMKALQNKPLRR------RKLDIHYSIPKDNPSEK 358
            +    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 = 49.3 bits (118), Expect = 2e-07
 Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 17/99 (17%)

Query: 352 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---F 403
                       T+ + NL      E L ++   +G+++ +      DT+H    K   F
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH---SKGCAF 61

Query: 404 IEFYDIRAAETALRTLNRS------DVAGKQIKLEASRP 436
            +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 = 7e-10
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
           P+  L V  ++    + +L+ +F ++G I  +         + RGF  + + ++  A+ A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 331 MKALQNKPLRRRKLDIHYSIPK 352
            +      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 = 3e-09
 Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 5/91 (5%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 405
                         L VF L    +  +L ++F  YG I ++     + + +     F+ 
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94

Query: 406 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 8e-10
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 257 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----- 311
             Q        G  P       +L V N+        L+ +FE++G +  +Y        
Sbjct: 27  GQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 86

Query: 312 KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 352
           + 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 = 7e-09
 Identities = 24/128 (18%), Positives = 51/128 (39%), Gaps = 6/128 (4%)

Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEE 378
           S++    +   +    +         +            D    T L V NL    S + 
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDT 63

Query: 379 LHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA 433
           L ++F  YG + ++     R T+      F+ F+D R AE A+  ++ + + G++++++ 
Sbjct: 64  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

Query: 434 SRPGGARR 441
           +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 = 55.3 bits (134), Expect = 1e-09
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 6/89 (6%)

Query: 260 GVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRG 315
           G S  S  G  P  E   RT+FV N+ + V +  L  LF Q G +  +        K + 
Sbjct: 1   GSSGSS--GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS 58

Query: 316 FVMISYYDIRAARNAMKALQNKPLRRRKL 344
           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 = 52.2 bits (126), Expect = 1e-08
 Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDI 409
           P++++A++ T+ V NL++ V  E L+++F   G + ++     R+ + K +  F+ F   
Sbjct: 10  PAQEEADR-TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK-SFGFVCFKHP 67

Query: 410 RAAETALRTLNRSDVAGKQIK 430
            +   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: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
            + T+ V N++ +  +++L+ LF  FG I  IY A      + +GF  IS++    A  A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           +  +         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 = 54.9 bits (133), Expect = 2e-09
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDI 409
           P+ +  +  T+ V NL       +L ++F  +G I  I     + T       FI F+  
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 410 RAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
             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 = 55.7 bits (135), Expect = 1e-09
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
            P  +     T+ V  LD  VS   L ++F   G +        R T     + F+EF  
Sbjct: 7   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66

Query: 409 IRAAETALRTLNRSDVAGKQIKLEASRP 436
              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 = 53.4 bits (129), Expect = 6e-09
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 5/88 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
              T++V  ++  V +  L  LF Q G +   +        +H+G+  + +     A  A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEK 358
           +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 = 55.8 bits (135), Expect = 1e-09
 Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 5/90 (5%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIR 325
           P        LFV +I+   ++ E++  F  +G+I+ I+          +G+ ++ Y   +
Sbjct: 20  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79

Query: 326 AARNAMKALQNKPLRRRKLDIHYSIPKDNP 355
            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 = 55.4 bits (134), Expect = 1e-09
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L V ++      +E+ + F  YGEI+ I     R T     +  +E+   + A  A   
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           LN +++ G+ I+++     G +R
Sbjct: 88  LNGAEIMGQTIQVDWCFVKGPKR 110

>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 = 56.3 bits (136), Expect = 1e-09
 Identities = 22/116 (18%), Positives = 48/116 (41%), Gaps = 7/116 (6%)

Query: 326 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGI 385
           A    M+   +K +           P     +K+ ++ ++ V N+D   + ++L   F  
Sbjct: 1   AIAPCMQTTHSK-MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSS 59

Query: 386 YGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
            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 = 46.6 bits (111), Expect = 2e-06
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAAR 328
           E   R+++V N++      +L+A F   G I  I   C       +G+  I + +  +  
Sbjct: 33  EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92

Query: 329 NAMKALQNKPLRRRKL 344
            A+ A+     R R +
Sbjct: 93  AAV-AMDETVFRGRTI 107

>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 = 1e-09
 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
               LFV  ++    + ++   F ++G+I+ I+          +G+ ++ Y   + A+ A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNP 355
           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 = 2e-08
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L V  +    + E++H  F  YGEI+ I     R T +   +  +E+   + A+ A+  
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 419 LNRSDVAGKQIKLEASRP 436
           LN  D+ G+ I ++    
Sbjct: 85  LNGQDLMGQPISVDWCFV 102

>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 = 55.7 bits (135), Expect = 1e-09
 Identities = 18/113 (15%), Positives = 43/113 (38%), Gaps = 15/113 (13%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-------HRGFVMISYYDIRAARN 329
           S  +F++N++ ++++  L   F  FG+I     +CK        +G+  + +    AA  
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNI----LSCKVVCDENGSKGYGFVHFETQEAAER 60

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDN----PSEKDANQGTLVVFNLDSSVSTEE 378
           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 = 54.2 bits (131), Expect = 4e-09
 Identities = 18/91 (19%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 363 GTLVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHNHKFIEFYDIRAAETALRTL 419
           G + + NLD S+  + L+  F  +G I   + + D      + F+ F    AAE A+  +
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 420 NRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
           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 = 56.3 bits (136), Expect = 1e-09
 Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 12/106 (11%)

Query: 334 LQNKPLRRRKLDIHYSIPKDNPSEKDANQG-TLVVFNLDSSVSTEELHQIFGIYGEIREI 392
           +    +   +  +         S   A     L V  L   V  + LH  F  +G+I +I
Sbjct: 34  VAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDI 93

Query: 393 -----RDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIK 430
                 +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 = 54.8 bits (132), Expect = 5e-09
 Identities = 23/88 (26%), Positives = 31/88 (35%), Gaps = 5/88 (5%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGF 316
                 G         R L+V  +   V+D  L A F  FGDI  I         KHRGF
Sbjct: 48  GGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGF 107

Query: 317 VMISYYDIRAARNAMKALQNKPLRRRKL 344
             + +     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 = 55.1 bits (133), Expect = 2e-09
 Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 13/100 (13%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRT----------IYT---ACKHRGFVMISYY 322
            + T+FV+ +  NV    +   F+Q G I+T          +YT     K +G   +S+ 
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
           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 = 50.1 bits (120), Expect = 1e-07
 Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 14/94 (14%)

Query: 357 EKDANQ-GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--------KHNHK----- 402
           E+D +   T+ V  L  +V+ E +   F   G I+  + T          +   K     
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 403 FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
            + 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 = 2e-09
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 5/94 (5%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKF 403
           S               L VF L    +  +L ++F  YG I ++     + ++      F
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG 437
           + 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 = 4e-09
 Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
           P+  L V  ++    + +L+ +F ++G I  +         + RGF  + + ++  A+ A
Sbjct: 14  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73

Query: 331 MKALQNKPLRRRKLDIHYS 349
            +      L  R++ +   
Sbjct: 74  KERANGMELDGRRIRVSGP 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 53.9 bits (130), Expect = 3e-09
 Identities = 16/94 (17%), Positives = 34/94 (36%), Gaps = 13/94 (13%)

Query: 267 VGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG-----DIRTIY--TACKHRGFVMI 319
           +G H    H   T+ +RNI  +     +      +      +IR I      ++RGF  +
Sbjct: 1   MGHHH--HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFV 58

Query: 320 SYYDIRAARNAMKALQNKPLRR----RKLDIHYS 349
                  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: 364 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETAL 416
           T+++ N+      + +      Y    +  IR  + K   +     F++      A   L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 417 RTLNRSD----VAGKQIKLEASRPG 437
           + 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 = 4e-09
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 11/75 (14%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHK---FIEFYDIRAAETA 415
            L V  L   V  + LH  F  +G+I +I      +T+    H+   F+EF     A  A
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE---KHRGFAFVEFELAEDAAAA 65

Query: 416 LRTLNRSDVAGKQIK 430
           +  +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 = 4e-09
 Identities = 22/74 (29%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
             R L+V  +   V+D  L A F  FGDI  I         KHRGF  + +     A  A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 331 MKALQNKPLRRRKL 344
           +  +    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 = 52.9 bits (128), Expect = 5e-09
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDI---RTIY---TACKHRGFVMISYYDIRAARNA 330
           +  LFV ++N NV+D  L+  F+ F        ++   T    RG+  +S+     A+NA
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG-SSRGYGFVSFTSQDDAQNA 59

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           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: 369 NLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           +L+ +V  E L   F  +             T     + F+ F     A+ A+ ++   D
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD 67

Query: 424 VAGKQIKLEASRP 436
           + 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 = 6e-09
 Identities = 21/94 (22%), Positives = 43/94 (45%), Gaps = 5/94 (5%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAA 327
           G   S  L+V +++ N+ +  L+ +FE FG I  I         + +G+  I++ D   A
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
           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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L V +L  +++ + L  IF  +G+I  I      DT     + FI F D   A  AL  
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 419 LNRSDVAGKQIKLEASRP 436
           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 = 53.4 bits (129), Expect = 6e-09
 Identities = 20/103 (19%), Positives = 48/103 (46%), Gaps = 7/103 (6%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRA 326
           P G+    T+FV  I+  ++++E+++ F ++G ++ +          +G+  +S+Y+   
Sbjct: 3   PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFN 369
            +  ++         +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 = 5e-04
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD-TQHKHNHKFIEFYDIRAA 412
           E      T+ V  +D  +   E+   F  YG ++E   I D T     + F+ FY+    
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63

Query: 413 ETALRTLNRSDVAGKQIK 430
           +  +   ++ +  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 = 53.4 bits (129), Expect = 6e-09
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 10/97 (10%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARN 329
               R LFV  +N    + ++  LF+ FG I             +G   + +     A+ 
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71

Query: 330 AMKALQNK---PLRRRKLDIHYSIPKDNPSEKDANQG 363
           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 = 45.7 bits (109), Expect = 3e-06
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 14/90 (15%)

Query: 354 NPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEF 406
           + SE    +   L V  L+   S E++ ++F  +G I E   +R      + K   F++F
Sbjct: 6   SGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG--PDGSSKGCAFVKF 63

Query: 407 YDIRAAETALRTLNRSDVAGKQIKLEASRP 436
                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 = 53.1 bits (128), Expect = 7e-09
 Identities = 16/86 (18%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAET 414
              +  L +  L  S + EEL +I   +G ++++R             ++E+ +   A  
Sbjct: 14  SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQ 73

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGAR 440
           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 = 51.9 bits (125), Expect = 2e-08
 Identities = 11/83 (13%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAM 331
               LF+  +  +    EL+ + +  G ++ +        K +G   + Y +   A  A+
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75

Query: 332 KALQNKPLRRRKLDIHYSIPKDN 354
             +    ++   + +  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 = 52.8 bits (127), Expect = 8e-09
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR--GFVMISYYDIRAARNAMKAL 334
            R L +RNI  +++   L +L  Q+G + +            V ++Y     AR A+  L
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKL 74

Query: 335 QNKPLRRRKLDIHYSIPK 352
               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 = 52.5 bits (126), Expect = 1e-08
 Identities = 12/71 (16%), Positives = 22/71 (30%), Gaps = 2/71 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK--FIEFYDIRAAETALRTLNR 421
            L + N+   +  E L  +   YG +                + +     A  AL  LN 
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76

Query: 422 SDVAGKQIKLE 432
             +    +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 = 53.1 bits (128), Expect = 8e-09
 Identities = 19/93 (20%), Positives = 47/93 (50%), Gaps = 8/93 (8%)

Query: 356 SEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHNHK---FIEFYD 408
           S+K+  +G  L +++L      ++L Q+F  +G +   +   D Q   + K   F+ + +
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS-KCFGFVSYDN 76

Query: 409 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
             +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 = 50.0 bits (120), Expect = 1e-07
 Identities = 20/118 (16%), Positives = 49/118 (41%), Gaps = 14/118 (11%)

Query: 254 GGVSNQGVSAGSVVGEHPYGEHPSRT-LFVRNINSNVEDSELKALFEQFGDIRTIYTACK 312
           G   + G++  S+       E P    LF+ ++     D +L  +F  FG++     + K
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNV----VSAK 56

Query: 313 ---------HRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
                     + 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 = 1e-08
 Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK---FIE 405
           S      SE  +    L V N+       +L Q+FG +G+I ++    ++   K   F+ 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 406 FYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 51.9 bits (125), Expect = 2e-08
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARNAMK 332
             + L V NI     D +L+ +F QFG I     I+     +GF  +++ +   A  A +
Sbjct: 14  TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73

Query: 333 ALQNKPLRRRKLDIHYSIPKDNPSEK 358
            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 = 1e-08
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 5/93 (5%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
             S   +++G L V  L    + + L Q+F  YG+I E+     R+TQ      F+ F +
Sbjct: 4   GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63

Query: 409 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 6e-08
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
               LFV  ++ +  +  L+ +F ++G I  +         + RGF  +++ +I  A++A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           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 = 1e-08
 Identities = 11/69 (15%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 274 EHPSRTLFVRN--INSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAM 331
            + +++L V N  + + V  ++L  + E+ G +  +     ++ +    Y     ++ A 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAY 80

Query: 332 KALQNKPLR 340
             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 = 9e-08
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 364 TLVVFN--LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
           +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: 274 EHPSRTLFVRNI-NSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           +   R + + N+ +S   DS +  L E +G I+      + +    I       A   + 
Sbjct: 22  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVD 80

Query: 333 ALQNKP--LRRRKLDIHYS 349
               K    + R + +  S
Sbjct: 81  HCLKKALWFQGRCVKVDLS 99

>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 = 52.8 bits (127), Expect = 2e-08
 Identities = 28/128 (21%), Positives = 57/128 (44%), Gaps = 13/128 (10%)

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTE 377
           ++S YD       ++ LQ +  +         IP    + +      L+V  + ++V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQH--------IPPTQMNPEPDVLRNLMVNYIPTTVDEV 57

Query: 378 ELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
           +L Q+F  YG I  +     R+T+    + F++F    +A+ A+  LN  ++  K++K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 433 ASRPGGAR 440
            +  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 = 48.2 bits (115), Expect = 1e-06
 Identities = 20/115 (17%), Positives = 40/115 (34%), Gaps = 13/115 (11%)

Query: 258 NQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK----- 312
            Q         +        R L V  I + V++ +L+ LFE++G I     + K     
Sbjct: 23  QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI----ESVKIVCDR 78

Query: 313 ----HRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
                RG+  + +    +A+ A+  L    +  ++L +  +             G
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVG 133

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 52.4 bits (126), Expect = 2e-08
 Identities = 23/108 (21%), Positives = 44/108 (40%), Gaps = 10/108 (9%)

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGE 388
           +  AL   PL    L    +       E    +G  L +++L    +  +L   F  +G 
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEG--PEGCNLFIYHLPQEFTDTDLASTFLPFGN 66

Query: 389 I---REIRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIK 430
           +   +   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 = 6e-06
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 13/74 (17%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRAARNA 330
           LF+ ++     D++L + F  FG++     + K          + F  +S+ +  +A+ A
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNV----ISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98

Query: 331 MKALQNKPLRRRKL 344
           +KA+    +  ++L
Sbjct: 99  IKAMNGFQVGTKRL 112

>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 = 2e-08
 Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 14/105 (13%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------K 312
           S+GS        +     +FV  +  +  D+ L+  FE FGDI                K
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDI----EEAVVITDRQTGK 57

Query: 313 HRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE 357
            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 = 5e-04
 Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 8/97 (8%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FI 404
              + S+KD     + V  L    +   L + F  +G+I E   I D Q     +   F+
Sbjct: 6   SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGK-SRGYGFV 64

Query: 405 EFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
              D  AAE A +  N   + G++  +  +  G   R
Sbjct: 65  TMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPR 100

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 4/92 (4%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC----KHRGFVMISYYDIRAARNAM 331
               LF+  +N    +  LKA+F + G I  +        K RGF  I++ +   A+NA 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 332 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
           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 = 8e-08
 Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 13/97 (13%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEFYDIRAAET 414
           + G L +  L+   + + L  +FG +G I E   I+D   K   +   FI F +   A+ 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKS--RGFAFITFENPADAKN 63

Query: 415 ALRTLNRSDVAGKQIKLE-----ASRPGGARRFMVQS 446
           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 = 51.5 bits (124), Expect = 2e-08
 Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 8/89 (8%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YTACKHRG 315
           S+GS             T++V N+  ++ +++L  +F ++G +  +       T  K +G
Sbjct: 2   SSGSSGMSGGLAP-SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTR-KSKG 59

Query: 316 FVMISYYDIRAARNAMKALQNKPLRRRKL 344
              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 = 8e-08
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 405
                     ++ T+ V NL  S++  +L++IF  YG++ ++   + K   K     FI 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 406 FYDIRAAETALRTLNRSDVAGKQIK 430
           F D  +A+   R +N   + G+ IK
Sbjct: 65  FLDKDSAQNCTRAINNKQLFGRVIK 89

>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 = 2e-08
 Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 8/93 (8%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 322
           G     +H +  LF+  I  N+++ +LK LFE+FG I  +          H+G   ++Y 
Sbjct: 4   GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63

Query: 323 DIRAARNAMKALQNK---PLRRRKLDIHYSIPK 352
           +  +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 = 41.2 bits (97), Expect = 1e-04
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 12/88 (13%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---FIEFYD 408
              KD +   L +  +  ++  ++L  +F  +G+I E   ++D +    HK   F+ + +
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKD-RFTGMHKGCAFLTYCE 64

Query: 409 IRAAETALRTLNRSDVAGKQIKLEASRP 436
             +A  A   L+      ++     +RP
Sbjct: 65  RESALKAQSALH-----EQKTLPGMNRP 87

>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 = 51.5 bits (124), Expect = 3e-08
 Identities = 20/97 (20%), Positives = 44/97 (45%), Gaps = 5/97 (5%)

Query: 263 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFV 317
           A ++      G      L+V +++ N+ +  L+ +FE FG I +I         + +G+ 
Sbjct: 12  AAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYG 71

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
            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 = 4e-07
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 5/91 (5%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIE 405
             +N  +  A    L V +L  +++ + L  IF  +G I  I      +T     + FI 
Sbjct: 15  MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74

Query: 406 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 3e-08
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-HNHKFIEFYDIRAAETALRTLNRSD 423
           ++V NL   V+ + LHQIF  +G + +I            +++ D  +A+ A  +L+  +
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90

Query: 424 V--AGKQIKLEASRP 436
           +  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 = 8e-08
 Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 262 SAGSVVGEHPYGEHPSRTLF--VRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VM 318
           ++ + V         S  L   V N+   V    L  +F +FG +  I T  K+  F  +
Sbjct: 11  ASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQAL 70

Query: 319 ISYYDIRAARNAMKALQNKPL--RRRKLDIHYSIPKD 353
           + Y D  +A++A  +L  + +      L I +S    
Sbjct: 71  LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107

>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: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           S  L ++N+ + ++   L+ L  Q G + + +      G  +  Y     A  A  AL N
Sbjct: 7   SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-GIALCKYTTREEANKAQMALNN 65

Query: 337 KPLRRRKLDIHYSIPKDNPSEKDANQ 362
             L         +I  ++PSE +   
Sbjct: 66  CVLANT------TIFAESPSENEVQS 85

>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 = 4e-08
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 15/93 (16%)

Query: 267 VGEHPYGEHP--SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----------- 313
           +G H +      + T+FV+ +  NV    +   F+Q G I+T     +            
Sbjct: 1   MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60

Query: 314 --RGFVMISYYDIRAARNAMKALQNKPLRRRKL 344
             +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 = 1e-07
 Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 13/94 (13%)

Query: 352 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQH--------KHNHK- 402
             +     ++  T+ V  L  +V+ E +   F   G I+  + T          +   K 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 403 ----FIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
                + F D  +A+ A+   +  + +G  IK+ 
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96

>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 = 51.2 bits (123), Expect = 4e-08
 Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 6/108 (5%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKF 403
           S       +  +N   + V +L   ++TE++   F  +G I +        T     + F
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKL-EASRPGGARRFMVQSEQEQ 450
           + 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 = 51.2 bits (123), Expect = 5e-08
 Identities = 20/108 (18%), Positives = 43/108 (39%), Gaps = 7/108 (6%)

Query: 263 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YTACKHRGF 316
             S              +FV +++  +   ++KA F  FG I          T  K +G+
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATG-KSKGY 59

Query: 317 VMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGT 364
             +S+++   A NA++ +  + L  R++  +++  K    +      T
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT 107

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.8 bits (122), Expect = 4e-08
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 1/74 (1%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           G    R++FV      V+ ++L   F  FG + ++        F ++   D+ A    + 
Sbjct: 4   GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL- 62

Query: 333 ALQNKPLRRRKLDI 346
           +     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 = 7e-06
 Identities = 12/73 (16%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           ++ V      V + +L + F  +G +  +   + K     +E  D+ A E  L   ++  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHS 68

Query: 424 VAGKQIKLEASRP 436
           + G ++++     
Sbjct: 69  LGGHRLRVRPREQ 81

>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 = 5e-08
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAE 413
           +A+  ++ V N+D   + EEL   F   G +  +     + + H     +IEF D  +  
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 414 TALRTLNRSDVAGKQIKLEASRP 436
           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: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAAR 328
           E  +R+++V N++      EL+A F   G +  +   C       +GF  I + D  + R
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 329 NAMKALQNKPLRRRKLDIHYSIPK 352
            ++ 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 = 5e-08
 Identities = 19/99 (19%), Positives = 41/99 (41%), Gaps = 14/99 (14%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----------RGFVMISYY 322
           G   S  +F+ N++  +++  L   F  FG I                   +G+  I++ 
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVI----LQTPKIMRDPDTGNSKGYAFINFA 56

Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
              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: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI------RDTQHKHNHKFIEFYDIRAAET 414
               + + NLD  +  + L+  F  +G I +        DT +   + FI F    A++ 
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 51.2 bits (123), Expect = 6e-08
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 4/94 (4%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT---IYTAC-KHRGFVMISYYDIRAAR 328
           G      L V N++  V D++++ LF +FG ++     Y    +  G   + +     A 
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 90

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
            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 = 8e-05
 Identities = 14/82 (17%), Positives = 32/82 (39%), Gaps = 4/82 (4%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD-TQHKHNHKFIEFYDIRAAETALRTL 419
            L+V NLD  VS  ++ ++F  +G +++     D +        + F     A  A++  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96

Query: 420 NRSDVAGKQIKLEASRPGGARR 441
               + 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 = 50.3 bits (121), Expect = 7e-08
 Identities = 19/94 (20%), Positives = 29/94 (30%), Gaps = 11/94 (11%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI--REIRDTQHKHNHK-----FIEFY 407
              +      L + NL+ + S  EL              + D             +++F 
Sbjct: 10  EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD---VRTGTNRKFGYVDFE 66

Query: 408 DIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
                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 = 8e-06
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGD-----IRTIYTACKHRGFVMISYYDIRAARNA 330
               LF+ N+N N   +ELK    +        +  + T   +R F  + +        A
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTG-TNRKFGYVDFESAEDLEKA 74

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           +  L    +   ++ +     +D 
Sbjct: 75  L-ELTGLKVFGNEIKLEKPKGRDG 97

>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 = 50.5 bits (121), Expect = 7e-08
 Identities = 19/100 (19%), Positives = 39/100 (39%), Gaps = 14/100 (14%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-------------RGFVMISYYD 323
           +  ++V+ +N +V   +L   F+Q G ++      +              +G   +SY D
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

Query: 324 IRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
              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 = 49.7 bits (119), Expect = 2e-07
 Identities = 18/101 (17%), Positives = 39/101 (38%), Gaps = 13/101 (12%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK------ 402
           S       ++D++   + V  L+ SV+ ++L   F   G ++  + T     H       
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 403 -------FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
                   + + D   A+ A+   +  D  G ++K+  +R 
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102

>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 = 9e-08
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 3/78 (3%)

Query: 367 VFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           V NLD  +  E L + F  +G I     + +        F+ F     A  A+  +N   
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI 79

Query: 424 VAGKQIKLEASRPGGARR 441
           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: 280 LFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
           L+V+N++  ++D  L+  F  FG I   + +    + +GF  + +     A  A+  +  
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 337 KPLRRRKLDIHYSIPKDNPSEKDAN 361
           + +  + L +  +  K+      ++
Sbjct: 78  RIVATKPLYVALAQRKEERQSGPSS 102

>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 = 9e-08
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFG---DIRTIY---TACKHRGFVMISYYDIRAARN 329
               +FV +++  +  + + A F  FG   D R +    T  K +G+  +S+++   A N
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATG-KSKGYGFVSFFNKWDAEN 63

Query: 330 AMKALQNKPLRRRKLDIHYSIPK 352
           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: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAE 413
             +   + V +L   ++T  +   F  +G I + R      T     + F+ F++   AE
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 414 TALRTLNRSDVAGKQIKLEASRP 436
            A++ +    + G+QI+   +  
Sbjct: 63  NAIQQMGGQWLGGRQIRTNWATR 85

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 49.4 bits (119), Expect = 9e-08
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 9/79 (11%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YT-ACKHRGFVMISYYDIR 325
           G   S  L++R +     D +L  L + +G I +        T  CK  GFV   +    
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFV--DFDSPS 58

Query: 326 AARNAMKALQNKPLRRRKL 344
           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: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNR 421
           +  L    + ++L ++   YG+I   +    K  +K     F++F    AA+ A+  L  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 422 SDVAGKQIKLEASRPG 437
           S V  +  K      G
Sbjct: 70  SGVQAQMAKQSGPSSG 85

>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 = 52.8 bits (126), Expect = 1e-07
 Identities = 26/172 (15%), Positives = 53/172 (30%), Gaps = 18/172 (10%)

Query: 199 DEDDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGMELEGDDRLFAVQKNSDFVGGVSN 258
           D  + F+   +  GH+     +D  +D    S+  G   E  D         D +     
Sbjct: 1   DVGEEFNQEAEYGGHDQ----IDLYDDVISPSANNGDAPEDRD-------YMDTLPPTVG 49

Query: 259 QGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYTAC----- 311
             V  G+              L++ N+     D +L       G  DI  I         
Sbjct: 50  DDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG 109

Query: 312 KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
           + +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 = 45.1 bits (106), Expect = 3e-05
 Identities = 15/94 (15%), Positives = 38/94 (40%), Gaps = 7/94 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETAL 416
            L + NL    + E+L +     G  +I EI+  +++ N +      +      +++  +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 417 RTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
             L + ++ G+   +         +F +QS +  
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTT 163

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 49.5 bits (119), Expect = 1e-07
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARN 329
           G   +  +FVRN+  +     LK  F + G +          K +G  ++ +     A  
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 63

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPS 356
           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 = 48.7 bits (117), Expect = 2e-07
 Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 3/89 (3%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAA 412
           S   +    + V NL    + + L   F   G +       +         ++F     A
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61

Query: 413 ETALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 1e-07
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRA 411
            +E  +    L V N+       +L Q+FG +G+I +   I + +      F+ F +   
Sbjct: 22  NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 81

Query: 412 AETALRTLNRSDVAGKQIKLEASRP 436
           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 = 1e-07
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI---RTIYTACKHRGFVMISYYDIRAARN 329
            +   + L V NI     D +L+ +F QFG I     I+     +GF  +++ +   A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84

Query: 330 AMKALQNKPLRRRKLDIHYSIPK 352
           A + L    +  RK++++ +  +
Sbjct: 85  AREKLHGTVVEGRKIEVNNATAR 107

>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 = 1e-07
 Identities = 15/104 (14%), Positives = 38/104 (36%), Gaps = 6/104 (5%)

Query: 263 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIY---TACKHRGFV 317
             S        + P  T F+ N+  +V +  +K  F       +R         + +GF 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
              + 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 = 44.9 bits (107), Expect = 5e-06
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK---FIEFYDIRAAETALRT 418
           T  + NL   V+ E + + F       +R  R+  +    K   + EF D+ +  +AL +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           LN   +  K+I+++ +     + 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>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: 263 AGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFV 317
             S       G+     + V+N+   V   E+   F  +  I        +      G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYS 349
           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 = 1e-05
 Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 5/92 (5%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 405
                S        + V N+  +VS +E+   F  Y  I      ++           + 
Sbjct: 4   GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 406 FYDIRAAETALRTLNRSDVAGKQIKLEASRPG 437
           F     A  A+  LN   +  +++KL     G
Sbjct: 64  FESRDEATAAVIDLNDRPIGSRKVKLSGPSSG 95

>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 = 49.2 bits (118), Expect = 2e-07
 Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 6/92 (6%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIY---TACKHRGFVMISYY 322
                 + P  T F+ N+  +V +  +K  F       +R         + +GF    + 
Sbjct: 10  HRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFE 69

Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
           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 = 4e-05
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK---FIEFYDIRAAETALRT 418
           T  + NL   V+ E + + F       +R  R+  +    K   + EF D+ +  +AL +
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 419 LNRSDVAGKQIKLEASRP 436
           LN   +  ++I+++ +  
Sbjct: 80  LNEESLGNRRIRVDVADQ 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 = 48.1 bits (115), Expect = 4e-07
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 11/96 (11%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRD--TQHKHNHKFIEFYD 408
            S       +L + +L+  +    + + F   GE    ++ IR+  T     + F+EF D
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 409 IRAAETALRTLNRSDVAG----KQIKL-EASRPGGA 439
           +  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 = 43.8 bits (104), Expect = 1e-05
 Identities = 12/71 (16%), Positives = 30/71 (42%), Gaps = 8/71 (11%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGD-------IRTIYTACKHRGFVMISYYDIRAAR 328
            + +L++ ++   ++++ +   F   G+       IR   T     G+  + + D+  A 
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTG-IPAGYCFVEFADLATAE 66

Query: 329 NAMKALQNKPL 339
             +  +  KPL
Sbjct: 67  KCLHKINGKPL 77

>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 = 4e-07
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           G   S  +FV     ++ + EL+  F Q+GD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 333 ALQNKPLRRRKLDIHYSIPKDNPS 356
             ++  ++   + I  + PK N +
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSN 82

>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 = 4e-07
 Identities = 16/94 (17%), Positives = 32/94 (34%), Gaps = 5/94 (5%)

Query: 264 GSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVM 318
            S       G+     + V+N+   V   E+   F  +  I        +      G  M
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 319 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 352
           +++     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 = 1e-05
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 5/91 (5%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIE 405
                S        + V N+  +VS +E+   F  Y  I      ++           + 
Sbjct: 4   GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

Query: 406 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 48.1 bits (115), Expect = 5e-07
 Identities = 15/95 (15%), Positives = 30/95 (31%), Gaps = 12/95 (12%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDIRAA 327
              T+FV N++  V   +LK +F   G +                 RG   +++     A
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVV----VRADILEDKDGKSRGIGTVTFEQSIEA 69

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
             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 = 43.8 bits (104), Expect = 2e-05
 Identities = 17/111 (15%), Positives = 39/111 (35%), Gaps = 9/111 (8%)

Query: 351 PKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHK---F 403
              + + +    G+ + V NLD  V  ++L ++F + G +     + D   K   +    
Sbjct: 3   SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS--RGIGT 60

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLN 454
           + 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 = 48.0 bits (115), Expect = 5e-07
 Identities = 16/116 (13%), Positives = 34/116 (29%), Gaps = 19/116 (16%)

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIY 386
             +    L+   ++ +              +   N   L + NL  S+  +EL  +   +
Sbjct: 1   GSSGSSGLKASGVQAQM--------AKQQEQDPTN---LYISNLPLSMDEQELENMLKPF 49

Query: 387 GEI---REIRDTQHKHNHK---FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 46.9 bits (112), Expect = 1e-06
 Identities = 11/90 (12%), Positives = 29/90 (32%), Gaps = 15/90 (16%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDIRAARNAM 331
           L++ N+  ++++ EL+ + + FG +     + +         RG               +
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQV----ISTRILRDSSGTSRGVGFARMESTEKCEAVI 83

Query: 332 KALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
                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 = 47.9 bits (114), Expect = 6e-07
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNA 330
           P        + V  +  +    +LK    + GD+   Y      G  ++ +        A
Sbjct: 10  PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKEDMTYA 67

Query: 331 MKALQNKPLRRRKLDIHY 348
           ++ 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 = 41.7 bits (98), Expect = 9e-05
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            +VV  L  S S ++L       G++       ++     +EF        A+R L+ + 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKEDMTYAVRKLDNTK 75

Query: 424 VAGKQIKLEASRP 436
               + +    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 = 47.8 bits (114), Expect = 6e-07
 Identities = 10/77 (12%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARN 329
           +  +R+++++   ++    ++K   E  G +  I          +G + + +  I +A+ 
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 330 AMKALQNKPLRRRKLDI 346
            ++    +  +   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 = 46.3 bits (110), Expect = 2e-06
 Identities = 11/98 (11%), Positives = 34/98 (34%), Gaps = 8/98 (8%)

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHNHK---FIEFYDIRAA 412
           + D    ++ +    +  + +++ +     G++  I+         K   F+ F  I +A
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65

Query: 413 ETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
           +  +            + +       A++     E++Q
Sbjct: 66  KKFV-ETPGQKYKETDLLILFKDDYFAKK---NEERKQ 99

>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 = 51.8 bits (123), Expect = 7e-07
 Identities = 22/132 (16%), Positives = 52/132 (39%), Gaps = 7/132 (5%)

Query: 325 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFG 384
              +   K  + +     +L +    P ++P+ +     TL V  ++   +  +L + F 
Sbjct: 67  MERKRREKIERRQQEVETELKMW--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124

Query: 385 IYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA 439
           +YG I+ I     K + K     FIE+   R   +A +  +   + G+++ ++  R    
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184

Query: 440 RRFMVQSEQEQD 451
           + +  +      
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 = 47.5 bits (112), Expect = 1e-05
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
             +TLFV  +N +  +S+L+  FE +G I+ I+        K RG+  I Y   R   +A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEK 358
            K    K +  R++ +     +     +
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWR 188

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 49.5 bits (118), Expect = 7e-07
 Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT---IYTAC-KHRGFVMISYYDIRA 326
             G      L V N++  V D++++ LF +FG ++     Y    +  G   + +     
Sbjct: 82  GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 141

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
           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 = 42.1 bits (99), Expect = 2e-04
 Identities = 18/113 (15%), Positives = 41/113 (36%), Gaps = 9/113 (7%)

Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIREIR 393
           + KPL  +    H          +    G  L+V NLD  VS  ++ ++F  +G +++  
Sbjct: 62  RPKPLPDKWQ--HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA- 118

Query: 394 DTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
              +  + +      + 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 = 48.8 bits (116), Expect = 7e-07
 Identities = 11/96 (11%), Positives = 37/96 (38%), Gaps = 7/96 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETAL 416
            + V +     + ++L Q+    G  ++ E++  +++ N +      +      +    L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 417 RTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQDD 452
             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 = 48.0 bits (114), Expect = 2e-06
 Identities = 12/114 (10%), Positives = 39/114 (34%), Gaps = 8/114 (7%)

Query: 257 SNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG-----DIRTIY--T 309
                   +++  +    +    ++V + +    D +L  +    G     +++      
Sbjct: 35  PKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94

Query: 310 ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK-DNPSEKDANQ 362
             + +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 = 50.2 bits (119), Expect = 8e-07
 Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 12/98 (12%)

Query: 268 GEHPYGEHPSRTLFVRNINSNV---------EDSELKALFEQFGDIRTI-YTACKHRGFV 317
           G        ++TL+V  I+  +          +S ++ +F + GDI  I Y   K+ GFV
Sbjct: 125 GGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFV 184

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNP 355
              +     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 = 49.8 bits (118), Expect = 1e-06
 Identities = 23/123 (18%), Positives = 42/123 (34%), Gaps = 11/123 (8%)

Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVST---------E 377
            + A++        R K   +        S +  N+ TL V  +D ++++          
Sbjct: 100 GKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNK-TLYVGGIDGALNSKHLKPAQIES 158

Query: 378 ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG 437
            +  +F   G+I  IR      N  F++F     AE A   ++   +     K    R  
Sbjct: 159 RIRFVFSRLGDIDRIR-YVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217

Query: 438 GAR 440
           G  
Sbjct: 218 GTG 220

>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 = 47.2 bits (112), Expect = 1e-06
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 12/83 (14%)

Query: 362 QGTLV-VFNLDSSVSTEEL---HQIFGIYGEIREI---RDTQHKHNHK-----FIEFYDI 409
           Q  LV V  L   ++  E+    + FG +G+I ++     T +  +       ++ +   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 410 RAAETALRTLNRSDVAGKQIKLE 432
             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 = 1e-04
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 11/85 (12%)

Query: 279 TLFVRNINSNVEDSEL---KALFEQFGDIRTIY--------TACKHRGFVMISYYDIRAA 327
            +FV  ++  + D E+      F +FG I  +          +        ++Y     A
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPK 352
             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: 276 PSRTLFVRNI-NSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
             R + + +         +L  L E FG I              I       A+ A+   
Sbjct: 14  TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYY 72

Query: 335 QNKP--LRRRKLDIHYSIPK 352
              P  +  + + +H S   
Sbjct: 73  TTTPALVFGKPVRVHLSQKY 92

>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 = 51.0 bits (121), Expect = 2e-06
 Identities = 70/464 (15%), Positives = 144/464 (31%), Gaps = 127/464 (27%)

Query: 3   FEIMDHRSGSAPTHFSEEIRFPAERQIGF-WKPNTMSDQQGSDGTVPMLGGKFVAS-SPM 60
           F  +  +       F EE+         F   P     +Q S  T       ++     +
Sbjct: 68  FWTLLSKQEEMVQKFVEEV---LRINYKFLMSPIKTEQRQPSMMTR-----MYIEQRDRL 119

Query: 61  EN----FSPVGIPSVD-WLELQQSTLARDKMKRLGIVGEEGAANLSENSWNSVNHHPKSW 115
            N    F+   +  +  +L+L+Q+ L     K + I G  G+               K+W
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG--------------KTW 165

Query: 116 SNLAVQPGINSLSGNRSGINGIQSESSLFSSSLSDIFTRKMKLSGNEILSRQ---PLNAV 172
             +A+     S          I      F  +L +  + +  L   + L  Q      + 
Sbjct: 166 --VALD-VCLSYKVQCKMDFKI------FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR 216

Query: 173 ASHHQ-PEEPFESLKEIEAQTIGNLL---PDEDDLFSGVTDDMGHNFQANTVDDLEDFDL 228
           + H    +    S++      +  LL   P E+ L   V  +         V + + ++ 
Sbjct: 217 SDHSSNIKLRIHSIQA----ELRRLLKSKPYENCLL--VLLN---------VQNAKAWNA 261

Query: 229 FSSGGGMELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGEHPYGEHP--SRTLFVRNIN 286
           F+    + L    +     + +DF+   +   +S    +  H     P   ++L ++ ++
Sbjct: 262 FNLSCKILLTTRFK-----QVTDFLSAATTTHIS----LDHHSMTLTPDEVKSLLLKYLD 312

Query: 287 SNVEDSELKALFEQFGDIRTIYTACKHRGFV--MISYYDIRAARNAMKALQN-KPLRRRK 343
              +D     L  +                   +I+     + R+ +    N K +   K
Sbjct: 313 CRPQD-----LPRE---------VLTTNPRRLSIIA----ESIRDGLATWDNWKHVNCDK 354

Query: 344 LD--IHYSIPKDNPSEKDANQGTLVVFNLDSSVST-------------------EELHQ- 381
           L   I  S+    P+E       L VF   + + T                    +LH+ 
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

Query: 382 -------------IFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 412
                        I  IY E++   + ++  +   ++ Y+I   
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 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 = 44.1 bits (103), Expect = 2e-04
 Identities = 91/678 (13%), Positives = 192/678 (28%), Gaps = 205/678 (30%)

Query: 175 HHQPEEPFESLKEIEAQTIGNLLPDEDDLFSGVTDDMGHNFQANTVDDL-------EDFD 227
           HH     FE   E +     ++L   +D F  V +     F    V D+       E+ D
Sbjct: 2   HHHHHMDFE-TGEHQ-YQYKDILSVFEDAF--VDN-----FDCKDVQDMPKSILSKEEID 52

Query: 228 -LFSSGGGMELEGDDRLFAV----QKN--SDFVGGVSNQG----VSAGSVVGEHPYGEHP 276
            +  S     + G  RLF      Q+     FV  V        +S        P     
Sbjct: 53  HIIMSKD--AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMM-- 108

Query: 277 SRTLFVRNINSNVEDSELKALF-----EQFGDIRTIYTACKHRGFVMISYYDIRAARNAM 331
              +++   +    D+++ A +     + +  +R      +    V+I         + +
Sbjct: 109 -TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI---------DGV 158

Query: 332 K----------ALQNKPLRRRKLD-IHY-SIPKDNPSEKDANQGTLVVFNLDSSVSTEEL 379
                         +  ++ +    I + ++   N  E        +++ +D +  T   
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN-WTSRS 217

Query: 380 HQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA 439
                I   I  I+        +       +  E  L  L   +V   +    A      
Sbjct: 218 DHSSNIKLRIHSIQA-------ELRRLLKSKPYENCLLVL--LNVQNAKA-WNA------ 261

Query: 440 RRFMVQSEQEQDDLNLCQIPFDDLSSGQMVSSGVITSTCMDNGSIQVLHSATRS------ 493
             F         +L+ C+I              ++T+          L +AT +      
Sbjct: 262 --F---------NLS-CKI--------------LLTTR--FKQVTDFLSAATTTHISLDH 293

Query: 494 PAIALTESHQTSSV--------PNGLPSLARVGS------IG----------KQFGHYEP 529
            ++ LT   +  S+        P  LP      +      I             + H   
Sbjct: 294 HSMTLTPD-EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352

Query: 530 N-------LSLDEMKFGNQHPSFHPHSLPEYHDSLANGLPYNSPSTIADIASSVGTKIKD 582
           +        SL+ ++         P    +  D L+   P +     A I + + + I  
Sbjct: 353 DKLTTIIESSLNVLE---------PAEYRKMFDRLSV-FPPS-----AHIPTILLSLIWF 397

Query: 583 GLDSRHIRGVSSNGHLMEPTGGVFGSPRNGSYSLHG-----NPYVWNNSNSHQQ---HPS 634
            +    +  V    + +     V   P+  + S+          + N    H+    H +
Sbjct: 398 DVIKSDVMVVV---NKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454

Query: 635 SPMVWPN---SPSFLNGLHANRVA-HMPG---------FPRVPPLMLN---------ATS 672
            P  + +    P +L+    + +  H+           F     + L+           S
Sbjct: 455 IPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM---VFLDFRFLEQKIRHDS 511

Query: 673 PAHHHIGSAPAVNPSLWDRQH--AYAGESPETSNFHLGSLGSGGFLGRSPSH-----HVD 725
            A +  GS   +  +L   +    Y  ++       + ++    FL +   +     + D
Sbjct: 512 TAWNASGS---ILNTLQQLKFYKPYICDNDPKYERLVNAILD--FLPKIEENLICSKYTD 566

Query: 726 IASQNILSHVGGNCMDMT 743
           +  +  L        +  
Sbjct: 567 LL-RIALMAEDEAIFEEA 583

>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 = 45.6 bits (108), Expect = 3e-06
 Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 5/82 (6%)

Query: 270 HPYGEHPSRT---LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRA 326
              G    R+   + V  +  +    +LK    + GD+   Y      G  ++ +     
Sbjct: 5   SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDV--CYADVYRDGTGVVEFVRKED 62

Query: 327 ARNAMKALQNKPLRRRKLDIHY 348
              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 = 2e-05
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            +VV  L  S S ++L       G++       ++     +EF        A+R L+ + 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD--VYRDGTGVVEFVRKEDMTYAVRKLDNTK 74

Query: 424 VAGKQIKLEASRP 436
               + +    R 
Sbjct: 75  FRSHEGETAYIRV 87

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 45.2 bits (108), Expect = 3e-06
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMK 332
           R ++V N+  +    ++K LF QFG +  +         K +GF  +   +  +   A+ 
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60

Query: 333 ALQNKPLRRRKLDIHYSIPKDNPSEKDAN 361
            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 = 42.9 bits (102), Expect = 2e-05
 Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            + V NL  S ++E++ ++F  +G++  +     R+T+      F+E  +  +   A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           L+ +D  G+ I++  + P  +  
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLE 84

>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 = 5e-06
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--------HRGFVMISYYDI 324
           G      L V N++  V D++++ LF +FG +                  G   + +   
Sbjct: 25  GVETGGKLLVSNLDFGVSDADIQELFAEFGTL----KKAAVHYDRSGRSLGTADVHFERK 80

Query: 325 RAARNAMKALQNKPLRRRKLDIHY 348
             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 = 4e-05
 Identities = 18/102 (17%), Positives = 39/102 (38%), Gaps = 5/102 (4%)

Query: 336 NKPLRRRKLDIHYSIPKDNPSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIRE--- 391
           ++P +      H               G  L+V NLD  VS  ++ ++F  +G +++   
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 392 IRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
             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 = 6e-06
 Identities = 19/87 (21%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 327
           G H +  H S+ +FV     ++   EL+  F Q+G++  ++     R F  +++ D + A
Sbjct: 3   GSHHHHHHGSK-VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDN 354
           ++     ++  ++   + 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: 280 LFVRNINSNVEDSELKALFEQFG-----DIRTIY---TACKHRGFVMISYYDIRAARNAM 331
           L++ N+     D +L       G     +I+         + +GF ++      +++  M
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG-QSKGFALVGVGSEASSKKLM 62

Query: 332 KALQNKPLRRRKLDIHYSIPKD 353
             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 = 1e-05
 Identities = 12/81 (14%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 369 NLDSSVSTEELHQIFGIYG--EIREIRDTQHKHNHK-----FIEFYDIRAAETALRTLNR 421
           NL    + E+L +     G  +I EI+  +++ N +      +      +++  +  L +
Sbjct: 8   NLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK 67

Query: 422 SDVAGKQIKLEASRPGGARRF 442
            ++ 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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKA 333
           +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 = 43.9 bits (104), Expect = 1e-05
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 9/75 (12%)

Query: 274 EHPSRTLFVRNINSNVEDSE------LKALFEQFGDIRTIYTAC---KHRGFVMISYYDI 324
           +     + V N+     D        +  +F +FG I   +      K +G++ + Y   
Sbjct: 12  DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASP 71

Query: 325 RAARNAMKALQNKPL 339
             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 = 2e-05
 Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 352 KDNPSEKDANQGTLVVFNL------DSSVSTEELHQIFGIYGEIREI---RDTQHKHNHK 402
           KD P E D     +VV N+              +H+IF  +G+I       +      + 
Sbjct: 5   KDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYI 64

Query: 403 FIEFYDIRAAETALRTLNRSDVAGK 427
           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: 253 VGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC- 311
           +G   +    +  +V    +       +F+  ++       L+  F QFG++      C 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEV----KECL 56

Query: 312 --------KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD 353
                   + 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 = 43.3 bits (103), Expect = 2e-05
 Identities = 21/94 (22%), Positives = 44/94 (46%), Gaps = 6/94 (6%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYY 322
           G        S  +FV  I  N  ++EL+  F++FG +  +         + RGF  I++ 
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
           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 = 3e-05
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 9/70 (12%)

Query: 279 TLFVRNINSNVED------SELKALFEQFGDIRTIYTAC---KHRGFVMISYYDIRAARN 329
            + V N+     D      + +  +F +FG I   +      K +G++ + Y     A +
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

Query: 330 AMKALQNKPL 339
           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 = 42.8 bits (101), Expect = 3e-05
 Identities = 12/107 (11%), Positives = 35/107 (32%), Gaps = 6/107 (5%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRDTQHKHN-HKF 403
           S       + ++ +    + N+  S++  ++ Q           +  + D   +      
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRFMVQSEQEQ 450
           ++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 = 42.8 bits (101), Expect = 4e-05
 Identities = 12/86 (13%), Positives = 29/86 (33%), Gaps = 6/86 (6%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFG----DIRTIYTAC-KHRGFVMISYYDIRAA 327
                    + NI  ++   ++    E        +  +     +  G  ++ + +   A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKD 353
           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 = 5e-05
 Identities = 12/68 (17%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-------TACKHRGFVMISYYDIR 325
           G   SR +FV  +  ++++ E+ A F +FG +   +       +    +G+  + + +  
Sbjct: 4   GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 326 AARNAMKA 333
           + +  + 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 = 6e-05
 Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 5/72 (6%)

Query: 363 GTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALR 417
           G  V+ +    V  + L  +F   G++  +       T       F+E   +  A+  ++
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 418 TLNRSDVAGKQI 429
           + +   +  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 = 8e-05
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 281 FVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKALQ 335
            + +    V    L +LF + G +  +         K +GF+ +    +  A+  +K+  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 336 NKPL 339
            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 = 7e-05
 Identities = 19/93 (20%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIR 410
           S   AN G + +  L    S EE+ Q F     +            +     F++F    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68

Query: 411 AAETALRTLNRSDVAGKQIKLEASRPGGARRFM 443
            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 = 7e-04
 Identities = 10/83 (12%), Positives = 24/83 (28%), Gaps = 6/83 (7%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFG----DIRTIY-TACKHRGFVMISYYDIRAARNA 330
               + +R +       E+   F         +        +  G   + +     A  A
Sbjct: 14  NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA 73

Query: 331 MKALQNKPLRRRKLDIHYSIPKD 353
           +K    + +  R ++I  S   +
Sbjct: 74  LK-KHKERIGHRYIEIFKSSRAE 95

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFG--DIRTIY---TACKHRGFVMISYYDIRAARNA 330
           P  T +V N+  N    ++ A+F+      +R +    T  K +GF  + + ++ + + A
Sbjct: 14  PPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTD-KFKGFCYVEFDEVDSLKEA 72

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSE 357
           +       L  R L +  +  +     
Sbjct: 73  L-TYDGALLGDRSLRVDIAEGRKQDKS 98

>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 = 1e-04
 Identities = 16/98 (16%), Positives = 38/98 (38%), Gaps = 14/98 (14%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVM 318
                 +   R LF+  ++    +  L+  +EQ+G +    T C         + RGF  
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKL----TDCVVMRDPASKRSRGFGF 73

Query: 319 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
           +++  +     AM A +   +  R ++   ++ ++   
Sbjct: 74  VTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESG 110

>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: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVM 318
           G +  G      LFV  ++ +     L++ F Q+G++      C         + RGF  
Sbjct: 7   GMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEV----VDCVIMKDKTTNQSRGFGF 62

Query: 319 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD 353
           + + D       + + +   L  R +D     P+ 
Sbjct: 63  VKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRG 96

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 39.8 bits (94), Expect = 2e-04
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 13/63 (20%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISYYDIRAARNA 330
           +FV  ++ N    ++K  FEQFG +                +HRGF  +++         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKV----DDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57

Query: 331 MKA 333
            + 
Sbjct: 58  CEI 60

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 6/95 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALF-EQFGDIRT----IYTACKHRGFVMISYYDIRAARNA 330
           P  +LFV ++  +V+D  L   F + +   R     +      +G+  + + D    + A
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRA 67

Query: 331 MKALQNKP-LRRRKLDIHYSIPKDNPSEKDANQGT 364
           +   Q    L  + + +  +IPK +  +   +  +
Sbjct: 68  LTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPS 102

>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 = 40.1 bits (94), Expect = 2e-04
 Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 11/80 (13%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA----------CKHRGFVMISYYDIRA 326
           +R L+V NI   + +  +   F     +  +  A           + + F  + +  +  
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65

Query: 327 ARNAMKALQNKPLRRRKLDI 346
              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 = 4e-04
 Identities = 12/78 (15%), Positives = 25/78 (32%), Gaps = 13/78 (16%)

Query: 369 NLDSSVSTEELHQIFGIYGEIREI----------RDTQHKHNHKFIEFYDIRAAETALRT 418
           N+   ++ E +   F     +  +                 N  F+EF  +     A+  
Sbjct: 13  NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA- 71

Query: 419 LNRSDVAGKQIKLEASRP 436
            +     G+ +K+   RP
Sbjct: 72  FDGIIFQGQSLKI--RRP 87

>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: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE----IREIRDTQHKHN-HKF 403
            + + + S   AN G + +  L    + EE+ Q F         I    D + K     F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARRF 442
           ++F     AE AL   ++  +  + I++  S     R +
Sbjct: 89  VQFASQELAEKALG-KHKERIGHRYIEVFKSSQEEVRSY 126

>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 = 41.4 bits (97), Expect = 2e-04
 Identities = 14/121 (11%), Positives = 36/121 (29%), Gaps = 4/121 (3%)

Query: 246 VQKNSDFVGGVSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--D 303
           V + S        Q +  GS   E          + +R +     ++++   F       
Sbjct: 15  VPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR 74

Query: 304 IRTIYTA-CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
           +        +  G   + +     A  AM       ++ R +++  +      +   ++Q
Sbjct: 75  VHIEIGPDGRVTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTGASNGAYSSQ 133

Query: 363 G 363
            
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 = 40.0 bits (93), Expect = 3e-04
 Identities = 18/91 (19%), Positives = 41/91 (45%), Gaps = 6/91 (6%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQI----FGIYGEIREIRDTQHK--HNHKFIEFYDI 409
           S    N   + V N+D  +S +EL Q+    F  +G+++ +  + H        ++  ++
Sbjct: 3   SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENL 62

Query: 410 RAAETALRTLNRSDVAGKQIKLEASRPGGAR 440
           + 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 = 3e-04
 Identities = 14/92 (15%), Positives = 27/92 (29%), Gaps = 9/92 (9%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI------YTACKHRGFVMISYYDI 324
                 +  L V  +     + +LK  F  FG++  +       T    +GF  + + + 
Sbjct: 9   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTG-HSKGFGFVRFTEY 67

Query: 325 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
                 M       +  R  D      K +  
Sbjct: 68  ETQVKVMSQRHM--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 = 3e-04
 Identities = 12/85 (14%), Positives = 29/85 (34%), Gaps = 4/85 (4%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYTA-CKHRGFVMISYYDI 324
           G          T+ +R    NV +  +           IR +  A     G++ + + + 
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNE 60

Query: 325 RAARNAMKALQNKPLRRRKLDIHYS 349
              + A+K    + +  R +++   
Sbjct: 61  EEVKQALK-CNREYMGGRYIEVFRE 84

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 13/72 (18%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISY 321
              E  +  +FV  ++ +    +LK  F +FG++      C         + RGF  I +
Sbjct: 5   SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV----VDCTIKMDPNTGRSRGFGFILF 60

Query: 322 YDIRAARNAMKA 333
            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 = 39.8 bits (93), Expect = 4e-04
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 8/87 (9%)

Query: 268 GEHPYGEHPSRT------LFVRNINSNVEDSELKALFEQFGD--IRTIYTACKHRGFVMI 319
           G  P G H S+       + ++N+       +LK L  +       +        G   +
Sbjct: 13  GLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGAL 72

Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDI 346
            +        A++ L N   R   + +
Sbjct: 73  EFPSEEILVEALERLNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 39.0 bits (91), Expect = 7e-04
 Identities = 15/80 (18%), Positives = 24/80 (30%), Gaps = 3/80 (3%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKH--NHKFIEFYDIRAAETALRTLNRS 422
           + + NL    S ++L  +               +       +EF        AL  LN  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 423 DVAGKQIKL-EASRPGGARR 441
           +  G  I +     P   RR
Sbjct: 91  EFRGSVITVERDDNPPPIRR 110

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 38.6 bits (91), Expect = 4e-04
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 13/63 (20%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISYYDIRAARNA 330
           +F+  ++       L+  F QFG++      C         + RGF  +++ D       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV----KECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 331 MKA 333
           +  
Sbjct: 59  LAQ 61

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 39.0 bits (91), Expect = 8e-04
 Identities = 9/90 (10%), Positives = 28/90 (31%), Gaps = 6/90 (6%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK----FIEF 406
               P   + +   + V  +  S    ++   F     +  +   +           ++F
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKF 63

Query: 407 YDIRAAETALRTLNRSDVAGKQIKLEASRP 436
              +    AL+  NR  +  + +++  +  
Sbjct: 64  LSPQDTFEALK-RNRMLMIQRYVEVSPATE 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	861
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.79
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.68
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.66
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.66
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.64
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.64
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.64
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.63
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.62
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.62
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.62
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.61
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.61
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.6
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.6
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.6
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.6
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.59
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.59
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.59
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.59
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.59
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.59
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.59
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.59
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.58
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.58
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.58
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.58
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.58
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.58
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.58
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.58
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.58
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.58
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.58
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.58
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.58
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.58
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.58
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.57
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.57
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.57
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.57
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.57
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.57
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.57
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.56
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.56
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.56
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.56
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.56
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.56
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.56
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.56
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.56
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.56
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.56
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.56
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.55
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.55
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.55
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.55
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.55
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.55
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.55
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.55
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.55
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.55
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.55
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.55
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.55
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.55
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.54
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.54
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.54
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.54
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.54
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.54
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.54
2div_A	99	TRNA selenocysteine associated protein; structural	99.54
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.54
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.54
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.54
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.53
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.53
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.53
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.53
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.53
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.53
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.53
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.53
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.53
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.53
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.53
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.53
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.53
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.53
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.53
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.53
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.53
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.53
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.53
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.53
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.53
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.53
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.53
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.53
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.53
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.53
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.53
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.53
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.53
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.53
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.52
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.52
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.52
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.52
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.52
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.52
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.52
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.52
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.52
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.52
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.52
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.52
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.52
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.52
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.52
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.52
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.52
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.52
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.52
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.52
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.52
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.51
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.51
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.51
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.51
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.51
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.51
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.51
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.51
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.51
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.51
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.51
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.51
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.51
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.51
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.51
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.51
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.51
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.51
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.5
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.5
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.5
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.5
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.5
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.5
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.5
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.5
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.5
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.5
1x5p_A	97	Negative elongation factor E; structure genomics,	99.5
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.5
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.5
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.5
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.5
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.5
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.5
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.5
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.5
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.5
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.5
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.5
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.5
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.5
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.5
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.5
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.5
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.5
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.49
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.49
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.49
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.49
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.49
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.49
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.49
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.49
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.49
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.49
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.49
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.49
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.49
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.49
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.49
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.49
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.49
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.49
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.49
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.49
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.48
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.48
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.48
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.48
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.48
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.48
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.48
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.48
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.48
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.48
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.48
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.48
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.48
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.48
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.48
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.48
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.48
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.47
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.47
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.47
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.47
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.47
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.47
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.47
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.47
2div_A	99	TRNA selenocysteine associated protein; structural	99.47
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.46
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.46
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.46
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.46
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.46
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.46
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.46
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.46
1x5p_A	97	Negative elongation factor E; structure genomics,	99.46
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.46
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.46
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.46
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.46
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.46
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.46
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.45
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.45
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.45
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.45
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.45
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.45
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.45
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.45
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.45
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.44
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.44
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.44
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.44
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.44
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.44
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.44
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.44
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.43
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.43
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.43
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.43
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.43
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.43
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.43
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.43
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.43
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.43
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.43
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.43
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.42
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.42
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.42
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.42
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.41
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.41
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.41
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.41
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.41
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.41
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.41
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.4
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.4
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.4
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.4
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.4
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.4
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.39
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.39
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.39
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.39
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.38
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.38
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.38
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.38
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.37
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.37
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.37
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.37
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.37
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.37
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.36
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.35
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.35
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.35
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.35
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.35
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.34
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.34
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.34
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.33
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.33
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.33
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.33
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.32
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.32
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.31
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.31
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.31
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.3
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.29
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.29
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.28
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.27
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.25
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.25
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.23
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.22
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.21
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.19
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.17
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.13
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.13
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.1
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.1
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.08
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.02
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.0
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.93
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.92
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.9
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.88
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.67
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.64
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.53
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.44
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.37
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.33
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.25
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.12
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.88
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.42
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.38
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.11
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.76
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.7
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.48
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.38
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.23
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	94.67
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	94.59
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	94.17
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	93.7
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.25
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.79
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.65
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	91.92
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	91.33
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	89.72
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	88.49

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=1.6e-30  Score=265.37  Aligned_cols=167  Identities=19%  Similarity=0.340  Sum_probs=147.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||+++||++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++..+.|+.|++.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            3457899999999999999999999999999999985     57899999999999999999999999999999999999


Q ss_pred             ecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe---CCCCccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          348 YSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD---TQHKHNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       348 ~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri---tgksKGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      ++.....  .......+|||+|||..+++++|+++|++||.|++|++   .+.++|||||+|.+.++|++|++.|||..|
T Consensus        91 ~~~~~~~--~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~  168 (213)
T 4f02_A           91 WSQRDPS--LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLL  168 (213)
T ss_dssp             ECCCCTH--HHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             ccccccc--ccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            9875433  22334678999999999999999999999999999886   344689999999999999999999999999


Q ss_pred             CCcEEEEEeccCCchhh
Q 002974          425 AGKQIKLEASRPGGARR  441 (861)
Q Consensus       425 ~Gr~IkVe~Akpk~~rr  441 (861)
                      .|++|+|.+++++..+.
T Consensus       169 ~g~~i~V~~a~~~~~~~  185 (213)
T 4f02_A          169 NDRKVFVGRFKSRKERE  185 (213)
T ss_dssp             TTEECEEEECCCHHHHH
T ss_pred             CCEEEEEEEcCCCcccc
Confidence            99999999999876443

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=2.1e-29  Score=242.32  Aligned_cols=157  Identities=20%  Similarity=0.342  Sum_probs=143.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      |+|||+|||.++++++|+++|++||.|..|++    .++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.++.
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    46689999999999999999999999999999999999997765


Q ss_pred             CCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcE
Q 002974          354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  428 (861)
Q Consensus       354 ~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~  428 (861)
                      ..  ......+|||+|||..+++++|+++|++||.|..+++     ++.++|||||+|.+.++|.+|++.|||..+.|++
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            42  3445779999999999999999999999999999876     3566899999999999999999999999999999


Q ss_pred             EEEEeccC
Q 002974          429 IKLEASRP  436 (861)
Q Consensus       429 IkVe~Akp  436 (861)
                      |+|.|+++
T Consensus       159 i~v~~a~~  166 (166)
T 3md3_A          159 LRINWAAK  166 (166)
T ss_dssp             CEEEESCC
T ss_pred             EEEEecCC
Confidence            99999874

>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=7e-29  Score=261.97  Aligned_cols=195  Identities=16%  Similarity=0.270  Sum_probs=171.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      .++++|||+|||.++++++|+++|++|| |..|++ ++++|||||+|.+.++|++|++.|+|..+.|+.|.|.++.    
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            4679999999999999999999999999 999998 8899999999999999999999999999999999999864    


Q ss_pred             CCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       355 ~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                            ..++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++.|+|..+.|++|
T Consensus        94 ------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A           94 ------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             ------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             ------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence                  2468999999999999999999999999999875     45568999999999999999999999999999999


Q ss_pred             EEEeccCCchhhhchhhhhhhccccCC-CCCCCCC-Ccccc----CCcccEEEEe---CCCCCccee
Q 002974          430 KLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDL-SSGQM----VSSGVITSTC---MDNGSIQVL  487 (861)
Q Consensus       430 kVe~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~-tee~L----s~fG~I~Sv~---~enG~srGF  487 (861)
                      +|.++.++....      .......++ +|||.++ ++++|    ..||.|.+++   ..+|.++||
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            999998764221      111222344 9999996 87888    8999998887   668888887

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.96  E-value=8.9e-29  Score=239.30  Aligned_cols=155  Identities=24%  Similarity=0.428  Sum_probs=142.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ++++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|.|.|+.
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            5799999999999999999999999999999985     56688999999999999999999999999999999999998


Q ss_pred             CCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       351 ~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                      ++..    .....+|||+|||..+++++|+++|++||.|..+++     .+.++|||||+|.+.++|.+|++.|||..+.
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            7543    345689999999999999999999999999999876     3455799999999999999999999999998


Q ss_pred             C--cEEEEEec
Q 002974          426 G--KQIKLEAS  434 (861)
Q Consensus       426 G--r~IkVe~A  434 (861)
                      |  ++|+|.+|
T Consensus       158 g~~~~l~V~~A  168 (168)
T 1b7f_A          158 GGSQPLSVRLA  168 (168)
T ss_dssp             TCSSCCEEEEC
T ss_pred             CCCeEEEEEeC
Confidence            8  99999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.96  E-value=1.3e-28  Score=237.03  Aligned_cols=155  Identities=25%  Similarity=0.435  Sum_probs=141.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ++++|||+|||+++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.
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            4689999999999999999999999999999985     67788999999999999999999999999999999999997


Q ss_pred             CCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       351 ~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                      ++..    .....+|||+|||..+++++|+++|++||.|..+++     .+.++|||||+|.+.++|.+|++.|||..+.
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            6533    345678999999999999999999999999999886     3446899999999999999999999999999


Q ss_pred             CcE--EEEEec
Q 002974          426 GKQ--IKLEAS  434 (861)
Q Consensus       426 Gr~--IkVe~A  434 (861)
                      |+.  |+|.||
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  888876

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.96  E-value=9e-29  Score=245.49  Aligned_cols=168  Identities=18%  Similarity=0.334  Sum_probs=141.8

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++. ++..+.|+.|.|
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            45567999999999999999999999999999999985     467899999999999999999975 899999999999


Q ss_pred             eecCCCCCCC--CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHh
Q 002974          347 HYSIPKDNPS--EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTL  419 (861)
Q Consensus       347 ~~a~~k~~~~--~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~L  419 (861)
                      .++.++....  ......++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++. 
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            9997764432  22345689999999999999999999999999999876     355789999999999999999986 


Q ss_pred             CCCeeCCcEEEEEeccCCchhh
Q 002974          420 NRSDVAGKQIKLEASRPGGARR  441 (861)
Q Consensus       420 NG~~I~Gr~IkVe~Akpk~~rr  441 (861)
                      ++..|.|+.|+|.++.++....
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            8999999999999999987544

>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=99.96  E-value=4.2e-29  Score=264.69  Aligned_cols=204  Identities=14%  Similarity=0.150  Sum_probs=164.3

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          270 HPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       270 ~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ......+.++|||+|||+++++++|+++|++||+|..|++   ...++|||||+|.+.++|++|++ +++..+.|+.|.|
T Consensus        34 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v  112 (292)
T 2ghp_A           34 ALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIV  112 (292)
T ss_dssp             --------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEE
Confidence            3446678999999999999999999999999999999986   23358999999999999999995 9999999999999


Q ss_pred             eecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccC-cEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCC
Q 002974          347 HYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNR  421 (861)
Q Consensus       347 ~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfG-eI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG  421 (861)
                      .++.           .++|||+|||..+++++|+++|++|| .|..|++.    +.++|||||+|.+.++|.+|++.|+|
T Consensus       113 ~~~~-----------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g  181 (292)
T 2ghp_A          113 SHLT-----------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG  181 (292)
T ss_dssp             EECC-----------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTT
T ss_pred             EECC-----------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            9863           57899999999999999999999999 99999863    35689999999999999999999999


Q ss_pred             CeeCCcEEEEEeccCCchhhhchhhhhhhccccCC-CCCCCC-CCcccc----CCcccEEEEe---CCC--CCccee
Q 002974          422 SDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNLC-QIPFDD-LSSGQM----VSSGVITSTC---MDN--GSIQVL  487 (861)
Q Consensus       422 ~~I~Gr~IkVe~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s-~tee~L----s~fG~I~Sv~---~en--G~srGF  487 (861)
                      ..+.|+.|+|.++.++......  .........+. +||+.+ +++++|    ..||.|..++   ...  |.++||
T Consensus       182 ~~~~g~~l~v~~a~~~~~~~~~--~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~  256 (292)
T 2ghp_A          182 LKIEGYTLVTKVSNPLEKSKRT--DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCC  256 (292)
T ss_dssp             CEETTEECEEEECCCC-----------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEE
T ss_pred             CEeCCcEEEEEECCCCcccccc--cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceE
Confidence            9999999999999887532211  01111222233 899999 999998    8999999998   333  888877

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.96  E-value=1.3e-28  Score=247.90  Aligned_cols=166  Identities=19%  Similarity=0.356  Sum_probs=147.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        25 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             cCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            345899999999999999999999999999999986     567899999999999999999999999999999999998


Q ss_pred             cCCCCCCC-------CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHH
Q 002974          349 SIPKDNPS-------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETAL  416 (861)
Q Consensus       349 a~~k~~~~-------~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL  416 (861)
                      +..+....       ......++|||+|||..+++++|+++|++||.|+.|++     +++++|||||+|.+.++|.+|+
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~  184 (216)
T 2qfj_A          105 PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV  184 (216)
T ss_dssp             CSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHH
Confidence            87654221       12245689999999999999999999999999999886     3456899999999999999999


Q ss_pred             HHhCCCeeCCcEEEEEeccCCch
Q 002974          417 RTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       417 ~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      +.|||..|.|++|+|.++.++..
T Consensus       185 ~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          185 SSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             HHHTTCBCSSSBCEEEECSSCSS
T ss_pred             HHccCCEeCCcEEEEEEecCCCC
Confidence            99999999999999999998753

>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=99.96  E-value=4.2e-28  Score=250.19  Aligned_cols=165  Identities=22%  Similarity=0.315  Sum_probs=148.5

Q ss_pred             CCCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          273 GEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       273 ~~~~srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ...++++|||+|||+ ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|+|..+.|+.|+|.++.+
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            446789999999999 9999999999999999999998666689999999999999999999999999999999999975


Q ss_pred             CCCCCCc-------------------------------ccCCcceEEecccCCCcHHHHHHHhcccC-cEEEEEeCCCCc
Q 002974          352 KDNPSEK-------------------------------DANQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDTQHKH  399 (861)
Q Consensus       352 k~~~~~k-------------------------------~~~~~tLfVgNLp~svTeedLrelFskfG-eI~sVritgksK  399 (861)
                      +.....+                               ....++|||+|||..+++++|+++|++|| +|..|++..+.+
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~  189 (229)
T 2adc_A          110 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR  189 (229)
T ss_dssp             CCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSST
T ss_pred             ccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCC
Confidence            5211100                               11257899999999999999999999999 999999977789


Q ss_pred             cEEEEEECCHHHHHHHHHHhCCCeeC-CcEEEEEeccCC
Q 002974          400 NHKFIEFYDIRAAETALRTLNRSDVA-GKQIKLEASRPG  437 (861)
Q Consensus       400 GfAFVeF~d~eaA~kAL~~LNG~~I~-Gr~IkVe~Akpk  437 (861)
                      |||||+|.+.++|.+|++.|||..+. |++|+|.|++++
T Consensus       190 g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             cEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99999999999999999999999999 999999999874

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.96  E-value=2.8e-28  Score=237.12  Aligned_cols=154  Identities=16%  Similarity=0.335  Sum_probs=141.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcce
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQF----G-------DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  343 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqf----G-------~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~  343 (861)
                      ++.++|||+|||+++++++|+++|++|    |       .|..+++ ++++|||||+|.+.++|++|+ .|+|..+.|+.
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~-~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~   79 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   79 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-ETTTTEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe-cCCCCEEEEEeCCHHHHHHHH-HhCCcEecCce
Confidence            467999999999999999999999999    7       8888887 677999999999999999999 89999999999


Q ss_pred             eeeeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHH
Q 002974          344 LDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRT  418 (861)
Q Consensus       344 L~V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~  418 (861)
                      |+|.++......    ....+|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++.
T Consensus        80 i~v~~~~~~~~~----~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~  155 (172)
T 2g4b_A           80 LKIRRPHDYQPL----PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  155 (172)
T ss_dssp             CEEECCSSCCCC----TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHH
T ss_pred             eeecCCcccCCC----CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            999998655332    34689999999999999999999999999999886     455689999999999999999999


Q ss_pred             hCCCeeCCcEEEEEec
Q 002974          419 LNRSDVAGKQIKLEAS  434 (861)
Q Consensus       419 LNG~~I~Gr~IkVe~A  434 (861)
                      |||..+.|++|+|++|
T Consensus       156 l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          156 LNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HTTCEETTEECEEEEC
T ss_pred             cCCCEECCeEEEEEeC
Confidence            9999999999999987

>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=99.96  E-value=5.3e-28  Score=254.99  Aligned_cols=163  Identities=24%  Similarity=0.458  Sum_probs=146.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~----elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      +..++++|||+|||.++++++|+    ++|++||.|..|++  +++++|||||+|.+.++|++|++.|+|..|.|+.|+|
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            45679999999999999999976    89999999999986  6789999999999999999999999999999999999


Q ss_pred             eecCCCCCCC----------------------------------------------------------------------
Q 002974          347 HYSIPKDNPS----------------------------------------------------------------------  356 (861)
Q Consensus       347 ~~a~~k~~~~----------------------------------------------------------------------  356 (861)
                      .|+..+....                                                                      
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            9987644200                                                                      


Q ss_pred             -------------------------------------CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCc
Q 002974          357 -------------------------------------EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKH  399 (861)
Q Consensus       357 -------------------------------------~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksK  399 (861)
                                                           ......++|||+|||..+++++|+++|++||.|++|++....+
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                                                 0112346799999999999999999999999999999877677


Q ss_pred             cEEEEEECCHHHHHHHHHHhCCCeeC-CcEEEEEecc
Q 002974          400 NHKFIEFYDIRAAETALRTLNRSDVA-GKQIKLEASR  435 (861)
Q Consensus       400 GfAFVeF~d~eaA~kAL~~LNG~~I~-Gr~IkVe~Ak  435 (861)
                      |||||+|.+.++|.+|++.|||..|. |+.|+|.|++
T Consensus       245 g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             cEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            99999999999999999999999999 9999999986

>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=99.96  E-value=1.1e-28  Score=238.84  Aligned_cols=157  Identities=18%  Similarity=0.401  Sum_probs=141.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +++++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.  +..+.|+.|.|.++
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            35799999999999999999999999999999985     577899999999999999999984  57899999999998


Q ss_pred             CCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          350 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       350 ~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      .++..    ....++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|.+|++ +++..+
T Consensus        79 ~~~~~----~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~  153 (167)
T 2cjk_A           79 IPRDE----QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDF  153 (167)
T ss_dssp             CCHHH----HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECS
T ss_pred             cchhh----ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEe
Confidence            75422    234679999999999999999999999999999986     35668999999999999999998 899999


Q ss_pred             CCcEEEEEeccCCc
Q 002974          425 AGKQIKLEASRPGG  438 (861)
Q Consensus       425 ~Gr~IkVe~Akpk~  438 (861)
                      .|++|+|.++.++.
T Consensus       154 ~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          154 KDRKIEIKRAEPRH  167 (167)
T ss_dssp             SSSCEEEEECCCCC
T ss_pred             CCeEEEEeecCCCC
Confidence            99999999999863

>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=99.96  E-value=2.5e-28  Score=238.89  Aligned_cols=162  Identities=20%  Similarity=0.280  Sum_probs=145.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE----EeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~sv----kitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ...+.++|||+|||.++++++|+++|.+||.|..+    ..+++++|||||+|.+.++|++|++ |+|..+.|++|+|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            45679999999999999999999999999864431    1357899999999999999999995 999999999999999


Q ss_pred             cCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcE
Q 002974          349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  428 (861)
Q Consensus       349 a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~  428 (861)
                      +.++...  .....++|||+|||..+++++|+++|++||+|..+..++.++|||||+|.+.++|.+|++.|||..|.|++
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  34457899999999999999999999999999998556788999999999999999999999999999999


Q ss_pred             EEEEeccCC
Q 002974          429 IKLEASRPG  437 (861)
Q Consensus       429 IkVe~Akpk  437 (861)
                      |+|.+++++
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            999999886

>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=99.96  E-value=6.6e-28  Score=234.28  Aligned_cols=157  Identities=18%  Similarity=0.377  Sum_probs=138.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CC--CcccEEEEEeCCHHHHHHHHHHcCccccC---cceee
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----AC--KHRGFVMISYYDIRAARNAMKALQNKPLR---RRKLD  345 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tg--ksrGyAFVeF~d~e~A~kALkaLnG~~L~---Gr~L~  345 (861)
                      ++++|||+|||+++++++|+++|++||+|..|++     ++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            4789999999999999999999999999999985     22  78999999999999999999999998876   67788


Q ss_pred             eeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCC
Q 002974          346 IHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNR  421 (861)
Q Consensus       346 V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG  421 (861)
                      +.++.++...   ....++|||+|||..+++++|+++|++||.|..|++    .++++|||||+|.+.++|.+|++.|||
T Consensus        82 ~~~~~~~~~~---~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g  158 (175)
T 3nmr_A           82 MKPADSEKNN---AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ  158 (175)
T ss_dssp             EEECGGGCCS---CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             Eccccccccc---cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcC
Confidence            8777654432   345679999999999999999999999999999886    345689999999999999999999999


Q ss_pred             CeeC---CcEEEEEecc
Q 002974          422 SDVA---GKQIKLEASR  435 (861)
Q Consensus       422 ~~I~---Gr~IkVe~Ak  435 (861)
                      ..+.   +++|+|.||.
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            9776   4999999974

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.95  E-value=2.4e-28  Score=257.85  Aligned_cols=231  Identities=16%  Similarity=0.172  Sum_probs=177.5

Q ss_pred             HhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-ccccCcchhhhccCCCcCCCccCCCCCCCcccCC
Q 002974          192 TIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVGE  269 (861)
Q Consensus       192 ~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~d~~~s~~~s~s~~~gg~~~~~~~ng~~~Ge  269 (861)
                      +||||.++. ++-|..++..+| +.....          ....|+ -++.....++..++..+++..-.....  ..   
T Consensus        26 ~V~nLp~~~te~~l~~~F~~~G-i~~~~~----------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i--~v---   89 (284)
T 3smz_A           26 LIRGLPGDVTNQEVHDLLSDYE-LKYCFV----------DKYKGTAFVTLLNGEQAEAAINAFHQSRLREREL--SV---   89 (284)
T ss_dssp             EEECCCTTCCHHHHHHHTTTSC-EEEEEE----------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEEC--EE---
T ss_pred             EEeCCCCCCCHHHHHHHHHHcC-CEEEEE----------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEE--EE---
Confidence            389998877 777788888776 322211          111222 222222222233333333211100000  00   


Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCccee
Q 002974          270 HPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  344 (861)
Q Consensus       270 ~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L  344 (861)
                        ....+.++|||+|||+++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.|
T Consensus        90 --~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A           90 --QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             --EECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             --EecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence              01235789999999999999999999999999999874     57789999999999999999999999999999999


Q ss_pred             eeeecCCCCCCCCcccCCcceEEecccCCC-cHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHh
Q 002974          345 DIHYSIPKDNPSEKDANQGTLVVFNLDSSV-STEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTL  419 (861)
Q Consensus       345 ~V~~a~~k~~~~~k~~~~~tLfVgNLp~sv-TeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~L  419 (861)
                      .|.++.++... ......++|||+|||..+ ++++|+++|++||.|..|++    .+.++|+|||+|.+.++|.+|++.|
T Consensus       168 ~v~~a~~~~~~-~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l  246 (284)
T 3smz_A          168 YVHWTDAGQLT-PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA  246 (284)
T ss_dssp             EEEECCGGGCC-TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCC-cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHh
Confidence            99999876543 233456899999999996 99999999999999999876    3456899999999999999999999


Q ss_pred             CCCeeCCcEEEEEeccCCchhh
Q 002974          420 NRSDVAGKQIKLEASRPGGARR  441 (861)
Q Consensus       420 NG~~I~Gr~IkVe~Akpk~~rr  441 (861)
                      ||..|.|++|+|.++.++..++
T Consensus       247 ~g~~~~g~~l~v~~a~~~~~~~  268 (284)
T 3smz_A          247 DGLSLGGSHLRVSFCAPGPPGR  268 (284)
T ss_dssp             TTCEETTEECEEEECCSSSCHH
T ss_pred             CCCccCCeEEEEEEecCCCccc
Confidence            9999999999999999998766

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=6e-28  Score=239.96  Aligned_cols=162  Identities=16%  Similarity=0.320  Sum_probs=144.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCccee
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQF----G-------DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  344 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqf----G-------~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L  344 (861)
                      .+++|||+|||+++++++|+++|++|    |       .|..+++ ++++|||||+|.+.++|++|+ .|+|..+.|+.|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i   80 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-ETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceE
Confidence            57999999999999999999999999    6       7888877 778999999999999999999 899999999999


Q ss_pred             eeeecCCCCCCCC----------------cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEE
Q 002974          345 DIHYSIPKDNPSE----------------KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKF  403 (861)
Q Consensus       345 ~V~~a~~k~~~~~----------------k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAF  403 (861)
                      +|.++..+.....                .....++|||+|||..+++++|+++|++||.|..|++     ++.++||||
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            9999876532211                1134689999999999999999999999999999886     344589999


Q ss_pred             EEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       404 VeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      |+|.+.++|.+|++.|||..|.|++|+|.+++++..
T Consensus       161 V~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999999998763

>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=5e-28  Score=242.05  Aligned_cols=162  Identities=22%  Similarity=0.323  Sum_probs=146.2

Q ss_pred             CCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          276 PSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       276 ~srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      .+++|||+|||+ ++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|+|..+.|+.|+|.++..+..
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~   81 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV   81 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCc
Confidence            368999999999 9999999999999999999998666689999999999999999999999999999999999875421


Q ss_pred             CCCc-------------------------------ccCCcceEEecccCCCcHHHHHHHhcccC-cEEEEEeCCCCccEE
Q 002974          355 PSEK-------------------------------DANQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDTQHKHNHK  402 (861)
Q Consensus       355 ~~~k-------------------------------~~~~~tLfVgNLp~svTeedLrelFskfG-eI~sVritgksKGfA  402 (861)
                      ...+                               ....++|||+|||..+++++|+++|++|| .|.+|++....+|+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~a  161 (198)
T 1qm9_A           82 QLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA  161 (198)
T ss_dssp             CCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCE
T ss_pred             CCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEE
Confidence            1100                               12267899999999999999999999999 999999977789999


Q ss_pred             EEEECCHHHHHHHHHHhCCCeeC-CcEEEEEeccCC
Q 002974          403 FIEFYDIRAAETALRTLNRSDVA-GKQIKLEASRPG  437 (861)
Q Consensus       403 FVeF~d~eaA~kAL~~LNG~~I~-Gr~IkVe~Akpk  437 (861)
                      ||+|.+.++|.+|++.|||..+. |++|+|.|++++
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

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.95  E-value=1.4e-27  Score=244.17  Aligned_cols=159  Identities=18%  Similarity=0.222  Sum_probs=138.0

Q ss_pred             CCcEEEEcCCC-CCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          276 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       276 ~srtLfVgNLP-~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      ++++|||+||| ..+++++|+++|++||.|.+|++....+|||||+|.+.++|++|++.|||..+.|++|+|.++..+..
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 89999999999999999999998667799999999999999999999999999999999999864321


Q ss_pred             CCC------------c---------------------ccCCcceEEecccCCCcHHHHHHHhcccCcE--EEEEeCC---
Q 002974          355 PSE------------K---------------------DANQGTLVVFNLDSSVSTEELHQIFGIYGEI--REIRDTQ---  396 (861)
Q Consensus       355 ~~~------------k---------------------~~~~~tLfVgNLp~svTeedLrelFskfGeI--~sVritg---  396 (861)
                      ...            +                     ....++|||+|||+.+++++|+++|++||.|  .+|++..   
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            100            0                     0123579999999999999999999999999  8888743   


Q ss_pred             CCccEEEEEECCHHHHHHHHHHhCCCeeCCc----EEEEEec
Q 002974          397 HKHNHKFIEFYDIRAAETALRTLNRSDVAGK----QIKLEAS  434 (861)
Q Consensus       397 ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr----~IkVe~A  434 (861)
                      ..+|||||+|.+.++|.+||..|||..|.|+    ++.|+++
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            3469999999999999999999999999875    5666664

>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=2.1e-27  Score=251.66  Aligned_cols=231  Identities=17%  Similarity=0.189  Sum_probs=173.4

Q ss_pred             HHhcCCCCCc-chhhhccccccCCCCCCCCCCCcccccccccCCcc-ccccCcchhhhccCCCcCCCccCCCCCCCcccC
Q 002974          191 QTIGNLLPDE-DDLFSGVTDDMGHNFQANTVDDLEDFDLFSSGGGM-ELEGDDRLFAVQKNSDFVGGVSNQGVSAGSVVG  268 (861)
Q Consensus       191 q~IGnLlpdd-DdLlagv~d~~g~~~~~~~~dD~ee~Dvf~s~GGm-Ele~d~~~s~~~s~s~~~gg~~~~~~~ng~~~G  268 (861)
                      -+||||.++. ++-|..++..+|.+.......|...     + .|+ -++.....++..++ .+++..-     ++... 
T Consensus        44 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-----~-~g~afV~f~~~~~A~~A~-~~~~~~~-----~g~~i-  110 (292)
T 2ghp_A           44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-----N-FRFARIEFARYDGALAAI-TKTHKVV-----GQNEI-  110 (292)
T ss_dssp             EEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-----S-SEEEEEEESSHHHHHHHH-TTTTCEE-----TTEEC-
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-----C-cEEEEEEECCHHHHHHHH-HhCCcEe-----CCcEE-
Confidence            3499999887 7778888888887655544433211     1 233 22222222222223 2332111     11000 


Q ss_pred             CCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcce
Q 002974          269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFG-DIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  343 (861)
Q Consensus       269 e~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG-~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~  343 (861)
                        .......++|||+|||+++++++|+++|++|| .|..|++    .+.++|||||+|.+.++|++|++.|+|..+.|+.
T Consensus       111 --~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  188 (292)
T 2ghp_A          111 --IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT  188 (292)
T ss_dssp             --EEEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             --EEEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence              00123589999999999999999999999999 9999985    3568999999999999999999999999999999


Q ss_pred             eeeeecCCCCCCCC---cccCCcceEEecccCC-CcHHHHHHHhcccCcEEEEEeC------CCCccEEEEEECCHHHHH
Q 002974          344 LDIHYSIPKDNPSE---KDANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDT------QHKHNHKFIEFYDIRAAE  413 (861)
Q Consensus       344 L~V~~a~~k~~~~~---k~~~~~tLfVgNLp~s-vTeedLrelFskfGeI~sVrit------gksKGfAFVeF~d~eaA~  413 (861)
                      |.|.++.++.....   .....++|||+|||.. +++++|+++|++||.|..|++.      +.++|||||+|.+.++|.
T Consensus       189 l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~  268 (292)
T 2ghp_A          189 LVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE  268 (292)
T ss_dssp             CEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHH
T ss_pred             EEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHH
Confidence            99999987655432   2345689999999999 9999999999999999999873      567899999999999999


Q ss_pred             HHHHHhCCCeeCCcEEEEEeccCC
Q 002974          414 TALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       414 kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      +|+ .|||..|.|++|+|.|++++
T Consensus       269 ~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          269 RAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHH-HhcCCEECCcEEEEEEecCC
Confidence            999 99999999999999999986

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.93  E-value=7.3e-26  Score=238.07  Aligned_cols=156  Identities=24%  Similarity=0.360  Sum_probs=142.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+|||+++|+++|+++|++||.|..|++ .+++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.+ 
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            3456899999999999999999999999999999998 67799999999999999999999999999999999999864 


Q ss_pred             CCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCC-CeeC--
Q 002974          353 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNR-SDVA--  425 (861)
Q Consensus       353 ~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG-~~I~--  425 (861)
                               ..+|||+|||..+++++|+++|++||.|..|++    +++++|||||+|.+.++|.+|++.||+ ..+.  
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                     468999999999999999999999999999876    456789999999999999999999954 4544  


Q ss_pred             -CcEEEEEeccCCch
Q 002974          426 -GKQIKLEASRPGGA  439 (861)
Q Consensus       426 -Gr~IkVe~Akpk~~  439 (861)
                       +++|.|.++.+...
T Consensus       167 ~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          167 TPRPVIVEPMEQFDD  181 (261)
T ss_dssp             SCCBCEEEECCCEES
T ss_pred             CCceEEEeeccccCc
Confidence             89999999987653

>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=99.81  E-value=1.2e-19  Score=175.36  Aligned_cols=127  Identities=20%  Similarity=0.273  Sum_probs=113.8

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHc-CccccCcceeeeeecCCCC------------CCCCcccCCcceEEecccCCCcHH
Q 002974          311 CKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKLDIHYSIPKD------------NPSEKDANQGTLVVFNLDSSVSTE  377 (861)
Q Consensus       311 gksrGyAFVeF~d~e~A~kALkaL-nG~~L~Gr~L~V~~a~~k~------------~~~~k~~~~~tLfVgNLp~svTee  377 (861)
                      .+-+|+++|+|.+.++|++|++.+ ||..+.| .+.+.++..+.            .........++|||+|||+.++++
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            467899999999999999999999 9999999 99999886531            112233457899999999999999


Q ss_pred             HHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          378 ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       378 dLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      +|+++|++||.|.+|++...++|||||+|.+.++|.+|++.|||..|.|++|+|++++++.
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            9999999999999999977789999999999999999999999999999999999998864

>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=99.79  E-value=7.3e-19  Score=170.69  Aligned_cols=130  Identities=19%  Similarity=0.285  Sum_probs=104.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee-------eeecCCCC--CCCCcccCCcceEEecccCCCcHHHHH
Q 002974          310 ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD-------IHYSIPKD--NPSEKDANQGTLVVFNLDSSVSTEELH  380 (861)
Q Consensus       310 tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~-------V~~a~~k~--~~~~k~~~~~tLfVgNLp~svTeedLr  380 (861)
                      ..+++|||||+|.+.++|++|++.+++....+..+.       ........  ..........+|||+|||+.+++++|+
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            457899999999999999999998876543322222       22222111  111223456899999999999999999


Q ss_pred             HHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          381 QIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       381 elFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ++|++||.|..|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|.+++++..
T Consensus        89 ~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           89 RVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             HHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             HHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999986     456789999999999999999999999999999999999998753

>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=99.78  E-value=4.7e-19  Score=164.63  Aligned_cols=103  Identities=16%  Similarity=0.315  Sum_probs=72.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .+.+|||+|||+++++++|+++|++||.|..|++   .+.+||||||+|.+.++|++|++.|+|..|.|++|+|.++.++
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            3678999999999999999999999999999985   4567999999999999999999999999999999999999876


Q ss_pred             CCCCC----cccCCcceEEecccCCCcHHH
Q 002974          353 DNPSE----KDANQGTLVVFNLDSSVSTEE  378 (861)
Q Consensus       353 ~~~~~----k~~~~~tLfVgNLp~svTeed  378 (861)
                      .....    .....++|||+|||+++|++.
T Consensus        84 ~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           84 KEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CC----------------------------
T ss_pred             cccccccccccCCCCceEeCCCCCCccccc
Confidence            54322    233456899999999999864

>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=99.68  E-value=7.8e-17  Score=149.64  Aligned_cols=105  Identities=17%  Similarity=0.238  Sum_probs=72.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe---CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD---TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri---tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ..++|||+|||+++++++|+++|++||.|++|++   .+.+||||||+|.+.++|++||+.|+|..|.|++|+|.+++++
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            3568999999999999999999999999999886   3446899999999999999999999999999999999999987


Q ss_pred             chhhhchhhhhhhccccCC-CCCCCCCCcc
Q 002974          438 GARRFMVQSEQEQDDLNLC-QIPFDDLSSG  466 (861)
Q Consensus       438 ~~rrl~qq~eq~q~E~~vg-kNLp~s~tee  466 (861)
                      ..+... .....+....++ +||+.++|++
T Consensus        84 ~~~~~~-~~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           84 KEREAE-LGARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             CC----------------------------
T ss_pred             cccccc-cccccCCCCceEeCCCCCCcccc
Confidence            654411 122222223345 8999988876

>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=99.66  E-value=1e-16  Score=147.73  Aligned_cols=104  Identities=26%  Similarity=0.398  Sum_probs=93.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++  ++.++|||||+|.+.++|++|++.|+|..+.|+.|.|.|+.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            3456899999999999999999999999999999986  57789999999999999999999999999999999999997


Q ss_pred             CCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCc
Q 002974          351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE  388 (861)
Q Consensus       351 ~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGe  388 (861)
                      ++...            .+++...++++|.++|++||.
T Consensus        84 ~~~~~------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           84 ANRAF------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHHT------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CChhh------------hhhhHhHhHHHHHHHHHHhCC
Confidence            54332            456778899999999999984

>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=99.66  E-value=2.4e-16  Score=143.21  Aligned_cols=76  Identities=22%  Similarity=0.489  Sum_probs=71.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..++|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|.|++
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            3678999999999999999999999999999985     57899999999999999999999999999999999999997


Q ss_pred             C
Q 002974          351 P  351 (861)
Q Consensus       351 ~  351 (861)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.64  E-value=4.6e-16  Score=158.46  Aligned_cols=121  Identities=22%  Similarity=0.219  Sum_probs=101.7

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||+++|+++|+++|++||+|++|++     +++++|||||+|.+.++|++|++.+++..+.|+.|+|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            34679999999999999999999999999999986     4567899999999999999999999999999999999998


Q ss_pred             cCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe--CCCCCccee
Q 002974          435 RPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC--MDNGSIQVL  487 (861)
Q Consensus       435 kpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~--~enG~srGF  487 (861)
                      .......       ......++ +||+.++++++|    ..||.|..++  ...+.++||
T Consensus        93 ~~~~~~~-------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~  145 (213)
T 4f02_A           93 QRDPSLR-------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY  145 (213)
T ss_dssp             CCCTHHH-------HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEE
T ss_pred             ccccccc-------ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceE
Confidence            8764222       11223344 999999999999    8999999988  445567876

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.64  E-value=7.5e-16  Score=154.77  Aligned_cols=127  Identities=21%  Similarity=0.278  Sum_probs=104.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||.++++++|+++|++||+|.+|++     +++.+|||||+|.+.++|++|++.|++..|.|+.|+|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            3578999999999999999999999999999987     45579999999999999999999999999999999999988


Q ss_pred             CCchhh-hchh-hhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          436 PGGARR-FMVQ-SEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       436 pk~~rr-l~qq-~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      ...... ...+ .........+. +||+.++++++|    ..||.|..++    .++|+++||
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~  169 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGY  169 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEE
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCce
Confidence            776443 2111 11222223344 999999999999    8999999988    357888887

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.64  E-value=2.1e-16  Score=151.33  Aligned_cols=121  Identities=20%  Similarity=0.325  Sum_probs=77.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe
Q 002974          315 GFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD  394 (861)
Q Consensus       315 GyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri  394 (861)
                      -++|++|.+...|..|++.++|....|+.- +.+..    +.......++|||+|||..+++++|+++|++||+|+.|++
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~----~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i   79 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGR----PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI   79 (135)
T ss_dssp             -------------------------------CCSCC----SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEEC
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcCC----CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE
Confidence            478999999999999999999877666542 22322    2234456789999999999999999999999999999987


Q ss_pred             -----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchh
Q 002974          395 -----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGAR  440 (861)
Q Consensus       395 -----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~r  440 (861)
                           +++.+|||||+|.+.++|++|++.||+..|.|++|+|++++++..+
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                 3466899999999999999999999999999999999999987543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=8.2e-16  Score=147.42  Aligned_cols=118  Identities=24%  Similarity=0.276  Sum_probs=100.5

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ++|||+|||.++++++|+++|++||+|.+|++.    ++++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.++.
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            479999999999999999999999999999873    4568999999999999999999999999999999999998765


Q ss_pred             hhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          439 ARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       439 ~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      ...       ......+. +||+.++++++|    ..||.|.++.    ..+|.++||
T Consensus        81 ~~~-------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~  131 (166)
T 3md3_A           81 QSS-------SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY  131 (166)
T ss_dssp             CCC-------CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEE
T ss_pred             CCC-------CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceE
Confidence            221       11122333 899999999999    8999999987    367888886

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.63  E-value=5.3e-16  Score=140.89  Aligned_cols=75  Identities=28%  Similarity=0.462  Sum_probs=70.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||+|||.++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|++|+|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            468999999999999999999999999999876     466789999999999999999999999999999999999986

>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=99.62  E-value=1.2e-15  Score=150.94  Aligned_cols=125  Identities=12%  Similarity=0.178  Sum_probs=100.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||.++++++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++. ++..+.|+.|+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            345789999999999999999999999999999876     355689999999999999999985 99999999999999


Q ss_pred             ccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          434 SRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       434 Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      +.++....   ..........++ +||+.++++++|    ..||.|..++    .++|.++||
T Consensus        89 ~~~~~~~~---~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~  148 (196)
T 1l3k_A           89 AVSREDSQ---RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF  148 (196)
T ss_dssp             CCC--------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEE
T ss_pred             ccCccccc---ccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccce
Confidence            98765322   111111223344 999999999999    8999999887    357888987

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=4.8e-16  Score=140.02  Aligned_cols=94  Identities=22%  Similarity=0.386  Sum_probs=82.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE  357 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~~~  357 (861)
                      ++|||+|||.++++++|+++|++||+|..|++...++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.++.....
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            58999999999999999999999999999997444899999999999999999999999999999999999987654321


Q ss_pred             ------cccCCcceEEeccc
Q 002974          358 ------KDANQGTLVVFNLD  371 (861)
Q Consensus       358 ------k~~~~~tLfVgNLp  371 (861)
                            ......+|||+||+
T Consensus        81 ~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           81 FDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCCCccccCCCceecCCCC
Confidence                  11235789999996

>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=99.62  E-value=1.8e-15  Score=145.23  Aligned_cols=117  Identities=26%  Similarity=0.363  Sum_probs=101.0

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||+|||..+++++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            478999999999999999999999999999886     455679999999999999999999999999999999999987


Q ss_pred             CchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          437 GGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       437 k~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      .....         ....+. +||+.++++++|    ..||.|..++    ..+|.++||
T Consensus        82 ~~~~~---------~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~  132 (167)
T 1fxl_A           82 SSASI---------RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV  132 (167)
T ss_dssp             CCGGG---------TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEE
T ss_pred             CcccC---------CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccce
Confidence            65221         112233 899999999999    8999999887    447888887

>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=99.61  E-value=1.9e-15  Score=145.69  Aligned_cols=118  Identities=25%  Similarity=0.322  Sum_probs=101.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      +.++|||+|||.++++++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++.|++..+.|++|+|.++.
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            3578999999999999999999999999999986     34467999999999999999999999999999999999998


Q ss_pred             CCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          436 PGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       436 pk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      ++....         ....+. +||+.++++++|    .+||.|..++    ..+|.++||
T Consensus        82 ~~~~~~---------~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~  133 (168)
T 1b7f_A           82 PGGESI---------KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV  133 (168)
T ss_dssp             CCSSTT---------TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEE
T ss_pred             CCcccC---------CCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceE
Confidence            765221         122233 899999999999    9999999887    347888886

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=4.3e-15  Score=133.58  Aligned_cols=83  Identities=14%  Similarity=0.288  Sum_probs=76.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..+.|+.|+|.
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            35567899999999999999999999999999999985    46788999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 002974          348 YSIPKDN  354 (861)
Q Consensus       348 ~a~~k~~  354 (861)
                      ++.++..
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=99.60  E-value=6e-16  Score=138.18  Aligned_cols=79  Identities=22%  Similarity=0.432  Sum_probs=71.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcC-ccccCcceeeeeec
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFG-DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQ-NKPLRRRKLDIHYS  349 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG-~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLn-G~~L~Gr~L~V~~a  349 (861)
                      +++|||+|||+++||++|+++|++|| .|..|++     ++++||||||+|.+.++|++|++.++ +..+.|++|+|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            57999999999999999999999999 7998874     57899999999999999999999874 56799999999999


Q ss_pred             CCCCCC
Q 002974          350 IPKDNP  355 (861)
Q Consensus       350 ~~k~~~  355 (861)
                      .++...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            887654

>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=99.60  E-value=4.7e-15  Score=132.89  Aligned_cols=83  Identities=24%  Similarity=0.410  Sum_probs=77.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3457899999999999999999999999999999996     57789999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++...
T Consensus        84 ~a~~~~~~   91 (99)
T 1whw_A           84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             EcCCCccc
Confidence            99887654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.60  E-value=2.7e-15  Score=139.05  Aligned_cols=79  Identities=19%  Similarity=0.379  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      +.+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|||+.|.|+.|+|.+
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            457899999999999999999999999999999985     588999999999999999999999999999999999999


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      +..+
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8644

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.60  E-value=2.4e-15  Score=138.09  Aligned_cols=80  Identities=16%  Similarity=0.309  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccc--cCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP--LRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~--L~Gr~L~V~~a~  350 (861)
                      ...++++|||+|||.++++++|+++|++||.|..|++ .+.||||||+|.+.++|++|++.|++..  +.||+|+|+|++
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            4567999999999999999999999999999999997 4578999999999999999999999876  789999999998


Q ss_pred             CCC
Q 002974          351 PKD  353 (861)
Q Consensus       351 ~k~  353 (861)
                      .++
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            754

>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=99.59  E-value=6.3e-15  Score=133.41  Aligned_cols=84  Identities=17%  Similarity=0.299  Sum_probs=77.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|
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            45567899999999999999999999999999999985     5778999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999876543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=3e-15  Score=138.51  Aligned_cols=83  Identities=22%  Similarity=0.322  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCc--cccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG--~~L~Gr~L~V~~a~  350 (861)
                      ...+.++|||+|||++++|++|+++|++||+|..|++. +.||||||+|.+.++|++|++.|++  ..|.|++|+|.|+.
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            35578999999999999999999999999999999973 3589999999999999999998864  78999999999998


Q ss_pred             CCCCCC
Q 002974          351 PKDNPS  356 (861)
Q Consensus       351 ~k~~~~  356 (861)
                      ++....
T Consensus        91 ~~~~~~   96 (105)
T 1sjq_A           91 HKELKT   96 (105)
T ss_dssp             SSSCCC
T ss_pred             CCCCCc
Confidence            876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=7.1e-15  Score=131.91  Aligned_cols=82  Identities=23%  Similarity=0.485  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ |++..|.|+.|+|.
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            4567899999999999999999999999999999986     46789999999999999999998 99999999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99887654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.59  E-value=8.1e-15  Score=135.01  Aligned_cols=84  Identities=20%  Similarity=0.407  Sum_probs=77.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|
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            45567999999999999999999999999999999985     5678999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .|+.++...
T Consensus        90 ~~a~~~~~~   98 (115)
T 2dgo_A           90 NWATRKPPA   98 (115)
T ss_dssp             EESSCCCCC
T ss_pred             EEccCCCCC
Confidence            999877654

>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=99.59  E-value=1.5e-15  Score=155.12  Aligned_cols=127  Identities=19%  Similarity=0.241  Sum_probs=99.6

Q ss_pred             CCcceEEeccc-CCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          361 NQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       361 ~~~tLfVgNLp-~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ...+|||+||+ ..+++++|+++|++||.|.+|++...++|||||+|.+.++|++|++.|||..+.|++|+|.+++.+..
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            35789999999 89999999999999999999999877899999999999999999999999999999999999975431


Q ss_pred             hhh-----c------hh-----------hhhhhc------cccCC-CCCCCCCCcccc----CCcccE--EEEe--CCCC
Q 002974          440 RRF-----M------VQ-----------SEQEQD------DLNLC-QIPFDDLSSGQM----VSSGVI--TSTC--MDNG  482 (861)
Q Consensus       440 rrl-----~------qq-----------~eq~q~------E~~vg-kNLp~s~tee~L----s~fG~I--~Sv~--~enG  482 (861)
                      ...     .      +.           ......      ...++ +||+.++++++|    .+||.|  .+++  ...|
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            100     0      00           000000      01133 899999999999    899998  7777  3345


Q ss_pred             Cccee
Q 002974          483 SIQVL  487 (861)
Q Consensus       483 ~srGF  487 (861)
                      ..+||
T Consensus       163 ~~~g~  167 (205)
T 3tyt_A          163 ERSSS  167 (205)
T ss_dssp             SSSEE
T ss_pred             CCceE
Confidence            55565

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.5e-15  Score=134.13  Aligned_cols=85  Identities=24%  Similarity=0.370  Sum_probs=77.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      +....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            445667899999999999999999999999999999986     367899999999999999999999999999999999


Q ss_pred             eeecCCCCCC
Q 002974          346 IHYSIPKDNP  355 (861)
Q Consensus       346 V~~a~~k~~~  355 (861)
                      |.++.++...
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999876543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=7.1e-15  Score=130.55  Aligned_cols=81  Identities=25%  Similarity=0.445  Sum_probs=75.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .++++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+.|++|+|.++
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            46899999999999999999999999999999985     4678999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002974          350 IPKDNP  355 (861)
Q Consensus       350 ~~k~~~  355 (861)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            887654

>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=99.59  E-value=2.7e-15  Score=147.59  Aligned_cols=123  Identities=18%  Similarity=0.270  Sum_probs=73.4

Q ss_pred             EEeCCHHHHHHHHHHcCccccC--cceeeeeecCCCC----------------CCCCcccCCcceEEecccCCCcHHHHH
Q 002974          319 ISYYDIRAARNAMKALQNKPLR--RRKLDIHYSIPKD----------------NPSEKDANQGTLVVFNLDSSVSTEELH  380 (861)
Q Consensus       319 VeF~d~e~A~kALkaLnG~~L~--Gr~L~V~~a~~k~----------------~~~~k~~~~~tLfVgNLp~svTeedLr  380 (861)
                      .+|++.++|+.|+..|++....  |+.+...+.....                ..+......++|||+|||..+++++|+
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            6899999999999999987765  6666665532210                011123345689999999999999999


Q ss_pred             HHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchhh
Q 002974          381 QIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGARR  441 (861)
Q Consensus       381 elFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~rr  441 (861)
                      ++|++||.|..|.+     ++..+|||||+|.+.++|++||+.|||..|.|++|+|.|+.++..++
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            99999999999886     34468999999999999999999999999999999999998876544

>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=99.58  E-value=5.1e-15  Score=128.09  Aligned_cols=77  Identities=29%  Similarity=0.477  Sum_probs=72.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      +.+|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.+
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            468999999999999999999999999999985     577899999999999999999999999999999999999987


Q ss_pred             CC
Q 002974          352 KD  353 (861)
Q Consensus       352 k~  353 (861)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.58  E-value=4.2e-15  Score=137.74  Aligned_cols=81  Identities=21%  Similarity=0.300  Sum_probs=74.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+||++.+++++|+++|++||+|++|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|+++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4579999999999999999999999999999986     46789999999999999999999999999999999999998


Q ss_pred             CCchhh
Q 002974          436 PGGARR  441 (861)
Q Consensus       436 pk~~rr  441 (861)
                      .+..++
T Consensus        85 ~~~~~~   90 (110)
T 3s8s_A           85 KGQQRM   90 (110)
T ss_dssp             TTHHHH
T ss_pred             CCcHHH
Confidence            776544

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.58  E-value=6.9e-15  Score=129.87  Aligned_cols=83  Identities=20%  Similarity=0.322  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3456899999999999999999999999999999985   5678999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002974          350 IPKDNP  355 (861)
Q Consensus       350 ~~k~~~  355 (861)
                      .++..+
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            876543

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.58  E-value=3.9e-15  Score=129.90  Aligned_cols=78  Identities=21%  Similarity=0.430  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.|+
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            46889999999999999999999999999999985     5678999999999999999999999999999999999999


Q ss_pred             CCC
Q 002974          350 IPK  352 (861)
Q Consensus       350 ~~k  352 (861)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=8.9e-15  Score=132.68  Aligned_cols=84  Identities=25%  Similarity=0.483  Sum_probs=76.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHc-CccccCccee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKL  344 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki------tgksrGyAFVeF~d~e~A~kALkaL-nG~~L~Gr~L  344 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++      +++++|||||+|.+.++|++|++.| ++..|.|+.|
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            35567899999999999999999999999999999986      4567999999999999999999999 9999999999


Q ss_pred             eeeecCCCCCC
Q 002974          345 DIHYSIPKDNP  355 (861)
Q Consensus       345 ~V~~a~~k~~~  355 (861)
                      +|.|+.++...
T Consensus        90 ~v~~a~~~~~~  100 (107)
T 2cph_A           90 VLEWADSEVTV  100 (107)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999887554

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=7.4e-15  Score=132.69  Aligned_cols=83  Identities=18%  Similarity=0.406  Sum_probs=77.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|++..|.|+.|+|.|+
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            4557999999999999999999999999999999986   4678999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002974          350 IPKDNP  355 (861)
Q Consensus       350 ~~k~~~  355 (861)
                      .++..+
T Consensus        91 ~~~~~~   96 (103)
T 2d9p_A           91 QRKEER   96 (103)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            887654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=6.4e-15  Score=133.10  Aligned_cols=84  Identities=24%  Similarity=0.455  Sum_probs=77.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|
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            34567899999999999999999999999999999985     5678999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .|+.++...
T Consensus        90 ~~a~~~~~~   98 (103)
T 2cq0_A           90 EWAKPSTNS   98 (103)
T ss_dssp             EESSCCCCS
T ss_pred             EECCCCCCC
Confidence            999877554

>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=99.58  E-value=4.8e-15  Score=140.03  Aligned_cols=92  Identities=22%  Similarity=0.329  Sum_probs=78.2

Q ss_pred             cccCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCc--cccCcc
Q 002974          265 SVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRRR  342 (861)
Q Consensus       265 ~~~Ge~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG--~~L~Gr  342 (861)
                      ...++......++++|||+|||++++|++|+++|++||.|..|++ .+.||||||+|.+.++|++|++.|++  ..|.|+
T Consensus        19 ~~~~~~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i-~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr   97 (119)
T 2ad9_A           19 SHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM-LKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   97 (119)
T ss_dssp             ---CCTTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEE-EGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTB
T ss_pred             cccccccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCCEEEEEECCHHHHHHHHHHhccCCceECCe
Confidence            344455556678999999999999999999999999999999997 34589999999999999999999985  579999


Q ss_pred             eeeeeecCCCCCCCC
Q 002974          343 KLDIHYSIPKDNPSE  357 (861)
Q Consensus       343 ~L~V~~a~~k~~~~~  357 (861)
                      +|+|.|+.++.....
T Consensus        98 ~l~V~~a~~k~~~~~  112 (119)
T 2ad9_A           98 PIYIQFSNHKELKTD  112 (119)
T ss_dssp             CCEEEECSSSSCCCC
T ss_pred             EEEEEEccCCCCCcc
Confidence            999999988765543

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.58  E-value=7.3e-15  Score=135.51  Aligned_cols=84  Identities=17%  Similarity=0.345  Sum_probs=77.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|
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            34557899999999999999999999999999999885     5788999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .|+.++...
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=99.58  E-value=1.5e-14  Score=130.76  Aligned_cols=84  Identities=21%  Similarity=0.385  Sum_probs=76.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++   ...++|||||+|.+.++|++|++.|++..|.|+.|+|.+
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            35567899999999999999999999999999999986   234799999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9887654

>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=99.58  E-value=8.7e-15  Score=133.74  Aligned_cols=83  Identities=16%  Similarity=0.325  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++  +++++|||||+|.+.++|++|++.|++..|.|+.|+|.|+.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            4567899999999999999999999999999999986  45678999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 002974          351 PKDNP  355 (861)
Q Consensus       351 ~k~~~  355 (861)
                      ++...
T Consensus        98 ~~~~~  102 (109)
T 1x4a_A           98 SGRGT  102 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            76543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=7.4e-15  Score=130.17  Aligned_cols=78  Identities=23%  Similarity=0.432  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
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            4567899999999999999999999999999999986     36788999999999999999999999999999999999


Q ss_pred             ecC
Q 002974          348 YSI  350 (861)
Q Consensus       348 ~a~  350 (861)
                      |++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>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=99.58  E-value=1.2e-14  Score=131.25  Aligned_cols=84  Identities=18%  Similarity=0.421  Sum_probs=76.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ....+.++|||+|||+++++++|+++|++||.|..|++   ...++|||||+|.+.++|++|++.|++..|.|+.|+|.|
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            35567899999999999999999999999999999986   344789999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9876543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=6e-15  Score=133.80  Aligned_cols=82  Identities=17%  Similarity=0.432  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            34567899999999999999999999999999999985     4778999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 002974          347 HYSIPKD  353 (861)
Q Consensus       347 ~~a~~k~  353 (861)
                      .|+.++.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9998654

>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=99.58  E-value=6.2e-15  Score=131.75  Aligned_cols=79  Identities=22%  Similarity=0.428  Sum_probs=73.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ++++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.
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     46789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7643

>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=99.57  E-value=9.5e-15  Score=134.41  Aligned_cols=82  Identities=17%  Similarity=0.262  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCcc--ccCcceeeeeec
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK--PLRRRKLDIHYS  349 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~--~L~Gr~L~V~~a  349 (861)
                      ....++++|||+|||+++++++|+++|++||.|..|++ .+.||||||+|.+.++|++|++.|++.  .|.|++|+|.|+
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE-ECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            45567899999999999999999999999999999997 345899999999999999999998765  489999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      ..+..
T Consensus        89 ~~~~~   93 (104)
T 1wex_A           89 TSKRI   93 (104)
T ss_dssp             SSSSC
T ss_pred             cCccc
Confidence            87654

>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=99.57  E-value=1.4e-14  Score=131.05  Aligned_cols=83  Identities=19%  Similarity=0.330  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCc---ceee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR---RKLD  345 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G---r~L~  345 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..+.|   +.|+
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            3456899999999999999999999999999999985    46779999999999999999999999999998   9999


Q ss_pred             eeecCCCCCC
Q 002974          346 IHYSIPKDNP  355 (861)
Q Consensus       346 V~~a~~k~~~  355 (861)
                      |.|+.++..+
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999876554

>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=99.57  E-value=7.3e-15  Score=127.65  Aligned_cols=77  Identities=29%  Similarity=0.484  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|
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            457899999999999999999999999999999985     566899999999999999999999999999999999999


Q ss_pred             cC
Q 002974          349 SI  350 (861)
Q Consensus       349 a~  350 (861)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.57  E-value=1.5e-14  Score=131.95  Aligned_cols=84  Identities=21%  Similarity=0.455  Sum_probs=77.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcC------ccccC
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQ------NKPLR  340 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLn------G~~L~  340 (861)
                      ....+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+      +..|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            35567899999999999999999999999999999986     36789999999999999999999999      99999


Q ss_pred             cceeeeeecCCCCCC
Q 002974          341 RRKLDIHYSIPKDNP  355 (861)
Q Consensus       341 Gr~L~V~~a~~k~~~  355 (861)
                      |+.|+|.|+.++...
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999999887654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=9e-15  Score=130.79  Aligned_cols=81  Identities=27%  Similarity=0.459  Sum_probs=74.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--------CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      .+.++|||+|||.++++++|+++|++||.|..|++        +++++|||||+|.+.++|++|++.|++..|.|+.|+|
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            46899999999999999999999999999999985        2278899999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876554

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=9.1e-15  Score=129.63  Aligned_cols=80  Identities=18%  Similarity=0.362  Sum_probs=74.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|
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            34567899999999999999999999999999999985     4678999999999999999999999999999999999


Q ss_pred             eecCC
Q 002974          347 HYSIP  351 (861)
Q Consensus       347 ~~a~~  351 (861)
                      .|+..
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

>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=99.57  E-value=6.2e-15  Score=154.84  Aligned_cols=114  Identities=18%  Similarity=0.226  Sum_probs=101.5

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ....++|||+|||.++|+++|+++|++||.|..|++. +.+|||||+|.+.++|.+|+..|+|..|.|+.|+|.++.+..
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~-~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~~~   97 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA   97 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecccCC
Confidence            3456799999999999999999999999999999974 579999999999999999999999999999999999998642


Q ss_pred             hhhhchhhhhhhccccCCCCCCCCCCcccc----CCcccEEEEe---CCCCCccee
Q 002974          439 ARRFMVQSEQEQDDLNLCQIPFDDLSSGQM----VSSGVITSTC---MDNGSIQVL  487 (861)
Q Consensus       439 ~rrl~qq~eq~q~E~~vgkNLp~s~tee~L----s~fG~I~Sv~---~enG~srGF  487 (861)
                                    ....+||+.++++++|    ..||.|..+.   ..+|+++||
T Consensus        98 --------------~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~  139 (261)
T 3sde_A           98 --------------ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGK  139 (261)
T ss_dssp             --------------EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEE
T ss_pred             --------------cccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcE
Confidence                          1222899999999999    8999999887   678889987

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=8.3e-15  Score=131.96  Aligned_cols=83  Identities=20%  Similarity=0.446  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.
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            4457899999999999999999999999999999986     45689999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>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=99.56  E-value=1.2e-14  Score=130.23  Aligned_cols=81  Identities=23%  Similarity=0.362  Sum_probs=74.8

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||+|..|++     +++.+|||||+|.+.++|++|++.||+..|.|++|+|+++
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            45689999999999999999999999999999987     4556899999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            988643

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=5.8e-15  Score=131.34  Aligned_cols=81  Identities=22%  Similarity=0.457  Sum_probs=74.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE-Ee-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTI-YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~sv-ki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .+.++|||+|||.++++++|+++|++||.|..| ++     +++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            468999999999999999999999999999888 64     466899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9887654

>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=99.56  E-value=1.9e-14  Score=128.88  Aligned_cols=81  Identities=27%  Similarity=0.467  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccC--cceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR--RRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~--Gr~L~V~~a~  350 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++.. .+|||||+|.+.++|++|++.|++..+.  |+.|+|.|+.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            345689999999999999999999999999999999843 4899999999999999999999999999  9999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      ++..
T Consensus        92 ~~~~   95 (97)
T 1why_A           92 SGPS   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=7.5e-15  Score=132.24  Aligned_cols=83  Identities=28%  Similarity=0.445  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
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             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99887654

>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=99.56  E-value=7.5e-15  Score=130.39  Aligned_cols=81  Identities=23%  Similarity=0.356  Sum_probs=73.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      +....+.++|||+|||+++++++|+++|++||+|..|++    +++++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            345667899999999999999999999999999999985    4667999999999999999999999999999999999


Q ss_pred             eecCC
Q 002974          347 HYSIP  351 (861)
Q Consensus       347 ~~a~~  351 (861)
                      .++..
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99853

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.8e-14  Score=129.55  Aligned_cols=82  Identities=20%  Similarity=0.316  Sum_probs=74.8

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      .....++|||+|||..+++++|+++|++||.|..|++.    ++.+|||||+|.+.++|++|++.||+..|.|++|+|++
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            34567899999999999999999999999999998863    45679999999999999999999999999999999999


Q ss_pred             ccCCch
Q 002974          434 SRPGGA  439 (861)
Q Consensus       434 Akpk~~  439 (861)
                      ++++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            998763

>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=99.56  E-value=7.1e-15  Score=142.34  Aligned_cols=118  Identities=19%  Similarity=0.253  Sum_probs=98.3

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----C--CCccEEEEEECCHHHHHHHHHHhCCCeeC---CcEEEE
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----Q--HKHNHKFIEFYDIRAAETALRTLNRSDVA---GKQIKL  431 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----g--ksKGfAFVeF~d~eaA~kAL~~LNG~~I~---Gr~IkV  431 (861)
                      .++|||+|||.++++++|+++|++||+|.+|++.     +  +++|||||+|.+.++|++|++.|++..+.   ++.+.+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            5789999999999999999999999999998762     1  57899999999999999999999998876   688888


Q ss_pred             EeccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe---CCCCCccee
Q 002974          432 EASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC---MDNGSIQVL  487 (861)
Q Consensus       432 e~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~---~enG~srGF  487 (861)
                      .++.+.....        .....+. +||+.++++++|    .+||.|.+++   ..+|.++||
T Consensus        83 ~~~~~~~~~~--------~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~  138 (175)
T 3nmr_A           83 KPADSEKNNA--------VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGC  138 (175)
T ss_dssp             EECGGGCCSC--------GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEE
T ss_pred             cccccccccc--------CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEE
Confidence            8876543211        1222344 999999999999    8999999887   567888887

>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=99.56  E-value=1.6e-14  Score=132.33  Aligned_cols=83  Identities=25%  Similarity=0.341  Sum_probs=73.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcC--ccccCcceeeeeec
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ--NKPLRRRKLDIHYS  349 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLn--G~~L~Gr~L~V~~a  349 (861)
                      ....++++|||+|||+++++++|+++|++||.|..|++. +.||||||+|.+.++|++|++.|+  +..+.|++|+|.|+
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  56799999999999


Q ss_pred             CCCCCC
Q 002974          350 IPKDNP  355 (861)
Q Consensus       350 ~~k~~~  355 (861)
                      .++...
T Consensus        89 ~~~~~~   94 (101)
T 2cq1_A           89 NHKELK   94 (101)
T ss_dssp             SCSSCC
T ss_pred             CcccCc
Confidence            876543

>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=99.56  E-value=1.1e-14  Score=133.85  Aligned_cols=82  Identities=23%  Similarity=0.459  Sum_probs=75.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||..+++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|
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            34567899999999999999999999999999999985     4678999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 002974          347 HYSIPKD  353 (861)
Q Consensus       347 ~~a~~k~  353 (861)
                      .++.++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998764

>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=99.56  E-value=7.6e-15  Score=134.95  Aligned_cols=80  Identities=16%  Similarity=0.190  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccc--cCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP--LRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~--L~Gr~L~V~~a  349 (861)
                      ...++++|||+|||+ ++++++|+++|++||.|..|++ .+.+|||||+|.+.++|++|++.|++..  |.|++|+|.|+
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i-~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   89 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   89 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEE-CSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEE-EcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEEC
Confidence            345799999999999 9999999999999999999998 4567999999999999999999998754  99999999999


Q ss_pred             CCCC
Q 002974          350 IPKD  353 (861)
Q Consensus       350 ~~k~  353 (861)
                      ..+.
T Consensus        90 ~~~~   93 (102)
T 1x4d_A           90 QKYK   93 (102)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            8654

>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=99.56  E-value=1.2e-14  Score=131.73  Aligned_cols=84  Identities=25%  Similarity=0.475  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCcccc---Ccce
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPL---RRRK  343 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L---~Gr~  343 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..+   .|+.
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            35667899999999999999999999999999999985     467899999999999999999999999987   8999


Q ss_pred             eeeeecCCCCCC
Q 002974          344 LDIHYSIPKDNP  355 (861)
Q Consensus       344 L~V~~a~~k~~~  355 (861)
                      |+|.++.++...
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

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.5e-14  Score=128.33  Aligned_cols=82  Identities=20%  Similarity=0.368  Sum_probs=75.3

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      .....+.++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         4 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   80 (92)
T 2dgt_A            4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLST   80 (92)
T ss_dssp             SCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC---SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE---CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            4456779999999999999999999999999999999983   6699999999999999999999999999999999998


Q ss_pred             CCCCC
Q 002974          351 PKDNP  355 (861)
Q Consensus       351 ~k~~~  355 (861)
                      ++...
T Consensus        81 ~~~~~   85 (92)
T 2dgt_A           81 SRLRT   85 (92)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            76543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.7e-14  Score=127.39  Aligned_cols=80  Identities=23%  Similarity=0.413  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|++..+.|++|+|.|+.++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   80 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNK   80 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCC
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCC
Confidence            34578999999999999999999999999999999984   899999999999999999999999999999999999877


Q ss_pred             CCC
Q 002974          353 DNP  355 (861)
Q Consensus       353 ~~~  355 (861)
                      ...
T Consensus        81 ~~~   83 (90)
T 2dnq_A           81 SKA   83 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.55  E-value=1.2e-14  Score=138.23  Aligned_cols=83  Identities=20%  Similarity=0.425  Sum_probs=76.6

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      .....+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            345677899999999999999999999999999999986     467899999999999999999999999999999999


Q ss_pred             eeecCCCC
Q 002974          346 IHYSIPKD  353 (861)
Q Consensus       346 V~~a~~k~  353 (861)
                      |.|+.++.
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998754

>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=99.55  E-value=1.3e-14  Score=132.62  Aligned_cols=83  Identities=19%  Similarity=0.390  Sum_probs=76.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|
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            34567899999999999999999999999999999986     4678999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 002974          347 HYSIPKDN  354 (861)
Q Consensus       347 ~~a~~k~~  354 (861)
                      .|+.++..
T Consensus       101 ~~a~~~~~  108 (110)
T 1oo0_B          101 DWCFVKGP  108 (110)
T ss_dssp             EESEESSC
T ss_pred             EEcccCCC
Confidence            99986543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.8e-14  Score=130.23  Aligned_cols=83  Identities=20%  Similarity=0.380  Sum_probs=76.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhc-CCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccc-cCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQ-FGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKP-LRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsq-fG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~-L~Gr~L~V  346 (861)
                      ...+.++|||+|||.++++++|+++|++ ||.|..|++    +++++|||||+|.+.++|++|++.|++.. +.|+.|+|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            4567899999999999999999999999 999999986    57789999999999999999999999999 99999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++...
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            999876554

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=2.2e-14  Score=131.10  Aligned_cols=81  Identities=30%  Similarity=0.445  Sum_probs=73.9

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ....++|||+|||..+++++|+++|++||.|+.|++  .++.++||||+|.+.++|++|++.||+..|.|++|+|+++++
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            445789999999999999999999999999999887  344689999999999999999999999999999999999988


Q ss_pred             Cch
Q 002974          437 GGA  439 (861)
Q Consensus       437 k~~  439 (861)
                      +..
T Consensus        99 ~~~  101 (109)
T 1x4a_A           99 GRG  101 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.8e-14  Score=130.19  Aligned_cols=84  Identities=23%  Similarity=0.299  Sum_probs=76.2

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      .....++|||+|||+.+++++|+++|++||+|..|++.   +..++||||+|.+.++|++|++.||+..|.|++|+|+++
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            34567899999999999999999999999999998863   467899999999999999999999999999999999999


Q ss_pred             cCCchhh
Q 002974          435 RPGGARR  441 (861)
Q Consensus       435 kpk~~rr  441 (861)
                      +++..+.
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            9876443

>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=6.9e-15  Score=132.01  Aligned_cols=73  Identities=21%  Similarity=0.294  Sum_probs=69.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .+..|||+||++.+||++|+++|.+||+|.++++ ..+||||||+|.+.++|++|++.||+..+.||+|+|+++
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            4789999999999999999999999999999997 458999999999999999999999999999999999987

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.3e-14  Score=126.22  Aligned_cols=78  Identities=23%  Similarity=0.414  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHc-CccccCcceeeeeecC
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKLDIHYSI  350 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaL-nG~~L~Gr~L~V~~a~  350 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++ .+++|||||+|.+.++|++|++.| ++..+.|++|+|.|++
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            34567899999999999999999999999999999997 357899999999999999999999 9999999999999974

>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=99.55  E-value=2.2e-14  Score=130.04  Aligned_cols=83  Identities=17%  Similarity=0.369  Sum_probs=75.5

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----C-CCcccEEEEEeCCHHHHHHHHHHcCccccCccee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----A-CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  344 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----t-gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L  344 (861)
                      +....+.++|||+|||.++++++|+++|++|| |..|++     + ++++|||||+|.+.++|++|+ .|++..|.|+.|
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 778999999999999999999 899999999999


Q ss_pred             eeeecCCCCCC
Q 002974          345 DIHYSIPKDNP  355 (861)
Q Consensus       345 ~V~~a~~k~~~  355 (861)
                      +|.++.++...
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999887654

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.55  E-value=1.3e-14  Score=126.51  Aligned_cols=77  Identities=21%  Similarity=0.362  Sum_probs=69.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+++++|+++|++||.|.+|++     ++..+|||||+|.+.++|++|++.|||..+.|++|+|++++
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            4578999999999999999999999999999886     44568999999999999999999999999999999999998


Q ss_pred             CC
Q 002974          436 PG  437 (861)
Q Consensus       436 pk  437 (861)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>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=99.55  E-value=3e-15  Score=169.63  Aligned_cols=146  Identities=20%  Similarity=0.331  Sum_probs=106.2

Q ss_pred             HHHHHhhcCCCEEEEEe-------CCCcccEE-----EEEeCCHHHHHHHHHHcCccccCccee-------------eee
Q 002974          293 ELKALFEQFGDIRTIYT-------ACKHRGFV-----MISYYDIRAARNAMKALQNKPLRRRKL-------------DIH  347 (861)
Q Consensus       293 dL~elFsqfG~I~svki-------tgksrGyA-----FVeF~d~e~A~kALkaLnG~~L~Gr~L-------------~V~  347 (861)
                      .|.+||.++|+|..|..       ..+..+|+     |+.|....++..++..++......+..             .+.
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            37899999999988831       11334444     888887666655554333322221100             011


Q ss_pred             ecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCC
Q 002974          348 YSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRS  422 (861)
Q Consensus       348 ~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~  422 (861)
                      ...+...........++|||+|||+.+|+++|+++|++||.|+.|.+     +++++|||||+|.+.++|++||..|||.
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            11122222222344679999999999999999999999999999987     4567999999999999999999999999


Q ss_pred             eeCCcEEEEEeccCCc
Q 002974          423 DVAGKQIKLEASRPGG  438 (861)
Q Consensus       423 ~I~Gr~IkVe~Akpk~  438 (861)
                      .|.|+.|+|.++.++.
T Consensus       168 ~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          168 KIDGRRVLVDVERGRT  183 (437)
T ss_pred             EECCEEEEEEEeCCCC
Confidence            9999999999999765

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.55  E-value=3.1e-15  Score=133.59  Aligned_cols=76  Identities=16%  Similarity=0.335  Sum_probs=69.4

Q ss_pred             cceEEecccCCCcHHHHHHHhcccC-cEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhC-CCeeCCcEEEEEecc
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYG-EIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLN-RSDVAGKQIKLEASR  435 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfG-eI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LN-G~~I~Gr~IkVe~Ak  435 (861)
                      ++|||+|||.++|+++|+++|++|| +|++|++     +++++|||||+|.+.++|++|++.++ +..+.|++|+|++++
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 8999876     46779999999999999999999875 568999999999999


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ++.
T Consensus        82 ~~~   84 (91)
T 2lxi_A           82 PKP   84 (91)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            875

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.55  E-value=2.4e-14  Score=129.81  Aligned_cols=83  Identities=19%  Similarity=0.416  Sum_probs=75.2

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCC------CCccEEEEEECCHHHHHHHHHHh-CCCeeCCcEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ------HKHNHKFIEFYDIRAAETALRTL-NRSDVAGKQIK  430 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritg------ksKGfAFVeF~d~eaA~kAL~~L-NG~~I~Gr~Ik  430 (861)
                      .....++|||+|||..+++++|+++|++||.|+.|++..      ..+|||||+|.+.++|++|++.| |+..|.|++|+
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            345678999999999999999999999999999998743      35899999999999999999999 99999999999


Q ss_pred             EEeccCCchh
Q 002974          431 LEASRPGGAR  440 (861)
Q Consensus       431 Ve~Akpk~~r  440 (861)
                      |++++++..+
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999987643

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.55  E-value=1.7e-14  Score=124.76  Aligned_cols=76  Identities=18%  Similarity=0.247  Sum_probs=71.0

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      .+|||+|||..+++++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|||..+.|++|+|++++++
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            57999999999999999999999999999876     3556899999999999999999999999999999999999986


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.5e-14  Score=131.07  Aligned_cols=83  Identities=19%  Similarity=0.395  Sum_probs=76.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|+|
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            35667899999999999999999999999999999985     567899999999999999999998 999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 2dh8_A           90 KPCTPRGMQ   98 (105)
T ss_dssp             CCSCCSSCC
T ss_pred             EEccCCCCC
Confidence            999887654

>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=99.54  E-value=1.3e-14  Score=130.32  Aligned_cols=81  Identities=26%  Similarity=0.481  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..|++ .+.+|||||+|.+.++|++|++.|+|..|.|++|+|.|+.++
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            4467899999999999999999999999999999998 456899999999999999999999999999999999999876


Q ss_pred             CC
Q 002974          353 DN  354 (861)
Q Consensus       353 ~~  354 (861)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpj_A           90 AS   91 (99)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.54  E-value=2.8e-14  Score=128.92  Aligned_cols=83  Identities=27%  Similarity=0.401  Sum_probs=74.9

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      .....++|||+|||..+++++|+++|++||.|+.|++.   ..++|||||+|.+.++|++|++.||+..|.|++|+|+++
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            34567899999999999999999999999999999873   236799999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2cqi_A           91 TTPSSQ   96 (103)
T ss_dssp             CCTTCC
T ss_pred             CCCccc
Confidence            987643

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=2.9e-14  Score=131.67  Aligned_cols=83  Identities=25%  Similarity=0.394  Sum_probs=75.3

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ..+.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.+++ .|.|+.|+|
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            35667899999999999999999999999999999986     467899999999999999999999998 899999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++..+
T Consensus        91 ~~a~~~~~~   99 (116)
T 2cqd_A           91 NLAYLGAKP   99 (116)
T ss_dssp             EESTTTCCC
T ss_pred             EEcccCCCc
Confidence            999775443

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=2.3e-14  Score=129.75  Aligned_cols=82  Identities=22%  Similarity=0.317  Sum_probs=75.0

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      .....++|||+|||..+++++|+++|++||.|+.|++     +++.+|||||+|.+.++|++|++.||+..|.|++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3445789999999999999999999999999999986     45578999999999999999999999999999999999


Q ss_pred             eccCCch
Q 002974          433 ASRPGGA  439 (861)
Q Consensus       433 ~Akpk~~  439 (861)
                      +++++..
T Consensus        91 ~a~~~~~   97 (105)
T 1x5u_A           91 KASAHNK   97 (105)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCc
Confidence            9998764

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.54  E-value=7e-15  Score=131.96  Aligned_cols=74  Identities=16%  Similarity=0.163  Sum_probs=69.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ...|||+||++.+|+++|+++|.+||+|+++++. .+||||||+|.+.++|++|++.||+..+.|++|+|++|..
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~-~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e   80 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY-LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSE   80 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEc-CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCH
Confidence            5679999999999999999999999999999975 4899999999999999999999999999999999999943

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.54  E-value=5.8e-15  Score=133.68  Aligned_cols=79  Identities=15%  Similarity=0.335  Sum_probs=70.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCC--EEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCcc----ccCc
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGD--IRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNK----PLRR  341 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~--I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~----~L~G  341 (861)
                      ....-.||||+|||+++|+++|+++|++||.  |..|++     ++++||||||+|.+.++|++|++.|||.    .|.|
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            4556889999999999999999999999995  556763     5889999999999999999999999997    4899


Q ss_pred             ceeeeeecCC
Q 002974          342 RKLDIHYSIP  351 (861)
Q Consensus       342 r~L~V~~a~~  351 (861)
                      |+|.|+||+.
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            9999999864

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.7e-14  Score=129.27  Aligned_cols=82  Identities=12%  Similarity=0.369  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEE-EEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcce---
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIR-TIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK---  343 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~-svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~---  343 (861)
                      ...+.++|||+|||+++++++|+++|++||.|. .|++     +++++|||||+|.+.++|++|++.|+|..+.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            345689999999999999999999999999999 8875     5678999999999999999999999999999999   


Q ss_pred             -eeeeecCCCCC
Q 002974          344 -LDIHYSIPKDN  354 (861)
Q Consensus       344 -L~V~~a~~k~~  354 (861)
                       |+|.|+.+...
T Consensus        85 ~l~v~~a~~~~~   96 (99)
T 2div_A           85 RFKLNYATYSGP   96 (99)
T ss_dssp             ECCEEETTCCSS
T ss_pred             eEEEeecCCCCC
Confidence             99999986543

>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=99.54  E-value=1.7e-14  Score=132.99  Aligned_cols=82  Identities=17%  Similarity=0.361  Sum_probs=74.8

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||.++++++|+++|++||.|++|++     +++.+|||||+|.+.++|++|++.||+..|.|++|+|++
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            345689999999999999999999999999999876     456689999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9987644

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.9e-14  Score=130.01  Aligned_cols=82  Identities=21%  Similarity=0.311  Sum_probs=74.9

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|..|++     +++.+|||||+|.+.++|++|++.||+..|.|++|+|++
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            455789999999999999999999999999999886     345689999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9987643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.54  E-value=1.1e-14  Score=129.82  Aligned_cols=82  Identities=24%  Similarity=0.400  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..+..+++++|||||+|.+.++|++|++.|+|..|.|+.|+|.++.++
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            45578999999999999999999999999999888778899999999999999999999999999999999999999876


Q ss_pred             CC
Q 002974          353 DN  354 (861)
Q Consensus       353 ~~  354 (861)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=4.6e-14  Score=129.56  Aligned_cols=82  Identities=20%  Similarity=0.227  Sum_probs=74.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|++..|.|+.|+|.+
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            4566899999999999999999999999999999885    466799999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002974          349 SIPKDN  354 (861)
Q Consensus       349 a~~k~~  354 (861)
                      +.....
T Consensus        91 a~~~~~   96 (114)
T 2do0_A           91 DERALP   96 (114)
T ss_dssp             CSCCCC
T ss_pred             cccCCC
Confidence            975433

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.53  E-value=2.3e-14  Score=124.52  Aligned_cols=76  Identities=26%  Similarity=0.449  Sum_probs=70.4

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||.|..|++     +++.+|||||+|.+.++|++|++.|||..+.|++|+|+++
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            45689999999999999999999999999999986     3446899999999999999999999999999999999998


Q ss_pred             c
Q 002974          435 R  435 (861)
Q Consensus       435 k  435 (861)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.53  E-value=2.1e-14  Score=134.37  Aligned_cols=85  Identities=19%  Similarity=0.472  Sum_probs=77.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      +....+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|.
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            345567899999999999999999999999999999986     677899999999999999999999999999999999


Q ss_pred             eeecCCCCCC
Q 002974          346 IHYSIPKDNP  355 (861)
Q Consensus       346 V~~a~~k~~~  355 (861)
                      |.|+.++...
T Consensus        96 v~~a~~~~~~  105 (126)
T 3ex7_B           96 VDWCFVRGPP  105 (126)
T ss_dssp             EEESEESSSC
T ss_pred             EEEecCCCCC
Confidence            9999876543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.53  E-value=2.3e-14  Score=136.56  Aligned_cols=82  Identities=27%  Similarity=0.392  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~----elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ...+.++|||+|||+.+++++|+    ++|++||+|..|.+  ++++||||||+|.+.++|++|++.|||..|.|++|+|
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    69999999999986  5689999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 002974          347 HYSIPKDN  354 (861)
Q Consensus       347 ~~a~~k~~  354 (861)
                      .|+..+..
T Consensus       105 ~~a~~~~~  112 (127)
T 2a3j_A          105 TFSETPQS  112 (127)
T ss_dssp             EECCCCCH
T ss_pred             EEccCcch
Confidence            99987643

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=3.6e-14  Score=128.36  Aligned_cols=82  Identities=20%  Similarity=0.417  Sum_probs=74.7

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++|| |..|++     +++++|||||+|.+.++|++|+ .|++..|.|+.|+|
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 999985     4778999999999999999999 89999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2dng_A           88 DIAEGRKQD   96 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEecCCCCC
Confidence            999876554

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.53  E-value=1.3e-14  Score=130.65  Aligned_cols=77  Identities=25%  Similarity=0.376  Sum_probs=72.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...++|||+|||.++++++|+++|++||.|..|++ .+++|||||+|.+.++|++|++.|+|..+.|+.|+|.|+.++
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            45789999999999999999999999999999998 478999999999999999999999999999999999999764

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=9.3e-15  Score=135.27  Aligned_cols=81  Identities=17%  Similarity=0.210  Sum_probs=73.2

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCC--CeeCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR--SDVAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG--~~I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||+++++++|+++|++||+|++|++.. .||||||+|.+.++|++|++.|++  ..|.|++|+|.+++++
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 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            4568999999999999999999999999999999764 489999999999999999998864  7899999999999987


Q ss_pred             chhh
Q 002974          438 GARR  441 (861)
Q Consensus       438 ~~rr  441 (861)
                      ..+.
T Consensus        93 ~~~~   96 (105)
T 1sjq_A           93 ELKT   96 (105)
T ss_dssp             SCCC
T ss_pred             CCCc
Confidence            6443

>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=99.53  E-value=5.8e-15  Score=130.76  Aligned_cols=77  Identities=18%  Similarity=0.283  Sum_probs=66.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFG--DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG--~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      .+|||+|||.++++++|+++|++||  .|..+++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++.
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            5899999999999999999999999  8888874     67899999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7644

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=3.1e-14  Score=126.20  Aligned_cols=78  Identities=21%  Similarity=0.406  Sum_probs=72.1

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||.|..|++.     ++.+|||||+|.+.++|++|++.||+..|.|++|+|++
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            3456899999999999999999999999999998863     56689999999999999999999999999999999999


Q ss_pred             ccC
Q 002974          434 SRP  436 (861)
Q Consensus       434 Akp  436 (861)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            976

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.53  E-value=2.3e-14  Score=132.57  Aligned_cols=79  Identities=18%  Similarity=0.341  Sum_probs=72.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|
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     4678999999999999999999999999999999999


Q ss_pred             eecC
Q 002974          347 HYSI  350 (861)
Q Consensus       347 ~~a~  350 (861)
                      +|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9874

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.8e-14  Score=126.71  Aligned_cols=80  Identities=26%  Similarity=0.345  Sum_probs=73.5

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+++++|+++|++||.|..|++     +++.+|||||+|.+.++|++|++.||+..|.|++|+|++++
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            4579999999999999999999999999999986     35568999999999999999999999999999999999999


Q ss_pred             CCchh
Q 002974          436 PGGAR  440 (861)
Q Consensus       436 pk~~r  440 (861)
                      ++..+
T Consensus        84 ~~~~~   88 (95)
T 2dnz_A           84 ERLDG   88 (95)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            87643

>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=99.53  E-value=2.4e-14  Score=133.38  Aligned_cols=82  Identities=24%  Similarity=0.444  Sum_probs=75.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ..+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.++
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            456899999999999999999999999999999986    5678899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 002974          350 IPKDNP  355 (861)
Q Consensus       350 ~~k~~~  355 (861)
                      .++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=3.2e-14  Score=127.63  Aligned_cols=81  Identities=20%  Similarity=0.418  Sum_probs=74.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|..|++.     ++.+|||||+|.+.++|++|++ |++..|.|++|+|++
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            3456899999999999999999999999999999873     4578999999999999999999 999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9987644

>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=99.53  E-value=4.2e-14  Score=129.04  Aligned_cols=82  Identities=20%  Similarity=0.355  Sum_probs=75.2

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhC------CCeeCCc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLN------RSDVAGK  427 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LN------G~~I~Gr  427 (861)
                      ....++|||+|||..+++++|+++|++||+|..|++.     +..+|||||+|.+.++|++|++.||      +..|.|+
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            3457899999999999999999999999999999874     5678999999999999999999999      9999999


Q ss_pred             EEEEEeccCCchh
Q 002974          428 QIKLEASRPGGAR  440 (861)
Q Consensus       428 ~IkVe~Akpk~~r  440 (861)
                      +|+|.++.++..+
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

>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=99.53  E-value=2e-14  Score=125.50  Aligned_cols=78  Identities=13%  Similarity=0.325  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeC------CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA------CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkit------gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ..++|||+|||.++++++|+++|++||.|..|++.      ++++|||||+|.+.++|++|++.|+|..+.|+.|+|.++
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            46899999999999999999999999999999851      228999999999999999999999999999999999999


Q ss_pred             CCCC
Q 002974          350 IPKD  353 (861)
Q Consensus       350 ~~k~  353 (861)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.53  E-value=3.6e-14  Score=130.67  Aligned_cols=83  Identities=22%  Similarity=0.372  Sum_probs=75.3

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||.|+.|++     ++..+|||||+|.+.++|++|++.||+..|.|+.|+|++
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            456789999999999999999999999999999886     345589999999999999999999999999999999999


Q ss_pred             ccCCchhh
Q 002974          434 SRPGGARR  441 (861)
Q Consensus       434 Akpk~~rr  441 (861)
                      ++++..+.
T Consensus        92 a~~~~~~~   99 (115)
T 2dgo_A           92 ATRKPPAP   99 (115)
T ss_dssp             SSCCCCCS
T ss_pred             ccCCCCCC
Confidence            99876443

>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=99.53  E-value=1.4e-14  Score=132.71  Aligned_cols=96  Identities=17%  Similarity=0.279  Sum_probs=82.5

Q ss_pred             cCcceeeeeecCCCCCCCCcccCCcceEEecccCC-CcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHH
Q 002974          339 LRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR  417 (861)
Q Consensus       339 L~Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~s-vTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~  417 (861)
                      ..|..|+|..+...... ......++|||+|||.. +++++|+++|++||+|+.|++   .++||||+|.+.++|++|++
T Consensus         5 ~~g~~~~~~~s~~~~~~-~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~   80 (110)
T 1wf1_A            5 SSGMSLKLQASNVTNKN-DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVL   80 (110)
T ss_dssp             CCSCCCCCCCCCSCCSC-CCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHH
T ss_pred             CCCcccccccCCCCCCC-CCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHH
Confidence            34677777776654332 22344689999999999 999999999999999999998   78999999999999999999


Q ss_pred             HhCCCeeCCcEEEEEeccCCc
Q 002974          418 TLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       418 ~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      .||+..|.|++|+|++++++.
T Consensus        81 ~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           81 GENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HHTTCEETTEECCEEESCCCC
T ss_pred             HcCCCEECCeEEEEEECCCCC
Confidence            999999999999999998654

>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=99.53  E-value=1.7e-14  Score=139.87  Aligned_cols=115  Identities=17%  Similarity=0.211  Sum_probs=98.4

Q ss_pred             CcceEEecccCCCcHHHHHHHhccc----C-------cEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIY----G-------EIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskf----G-------eI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      .++|||+|||.++++++|+++|++|    |       .|..+++ +.++|||||+|.+.++|++|+ .||+..+.|++|+
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~-~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-ETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe-cCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            5799999999999999999999999    7       7888875 467999999999999999999 8999999999999


Q ss_pred             EEeccCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          431 LEASRPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       431 Ve~Akpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      |.++.+.....         ....+. +|||.++++++|    .+||.|..++    .++|.++||
T Consensus        82 v~~~~~~~~~~---------~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~  138 (172)
T 2g4b_A           82 IRRPHDYQPLP---------GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY  138 (172)
T ss_dssp             EECCSSCCCCT---------TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEE
T ss_pred             ecCCcccCCCC---------CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceE
Confidence            99987653211         123334 899999999999    8999999887    358888987

>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=99.53  E-value=3.5e-14  Score=128.54  Aligned_cols=83  Identities=18%  Similarity=0.261  Sum_probs=74.6

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCC---cEEEE
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG---KQIKL  431 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G---r~IkV  431 (861)
                      ....++|||+|||..+++++|+++|++||.|+.|++    .++++|||||+|.+.++|++|++.||+..+.|   ++|+|
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            345789999999999999999999999999999886    34458999999999999999999999999998   99999


Q ss_pred             EeccCCchhh
Q 002974          432 EASRPGGARR  441 (861)
Q Consensus       432 e~Akpk~~rr  441 (861)
                      .+++++..++
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9999876543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2e-14  Score=129.52  Aligned_cols=82  Identities=24%  Similarity=0.426  Sum_probs=74.9

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|+.|++.     ++.+|||||+|.+.++|++|++.||+..|.|++|+|++
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            3457899999999999999999999999999999873     45789999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9987644

>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=99.53  E-value=3.9e-14  Score=128.32  Aligned_cols=80  Identities=26%  Similarity=0.523  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|++..|.|+.|+|.|+.++
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            34568999999999999999999999999999999983   789999999999999999999999999999999999877


Q ss_pred             CCC
Q 002974          353 DNP  355 (861)
Q Consensus       353 ~~~  355 (861)
                      ...
T Consensus        84 ~~~   86 (103)
T 2dgu_A           84 DQK   86 (103)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            554

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.53  E-value=6.4e-15  Score=133.43  Aligned_cols=78  Identities=18%  Similarity=0.273  Sum_probs=72.9

Q ss_pred             CCCcEEEEcCCCC------CCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCc-c
Q 002974          275 HPSRTLFVRNINS------NVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR-R  342 (861)
Q Consensus       275 ~~srtLfVgNLP~------~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G-r  342 (861)
                      ..+++|||+|||.      ++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.| +
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            4578999999999      9999999999999999999985     48899999999999999999999999999999 9


Q ss_pred             eeeeeecCCC
Q 002974          343 KLDIHYSIPK  352 (861)
Q Consensus       343 ~L~V~~a~~k  352 (861)
                      .|+|.++.++
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998753

>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=99.53  E-value=3.6e-14  Score=126.75  Aligned_cols=79  Identities=16%  Similarity=0.267  Sum_probs=73.3

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||+|||..+++++|+++|++||.|.+|++.     ++++|||||+|.+.++|++|++.|||..+.|+.|+|+++++
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            4789999999999999999999999999999873     55689999999999999999999999999999999999998


Q ss_pred             Cchh
Q 002974          437 GGAR  440 (861)
Q Consensus       437 k~~r  440 (861)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            8643

>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=99.53  E-value=4.8e-14  Score=127.34  Aligned_cols=83  Identities=20%  Similarity=0.348  Sum_probs=75.0

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      .....++|||+|||..+++++|+++|++||.|+.|++.   ...++||||+|.+.++|++|++.||+..|.|++|+|+++
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            34567899999999999999999999999999999874   235899999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2cq3_A           91 TARVMT   96 (103)
T ss_dssp             CSSCCC
T ss_pred             ccCCCC
Confidence            987643

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=1.9e-14  Score=130.54  Aligned_cols=80  Identities=24%  Similarity=0.390  Sum_probs=73.7

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|..|++.     +..+|||||+|.+.++|++|++.|||..|.|++|+|++
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            3456789999999999999999999999999999863     56689999999999999999999999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      ++++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98765

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=2.4e-14  Score=128.86  Aligned_cols=83  Identities=19%  Similarity=0.398  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..++. +++++|||||+|.+.++|++|++.|++..|.|+.|+|.|+.+
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            4567899999999999999999999999999955443 678899999999999999999999999999999999999987


Q ss_pred             CCCC
Q 002974          352 KDNP  355 (861)
Q Consensus       352 k~~~  355 (861)
                      +...
T Consensus        91 ~~~~   94 (101)
T 2fc9_A           91 RGSP   94 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=2.5e-14  Score=128.23  Aligned_cols=81  Identities=22%  Similarity=0.291  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .....++|||+|||+++++++|+++|++||.|....++++++|||||+|.+.++|++|++.|+|..|.|+.|+|.++.++
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            34568999999999999999999999999999633345788999999999999999999999999999999999999876


Q ss_pred             C
Q 002974          353 D  353 (861)
Q Consensus       353 ~  353 (861)
                      .
T Consensus        95 ~   95 (97)
T 2e5j_A           95 R   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2.3e-14  Score=131.52  Aligned_cols=83  Identities=23%  Similarity=0.367  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEE--------EEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCcccc
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIR--------TIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPL  339 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~--------svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L  339 (861)
                      ...+.++|||+|||.++++++|+++|++||.|.        .|++     +++++|||||+|.+.++|++|++.|++..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            456789999999999999999999999999998        4764     467899999999999999999999999999


Q ss_pred             CcceeeeeecCCCCCC
Q 002974          340 RRRKLDIHYSIPKDNP  355 (861)
Q Consensus       340 ~Gr~L~V~~a~~k~~~  355 (861)
                      .|+.|+|.++.++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999887554

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.53  E-value=3.5e-14  Score=135.03  Aligned_cols=83  Identities=20%  Similarity=0.419  Sum_probs=76.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.
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            4567899999999999999999999999999999985     46789999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++..+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99887654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.53  E-value=2.5e-14  Score=128.48  Aligned_cols=79  Identities=23%  Similarity=0.379  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--------EEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccc
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--------IYT-----ACKHRGFVMISYYDIRAARNAMKALQNKP  338 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~s--------vki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~  338 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..        +++     +++++|||||+|.+.++|++|++.|+|..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999999988        764     47789999999999999999999999999


Q ss_pred             cCcceeeeeecC
Q 002974          339 LRRRKLDIHYSI  350 (861)
Q Consensus       339 L~Gr~L~V~~a~  350 (861)
                      +.|+.|+|.+++
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            999999999874

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=5.2e-14  Score=124.71  Aligned_cols=77  Identities=26%  Similarity=0.422  Sum_probs=71.2

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|..|++.     ++.+|||||+|.+.++|++|++.||+..|.|++|+|++
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            4457899999999999999999999999999999873     45689999999999999999999999999999999999


Q ss_pred             cc
Q 002974          434 SR  435 (861)
Q Consensus       434 Ak  435 (861)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=2.7e-14  Score=126.09  Aligned_cols=77  Identities=29%  Similarity=0.416  Sum_probs=72.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ...++|||+|||..+++++|+++|++||+|+.|++.   ++||||+|.+.++|++|++.||+..+.|++|+|++++++..
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            456899999999999999999999999999999985   79999999999999999999999999999999999998764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.5e-14  Score=126.14  Aligned_cols=76  Identities=20%  Similarity=0.340  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|++.++
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            46899999999999999999999999999999985     4678999999999999999999999999999999999876


Q ss_pred             C
Q 002974          350 I  350 (861)
Q Consensus       350 ~  350 (861)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.52  E-value=3.3e-14  Score=127.27  Aligned_cols=79  Identities=19%  Similarity=0.352  Sum_probs=73.1

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeC--CcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA--GKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~--Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||..+++++|+++|++||+|+.|++.. .++||||+|.+.++|++|++.||+..|.  |++|+|++++++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            3457999999999999999999999999999999864 4899999999999999999999999999  999999999987


Q ss_pred             ch
Q 002974          438 GA  439 (861)
Q Consensus       438 ~~  439 (861)
                      ..
T Consensus        94 ~~   95 (97)
T 1why_A           94 PS   95 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.52  E-value=2.2e-14  Score=131.60  Aligned_cols=78  Identities=18%  Similarity=0.218  Sum_probs=72.0

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCe--eCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD--VAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~--I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||.++|+++|+++|++||.|++|++. +.||||||+|.+.++|.+|++.|++..  |.|++|+|++++++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~-~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM-PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            456799999999999999999999999999999975 468999999999999999999999885  78999999999986


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        98 ~   98 (100)
T 3r27_A           98 K   98 (100)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.52  E-value=2.8e-14  Score=130.40  Aligned_cols=82  Identities=21%  Similarity=0.347  Sum_probs=74.7

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||.|..|++.     +..+|||||+|.+.++|++|++.|||..|.|++|+|.+
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            3456799999999999999999999999999999873     45689999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus       103 a~~~~~~  109 (110)
T 1oo0_B          103 CFVKGPK  109 (110)
T ss_dssp             SEESSCC
T ss_pred             cccCCCC
Confidence            9987644

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.7e-14  Score=132.64  Aligned_cols=81  Identities=22%  Similarity=0.419  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ....+.++|||+|||.++++++|+++|++||+|..|++   .+.++|||||+|.+.++|++|++.|+|..+.|+.|+|.+
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            35567899999999999999999999999999999986   345799999999999999999999999999999999999


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9765

>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=99.52  E-value=1.6e-14  Score=128.82  Aligned_cols=82  Identities=28%  Similarity=0.619  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEeC--CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~----elFsqfG~I~svkit--gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ...++++|||+|||.++++++|+    ++|++||.|..|++.  ++++|||||+|.+.++|++|++.|+|..+.|+.|+|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            45678999999999999999999    999999999999873  467899999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 002974          347 HYSIPKDN  354 (861)
Q Consensus       347 ~~a~~k~~  354 (861)
                      .|+.++..
T Consensus        84 ~~a~~~~~   91 (97)
T 1nu4_A           84 QYAKTDSD   91 (97)
T ss_dssp             EECSSCCT
T ss_pred             EEccCCCc
Confidence            99987643

>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=99.52  E-value=1.5e-14  Score=133.68  Aligned_cols=78  Identities=13%  Similarity=0.272  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .+..++|||+|||+++++++|+++|++||.|..|++ .+.+|||||+|.+.++|++|++.|||..+.|+.|+|.|+...
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE-eCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            445789999999999999999999999999999998 468999999999999999999999999999999999999754

>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=99.52  E-value=8.4e-15  Score=132.19  Aligned_cols=82  Identities=24%  Similarity=0.441  Sum_probs=74.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .+.+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   83 (104)
T 1p1t_A            4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             cCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            3456799999999999999999999999999999885     56779999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 002974          348 YSIPKDN  354 (861)
Q Consensus       348 ~a~~k~~  354 (861)
                      ++.++..
T Consensus        84 ~a~~~~~   90 (104)
T 1p1t_A           84 NAASEKN   90 (104)
T ss_dssp             ETTCTTH
T ss_pred             eCCCccc
Confidence            9987643

>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=99.52  E-value=3.2e-14  Score=129.17  Aligned_cols=79  Identities=24%  Similarity=0.421  Sum_probs=73.5

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ....+.++|||+|||+.+++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.
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            34567999999999999999999999999999999885    56789999999999999999999999999999999999


Q ss_pred             ecC
Q 002974          348 YSI  350 (861)
Q Consensus       348 ~a~  350 (861)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            975

>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=99.52  E-value=6e-14  Score=128.43  Aligned_cols=81  Identities=14%  Similarity=0.206  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCc-----ceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR-----RKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~G-----r~L~V~  347 (861)
                      .....++|||+|||+++++++|+++|++||+|..|++...  |||||+|.+.++|++||+.|+++.|.|     +.|+|.
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            4466899999999999999999999999999999997333  999999999999999999999999999     999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (108)
T 1x4c_A           89 VDGPRSPS   96 (108)
T ss_dssp             ESSCCSCC
T ss_pred             eCCCCCCC
Confidence            99886543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.52  E-value=3.5e-14  Score=129.51  Aligned_cols=80  Identities=16%  Similarity=0.308  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCC------cHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcc-
Q 002974          273 GEHPSRTLFVRNINSNV------EDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR-  342 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~v------TEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr-  342 (861)
                      .....++|||+|||..+      ++++|+++|++||.|..|++   +++++|||||+|.+.++|++|++.|+|..|.|+ 
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            45568999999999999      78999999999999999986   567899999999999999999999999999999 


Q ss_pred             eeeeeecCCC
Q 002974          343 KLDIHYSIPK  352 (861)
Q Consensus       343 ~L~V~~a~~k  352 (861)
                      .|+|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999999754

>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=99.52  E-value=5.9e-15  Score=143.95  Aligned_cols=120  Identities=18%  Similarity=0.208  Sum_probs=99.8

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEE----EeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sV----ritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ....++|||+|||.++++++|+++|.+||.|..+    ..++.++|||||+|.+.++|++|++ |||..+.|++|+|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            4457899999999999999999999999865441    1256789999999999999999995 9999999999999999


Q ss_pred             cCCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEeCCCCCccee
Q 002974          435 RPGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTCMDNGSIQVL  487 (861)
Q Consensus       435 kpk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~~enG~srGF  487 (861)
                      .++..+.       ......+. +||+.++++++|    ..||.|..+ ..+|.++||
T Consensus        89 ~~~~~~~-------~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~  138 (175)
T 1fje_B           89 KGRDSKK-------VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGI  138 (175)
T ss_dssp             CCSSCST-------TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSE
T ss_pred             CCccccc-------cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceE
Confidence            8765321       11223344 999999999999    899999888 888889987

>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=2.7e-14  Score=124.62  Aligned_cols=78  Identities=23%  Similarity=0.400  Sum_probs=71.6

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCC-----C-CccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQ-----H-KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritg-----k-sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ..++|||+|||.++++++|+++|++||.|..|++..     . .+|||||+|.+.++|++|++.|||..+.|+.|+|+++
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            357899999999999999999999999999998632     2 6899999999999999999999999999999999999


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8765

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=1.8e-14  Score=134.74  Aligned_cols=80  Identities=15%  Similarity=0.186  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCc--cccCcceeeeeecC
Q 002974          274 EHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN--KPLRRRKLDIHYSI  350 (861)
Q Consensus       274 ~~~srtLfVgNLP~~-vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG--~~L~Gr~L~V~~a~  350 (861)
                      ..++++|||+|||++ +++++|+++|++||+|..|++ .+.||||||+|.+.++|++|++.|++  ..|.||+|+|.|+.
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            567999999999998 999999999999999999998 56799999999999999999998865  45999999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      .+..
T Consensus       101 ~~~~  104 (112)
T 1x4f_A          101 KYKK  104 (112)
T ss_dssp             SCSS
T ss_pred             cccc
Confidence            6654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=7.4e-14  Score=125.41  Aligned_cols=79  Identities=22%  Similarity=0.410  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcC--CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQF--GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqf--G~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ...+.++|||+|||+++++++|+++|++|  |.|..|++   .+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+.
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   47899999999999999999999999999999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      ++..
T Consensus        88 ~~~~   91 (99)
T 2cpd_A           88 PVDK   91 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.52  E-value=3.8e-14  Score=127.13  Aligned_cols=79  Identities=20%  Similarity=0.352  Sum_probs=72.4

Q ss_pred             cCCcceEEecccCCCcHHHHH----HHhcccCcEEEEEeCCC--CccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          360 ANQGTLVVFNLDSSVSTEELH----QIFGIYGEIREIRDTQH--KHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLr----elFskfGeI~sVritgk--sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      .+.++|||+|||..+++++|+    ++|++||+|++|++...  .++||||+|.+.++|++|++.|||..+.|++|+|++
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            345789999999999999999    99999999999998522  289999999999999999999999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      ++++.
T Consensus        87 a~~~~   91 (96)
T 2dgx_A           87 ATGAS   91 (96)
T ss_dssp             CCCSS
T ss_pred             cCCCC
Confidence            98875

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=4.5e-14  Score=124.65  Aligned_cols=80  Identities=18%  Similarity=0.372  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.|+|..+.|+.|+|.++.++
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            34578999999999999999999999999999999984   669999999999999999999999999999999999876


Q ss_pred             CCC
Q 002974          353 DNP  355 (861)
Q Consensus       353 ~~~  355 (861)
                      ...
T Consensus        82 ~~~   84 (90)
T 2dnp_A           82 QKK   84 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.52  E-value=4.4e-14  Score=126.67  Aligned_cols=81  Identities=15%  Similarity=0.274  Sum_probs=73.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHH----HHhhcCCCEEEEEeC--CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~----elFsqfG~I~svkit--gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .+.++|||+|||.++++++|+    ++|++||+|..|++.  ...+|||||+|.+.++|++|++.|+|..+.|++|+|.+
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            457899999999999999999    999999999999973  22389999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++..+
T Consensus        87 a~~~~~~   93 (96)
T 2dgx_A           87 ATGASGP   93 (96)
T ss_dssp             CCCSSCC
T ss_pred             cCCCCCC
Confidence            9876543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.52  E-value=2e-14  Score=133.94  Aligned_cols=78  Identities=18%  Similarity=0.136  Sum_probs=71.5

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccC-cEEEEEeC-CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYG-EIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfG-eI~sVrit-gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ...+|||+|||+++++++|+++|++|| +|..|++. .+++|||||+|.+.++|++|++.|||..|.|++|+|++++...
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            357999999999999999999999999 99999884 5689999999999999999999999999999999999998654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=3e-14  Score=128.73  Aligned_cols=81  Identities=23%  Similarity=0.413  Sum_probs=74.3

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||.|..|++.     ++.+|||||+|.+.++|++|++.||+..|.|++|+|++
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            3456899999999999999999999999999999873     56789999999999999999999999999999999999


Q ss_pred             ccCCch
Q 002974          434 SRPGGA  439 (861)
Q Consensus       434 Akpk~~  439 (861)
                      ++++..
T Consensus        90 a~~~~~   95 (103)
T 2dnm_A           90 ARYGRR   95 (103)
T ss_dssp             CSSCCS
T ss_pred             CCcCCC
Confidence            997653

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.2e-14  Score=129.18  Aligned_cols=82  Identities=27%  Similarity=0.487  Sum_probs=74.4

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|+.|++.     +..+|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3456899999999999999999999999999999873     34689999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++...
T Consensus        89 a~~~~~~   95 (102)
T 1x5s_A           89 AGKSSDN   95 (102)
T ss_dssp             EECCCCC
T ss_pred             CCCCCCC
Confidence            9987643

>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=99.51  E-value=1.1e-14  Score=140.45  Aligned_cols=116  Identities=16%  Similarity=0.277  Sum_probs=98.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||.++|+++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++  ++..+.|+.|.|.++.
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 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            3578999999999999999999999999999986     35568999999999999999999  4679999999999987


Q ss_pred             CCchhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          436 PGGARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       436 pk~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      ++...         .....++ +||+.++++++|    ..||.|.+++    .++|.++||
T Consensus        80 ~~~~~---------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~  131 (167)
T 2cjk_A           80 PRDEQ---------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGF  131 (167)
T ss_dssp             CHHHH---------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEE
T ss_pred             chhhc---------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceE
Confidence            65321         1122344 999999999999    8999999988    357889887

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=2.5e-14  Score=127.92  Aligned_cols=79  Identities=23%  Similarity=0.354  Sum_probs=72.5

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC------C--CCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT------Q--HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit------g--ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ..++|||+|||.++++++|+++|++||+|+.|++.      +  ..+|||||+|.+.++|++|++.||+..|.|++|+|+
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            45799999999999999999999999999998763      1  567999999999999999999999999999999999


Q ss_pred             eccCCch
Q 002974          433 ASRPGGA  439 (861)
Q Consensus       433 ~Akpk~~  439 (861)
                      +++++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9998763

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=5.4e-14  Score=128.81  Aligned_cols=80  Identities=19%  Similarity=0.197  Sum_probs=72.2

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHh--CCCeeCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~L--NG~~I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||+.+++++|+++|++||.|.+|++.. .||||||+|.+.++|++|++.|  ++..+.|++|+|.+++++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            4567999999999999999999999999999998754 4899999999999999999987  467899999999999987


Q ss_pred             chh
Q 002974          438 GAR  440 (861)
Q Consensus       438 ~~r  440 (861)
                      ..+
T Consensus        92 ~~~   94 (101)
T 2cq1_A           92 ELK   94 (101)
T ss_dssp             SCC
T ss_pred             cCc
Confidence            643

>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=99.51  E-value=5.4e-14  Score=129.28  Aligned_cols=83  Identities=20%  Similarity=0.384  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCE----EEEE-eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI----RTIY-TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I----~svk-itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|    ..++ .+++++|||||+|.+.++|++|++.|+|..|.|+.|+|.
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            44578999999999999999999999999998    4554 478999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      |+.++...
T Consensus       101 ~a~~~~~~  108 (115)
T 2cpx_A          101 FGKNKKQR  108 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EccCCCCC
Confidence            99887654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.51  E-value=3.1e-14  Score=125.70  Aligned_cols=80  Identities=19%  Similarity=0.249  Sum_probs=73.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe---CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD---TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri---tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ...++|||+|||..+++++|+++|++||+|..|++   .++.+|||||+|.+.++|++|++.||+..+.|++|+|+++++
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            45689999999999999999999999999999876   455789999999999999999999999999999999999998


Q ss_pred             Cch
Q 002974          437 GGA  439 (861)
Q Consensus       437 k~~  439 (861)
                      +..
T Consensus        86 ~~~   88 (92)
T 2dgv_A           86 ASG   88 (92)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            753

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=4.9e-14  Score=124.40  Aligned_cols=78  Identities=26%  Similarity=0.386  Sum_probs=72.6

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ....++|||+|||..+++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.||+..+.|++|+|++++++.
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            4457899999999999999999999999999999985   5699999999999999999999999999999999999875


Q ss_pred             h
Q 002974          439 A  439 (861)
Q Consensus       439 ~  439 (861)
                      .
T Consensus        83 ~   83 (90)
T 2dnp_A           83 K   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.51  E-value=5.5e-14  Score=128.07  Aligned_cols=83  Identities=19%  Similarity=0.308  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEeC------CCcccEEEEEeCCHHHHHHHHHHcC--ccccCccee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGD-IRTIYTA------CKHRGFVMISYYDIRAARNAMKALQ--NKPLRRRKL  344 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~-I~svkit------gksrGyAFVeF~d~e~A~kALkaLn--G~~L~Gr~L  344 (861)
                      ..+.++|||+|||.++++++|+++|++||. |..|++.      ++++|||||+|.+.++|++|++.|+  +..+.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            346899999999999999999999999998 9999863      4789999999999999999999996  589999999


Q ss_pred             eeeecCCCCCCC
Q 002974          345 DIHYSIPKDNPS  356 (861)
Q Consensus       345 ~V~~a~~k~~~~  356 (861)
                      +|.|+.++....
T Consensus        85 ~V~~a~~~~~~~   96 (109)
T 2dis_A           85 AVDWAEPEIDVD   96 (109)
T ss_dssp             EEEESCSSCSTT
T ss_pred             EEEEcCCCCCcC
Confidence            999998876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.51  E-value=1.2e-14  Score=131.72  Aligned_cols=76  Identities=18%  Similarity=0.361  Sum_probs=68.2

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCc--EEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCC----eeCCcEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGE--IREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRS----DVAGKQI  429 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGe--I~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~----~I~Gr~I  429 (861)
                      .-.+|||+|||+.+|+++|+++|++||.  |.+|++     ++++||||||+|.+.++|++|++.|||.    .|.||+|
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  556765     4677999999999999999999999997    4899999


Q ss_pred             EEEeccC
Q 002974          430 KLEASRP  436 (861)
Q Consensus       430 kVe~Akp  436 (861)
                      +|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999985

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.51  E-value=2.3e-14  Score=135.81  Aligned_cols=83  Identities=16%  Similarity=0.338  Sum_probs=75.0

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--EEe-----CCCcccEEEEEeCCHHHHHHHHHHcCcc----ccC
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--IYT-----ACKHRGFVMISYYDIRAARNAMKALQNK----PLR  340 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~s--vki-----tgksrGyAFVeF~d~e~A~kALkaLnG~----~L~  340 (861)
                      ....+.++|||+|||+++++++|+++|++||.|..  |++     ++++||||||+|.+. +|++|++.|+|.    .|.
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            34567899999999999999999999999999966  764     688999999999999 999999999999    999


Q ss_pred             cceeeeeecCCCCCC
Q 002974          341 RRKLDIHYSIPKDNP  355 (861)
Q Consensus       341 Gr~L~V~~a~~k~~~  355 (861)
                      |+.|+|.++.++...
T Consensus        97 gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           97 GKTINVEFAKGSKRD  111 (131)
T ss_dssp             GCCCCCEECCCSCCC
T ss_pred             CEEEEEEECCCCCCC
Confidence            999999999876543

>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=99.51  E-value=6.6e-14  Score=128.26  Aligned_cols=78  Identities=23%  Similarity=0.477  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          273 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~-vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      .....++|||+|||++ +++++|+++|++||.|..|++   ++|||||+|.+.++|++|++.|++..|.|+.|+|.++.+
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            3445799999999999 999999999999999999999   799999999999999999999999999999999999975


Q ss_pred             CC
Q 002974          352 KD  353 (861)
Q Consensus       352 k~  353 (861)
                      ..
T Consensus       100 ~~  101 (110)
T 1wf1_A          100 PK  101 (110)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.51  E-value=4.8e-14  Score=123.36  Aligned_cols=76  Identities=21%  Similarity=0.414  Sum_probs=70.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .+.+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ +++..+.|+.|+|+
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            4567899999999999999999999999999999985     47789999999999999999996 68888999999998


Q ss_pred             ec
Q 002974          348 YS  349 (861)
Q Consensus       348 ~a  349 (861)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=5.4e-14  Score=124.65  Aligned_cols=78  Identities=22%  Similarity=0.324  Sum_probs=72.6

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ....++|||+|||..+++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.||+..|.|++|+|++++++.
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            4557899999999999999999999999999999985   5699999999999999999999999999999999998875


Q ss_pred             h
Q 002974          439 A  439 (861)
Q Consensus       439 ~  439 (861)
                      .
T Consensus        84 ~   84 (92)
T 2dgt_A           84 R   84 (92)
T ss_dssp             S
T ss_pred             C
Confidence            3

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.51  E-value=2.4e-14  Score=127.51  Aligned_cols=82  Identities=24%  Similarity=0.342  Sum_probs=75.5

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      +....++|||+|||..+++++|+++|++||.|..+...++++|||||+|.+.++|++|++.|+|..|.|++|+|++++++
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            34456899999999999999999999999999888667888999999999999999999999999999999999999887


Q ss_pred             ch
Q 002974          438 GA  439 (861)
Q Consensus       438 ~~  439 (861)
                      ..
T Consensus        92 ~~   93 (96)
T 1fjc_A           92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.51  E-value=3e-14  Score=127.64  Aligned_cols=80  Identities=24%  Similarity=0.392  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          273 GEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       273 ~~~~srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ...+.++|||+|||. ++++++|+++|++||.|..|++   .+|||||+|.+.++|++|++.|+|..+.|++|+|.++.+
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            456799999999998 9999999999999999999998   589999999999999999999999999999999999987


Q ss_pred             CCCC
Q 002974          352 KDNP  355 (861)
Q Consensus       352 k~~~  355 (861)
                      +..+
T Consensus        83 ~~~~   86 (96)
T 2kvi_A           83 NARP   86 (96)
T ss_dssp             CCC-
T ss_pred             CCCC
Confidence            6543

>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=99.51  E-value=4.1e-14  Score=125.59  Aligned_cols=78  Identities=21%  Similarity=0.289  Sum_probs=71.4

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ....++|||+|||..+++++|+++|++||+|+.|++.    ++.+|||||+|.+.++|++|++.||+..|.|++|+|+++
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            3456899999999999999999999999999998863    445899999999999999999999999999999999998


Q ss_pred             cC
Q 002974          435 RP  436 (861)
Q Consensus       435 kp  436 (861)
                      +.
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.51  E-value=5.5e-14  Score=128.60  Aligned_cols=82  Identities=15%  Similarity=0.310  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .....++|||+|||.++++++|+++|++||.|..|++. ..+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+.++
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            34568999999999999999999999999999999973 33999999999999999999999999999999999999876


Q ss_pred             CCC
Q 002974          353 DNP  355 (861)
Q Consensus       353 ~~~  355 (861)
                      ...
T Consensus       100 ~~~  102 (109)
T 1x4g_A          100 PDM  102 (109)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.51  E-value=5.3e-14  Score=133.74  Aligned_cols=82  Identities=24%  Similarity=0.395  Sum_probs=74.9

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|++|++     +++.+|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            445689999999999999999999999999999886     345689999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus       119 a~~~~~~  125 (139)
T 1u6f_A          119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9987644

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=2.4e-14  Score=127.36  Aligned_cols=80  Identities=18%  Similarity=0.323  Sum_probs=73.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEE-EeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sV-rit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ..++|||+|||..+++++|+++|++||.|..| ++.     +..+|||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45799999999999999999999999999888 763     446899999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            987643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.50  E-value=3.1e-14  Score=123.47  Aligned_cols=71  Identities=18%  Similarity=0.385  Sum_probs=66.1

Q ss_pred             CcEEEEcCCCCCC------cHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcc-eeee
Q 002974          277 SRTLFVRNINSNV------EDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR-KLDI  346 (861)
Q Consensus       277 srtLfVgNLP~~v------TEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr-~L~V  346 (861)
                      +++|||+|||..+      ++++|+++|++||+|..|++   +++++|||||+|.+.++|++|++.|+|..+.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            4799999999999      77999999999999999986   567899999999999999999999999999999 8987


Q ss_pred             e
Q 002974          347 H  347 (861)
Q Consensus       347 ~  347 (861)
                      .
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=2.3e-14  Score=127.09  Aligned_cols=80  Identities=20%  Similarity=0.351  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCc-cccCcceeeeeecCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGD-IRTIYTACKHRGFVMISYYDIRAARNAMKALQN-KPLRRRKLDIHYSIP  351 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~-I~svkitgksrGyAFVeF~d~e~A~kALkaLnG-~~L~Gr~L~V~~a~~  351 (861)
                      ..+.++|||+|||.++++++|+++|++||. |..+.+  .++|||||+|.+.++|++|++.|+| ..+.|+.|+|.|+.+
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            456899999999999999999999999999 666666  5789999999999999999999999 999999999999988


Q ss_pred             CCCC
Q 002974          352 KDNP  355 (861)
Q Consensus       352 k~~~  355 (861)
                      +...
T Consensus        83 ~~~~   86 (93)
T 2cqh_A           83 KKLR   86 (93)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            7654

>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=99.50  E-value=3.8e-14  Score=128.48  Aligned_cols=82  Identities=16%  Similarity=0.311  Sum_probs=74.4

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCee---CCcEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDV---AGKQI  429 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I---~Gr~I  429 (861)
                      .....++|||+|||..+++++|+++|++||+|.+|++.     ++.+|||||+|.+.++|++|++.||+..+   .|++|
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            34567899999999999999999999999999999873     45689999999999999999999999988   89999


Q ss_pred             EEEeccCCch
Q 002974          430 KLEASRPGGA  439 (861)
Q Consensus       430 kVe~Akpk~~  439 (861)
                      +|.+++++..
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999998764

>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=99.50  E-value=4.3e-14  Score=145.48  Aligned_cols=129  Identities=21%  Similarity=0.323  Sum_probs=101.4

Q ss_pred             ccCCcceEEecccC-CCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          359 DANQGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       359 ~~~~~tLfVgNLp~-svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ....++|||+|||. .+++++|+++|++||.|.+|++....+|||||+|.+.++|++|++.|+|..+.|++|+|.+++++
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            34568999999999 99999999999999999999997777999999999999999999999999999999999999865


Q ss_pred             chhh-hch--------hhhh-----------h------hccccCC-CCCCCCCCcccc----CCcc-cEEEEeC-CCCCc
Q 002974          438 GARR-FMV--------QSEQ-----------E------QDDLNLC-QIPFDDLSSGQM----VSSG-VITSTCM-DNGSI  484 (861)
Q Consensus       438 ~~rr-l~q--------q~eq-----------~------q~E~~vg-kNLp~s~tee~L----s~fG-~I~Sv~~-enG~s  484 (861)
                      .... ...        ....           .      .....++ +||+.++++++|    ..|| .|..++. ...+.
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            3111 000        0000           0      0011233 899999999999    8999 9999984 44444


Q ss_pred             cee
Q 002974          485 QVL  487 (861)
Q Consensus       485 rGF  487 (861)
                      .+|
T Consensus       191 ~af  193 (229)
T 2adc_A          191 MAL  193 (229)
T ss_dssp             CEE
T ss_pred             EEE
Confidence            555

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=4.9e-14  Score=126.91  Aligned_cols=83  Identities=22%  Similarity=0.442  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ...+.++|||+|||.++++++|+++|++|+.|..++.  +++++|||||+|.+.++|++|++.|++..|.|+.|+|.|+.
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            4567899999999999999999999999988777763  67889999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 002974          351 PKDNP  355 (861)
Q Consensus       351 ~k~~~  355 (861)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87654

>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=99.50  E-value=3.3e-14  Score=130.98  Aligned_cols=82  Identities=18%  Similarity=0.272  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHH---HHhhcCCCEEEEEeC--------CCcccEEEEEeCCHHHHHHHHHHcCccccCc
Q 002974          273 GEHPSRTLFVRNINSNVEDSELK---ALFEQFGDIRTIYTA--------CKHRGFVMISYYDIRAARNAMKALQNKPLRR  341 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~---elFsqfG~I~svkit--------gksrGyAFVeF~d~e~A~kALkaLnG~~L~G  341 (861)
                      .....++|||+|||+++++++|+   ++|++||+|..|++.        ++++|||||+|.+.++|++|++.|||..|.|
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            44568999999999999999999   999999999999851        2456999999999999999999999999999


Q ss_pred             ceeeeeecCCCCC
Q 002974          342 RKLDIHYSIPKDN  354 (861)
Q Consensus       342 r~L~V~~a~~k~~  354 (861)
                      +.|+|.|+.++..
T Consensus        91 r~l~V~~a~~k~~  103 (111)
T 2cpi_A           91 RTLKASLGTTKYC  103 (111)
T ss_dssp             EEEEEESCCCCSC
T ss_pred             EEEEEEecccccc
Confidence            9999999988753

>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=99.50  E-value=4.5e-14  Score=123.69  Aligned_cols=76  Identities=22%  Similarity=0.454  Sum_probs=71.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|+ .|+|..+.|+.|+|.++.
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            4689999999999999999999999999999985     5778999999999999999999 899999999999999997


Q ss_pred             CC
Q 002974          351 PK  352 (861)
Q Consensus       351 ~k  352 (861)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.50  E-value=2.5e-14  Score=141.75  Aligned_cols=125  Identities=16%  Similarity=0.177  Sum_probs=98.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhccc----C-------cEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIY----G-------EIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskf----G-------eI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                      ..++|||+|||.++++++|+++|++|    |       .|..+++ +.++|||||+|.+.++|++|+ .|||..|.|++|
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            35799999999999999999999999    5       6777775 567999999999999999999 799999999999


Q ss_pred             EEEeccCCchhhhc-hhh----------hhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          430 KLEASRPGGARRFM-VQS----------EQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       430 kVe~Akpk~~rrl~-qq~----------eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      +|.++.+....... ...          ........+. +||+.++++++|    .+||.|..++    .++|.++||
T Consensus        81 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~  158 (198)
T 2yh0_A           81 KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY  158 (198)
T ss_dssp             EEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEE
T ss_pred             EEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceE
Confidence            99998775322110 000          0001112233 999999999999    8999999887    358888887

>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=99.50  E-value=1.2e-13  Score=124.82  Aligned_cols=82  Identities=17%  Similarity=0.318  Sum_probs=74.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++  ++..|.|+.|+|
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            35567899999999999999999999999999999985     47889999999999999999998  478899999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqg_A           88 KLPNSKQSQ   96 (103)
T ss_dssp             ECCCTTCCC
T ss_pred             EecCCCCcC
Confidence            999887654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=1.2e-13  Score=123.85  Aligned_cols=80  Identities=18%  Similarity=0.313  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+||  ++++++|+++|++||.|..|++ .+++|||||+|.+.++|++|++.|++..|.|+.|+|.|+.++
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            4557899999996  8999999999999999999998 688999999999999999999999999999999999999876


Q ss_pred             CCC
Q 002974          353 DNP  355 (861)
Q Consensus       353 ~~~  355 (861)
                      ...
T Consensus        88 ~~~   90 (97)
T 1x5p_A           88 PML   90 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.50  E-value=7e-14  Score=126.04  Aligned_cols=77  Identities=25%  Similarity=0.396  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          273 GEHPSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       273 ~~~~srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ...++++|||+|||. ++++++|+++|++||.|..|++   .+|||||+|.+.++|++|++.|+|..+.|++|+|.++.+
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            456799999999998 9999999999999999999998   489999999999999999999999999999999999976


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      +
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.50  E-value=5.2e-14  Score=129.43  Aligned_cols=81  Identities=28%  Similarity=0.370  Sum_probs=74.0

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      .....++|||+|||..+++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|+
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            3455789999999999999999999999999999886     34568999999999999999999999999999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      +++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            999874

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.50  E-value=8.9e-14  Score=131.57  Aligned_cols=77  Identities=29%  Similarity=0.495  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4567899999999999999999999999999999986     46789999999999999999999999999999999998


Q ss_pred             ec
Q 002974          348 YS  349 (861)
Q Consensus       348 ~a  349 (861)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            85

>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=99.50  E-value=5.6e-14  Score=122.20  Aligned_cols=77  Identities=30%  Similarity=0.436  Sum_probs=71.2

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHh-CCCeeCCcEEEEEecc
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL-NRSDVAGKQIKLEASR  435 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~L-NG~~I~Gr~IkVe~Ak  435 (861)
                      .+...++|||+|||..+++++|+++|++||.|..|++. ..+|||||+|.+.++|++|++.| ++..+.|++|+|+|++
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~-~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEE-CCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            34567899999999999999999999999999999975 36899999999999999999999 9999999999999985

>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=99.50  E-value=6.1e-14  Score=127.08  Aligned_cols=80  Identities=21%  Similarity=0.337  Sum_probs=73.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC------CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT------QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit------gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ....++|||+|||..+++++|+++|++|| |..|++.      ++.+|||||+|.+.++|++|| .||+..|.|++|+|+
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 9999873      566899999999999999999 899999999999999


Q ss_pred             eccCCchh
Q 002974          433 ASRPGGAR  440 (861)
Q Consensus       433 ~Akpk~~r  440 (861)
                      +++++..+
T Consensus        90 ~a~~~~~~   97 (104)
T 1wi8_A           90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99987643

>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=5.3e-14  Score=129.45  Aligned_cols=79  Identities=19%  Similarity=0.192  Sum_probs=71.5

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCC--eeCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS--DVAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~--~I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||+.+++++|+++|++||+|.+|.+.. .||||||+|.+.++|++|++.|++.  .|.|++|+|++++++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            4567999999999999999999999999999998754 5899999999999999999998765  599999999999987


Q ss_pred             ch
Q 002974          438 GA  439 (861)
Q Consensus       438 ~~  439 (861)
                      ..
T Consensus        92 ~~   93 (104)
T 1wex_A           92 RI   93 (104)
T ss_dssp             SC
T ss_pred             cc
Confidence            53

>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=3.7e-14  Score=130.41  Aligned_cols=78  Identities=19%  Similarity=0.232  Sum_probs=70.9

Q ss_pred             cCCcceEEecccC-CCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCC--eeCCcEEEEEeccC
Q 002974          360 ANQGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS--DVAGKQIKLEASRP  436 (861)
Q Consensus       360 ~~~~tLfVgNLp~-svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~--~I~Gr~IkVe~Akp  436 (861)
                      ...++|||+|||+ .+++++|+++|++||+|.+|++. +.++||||+|.+.++|++|++.|++.  .|.|++|+|.+++.
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 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEE-cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            3568999999999 99999999999999999999986 46799999999999999999999864  59999999999986


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      +.
T Consensus        92 ~~   93 (102)
T 1x4d_A           92 YK   93 (102)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>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=99.50  E-value=3e-14  Score=128.71  Aligned_cols=79  Identities=19%  Similarity=0.396  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      .....++|||+|||.++++++|+++|++|| |..|++      +++++|||||+|.+.++|++|+ .|+|..|.|+.|+|
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            445689999999999999999999999999 999985      4667999999999999999999 89999999999999


Q ss_pred             eecCCCC
Q 002974          347 HYSIPKD  353 (861)
Q Consensus       347 ~~a~~k~  353 (861)
                      .++.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9998754

>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=99.50  E-value=7.2e-14  Score=135.73  Aligned_cols=82  Identities=26%  Similarity=0.394  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|++..|.|+.|+|.
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            4457899999999999999999999999999999986     57789999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 002974          348 YSIPKDN  354 (861)
Q Consensus       348 ~a~~k~~  354 (861)
                      |+.++..
T Consensus       115 ~a~~~~~  121 (156)
T 1h2v_Z          115 WDAGFKE  121 (156)
T ss_dssp             EESCCCT
T ss_pred             ECCCCCC
Confidence            9987544

>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=99.50  E-value=6.3e-14  Score=126.91  Aligned_cols=79  Identities=27%  Similarity=0.493  Sum_probs=73.2

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ...++|||+|||..+++++|+++|++||.|..|++.   ++||||+|.+.++|++|++.||+..|.|++|+|++++++..
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            356899999999999999999999999999999975   67999999999999999999999999999999999998764


Q ss_pred             hh
Q 002974          440 RR  441 (861)
Q Consensus       440 rr  441 (861)
                      +.
T Consensus        86 ~~   87 (103)
T 2dgu_A           86 KR   87 (103)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=6.7e-14  Score=123.62  Aligned_cols=79  Identities=11%  Similarity=0.240  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .....++|||+|||.++++++|+++|++| .|..|++    +++++|||||+|.+.++|++|++ |++..|.|+.|.|.+
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            45568999999999999999999999999 8988875    57789999999999999999999 999999999999999


Q ss_pred             cCCCC
Q 002974          349 SIPKD  353 (861)
Q Consensus       349 a~~k~  353 (861)
                      +.++.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>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=99.50  E-value=1.1e-14  Score=128.97  Aligned_cols=77  Identities=16%  Similarity=0.168  Sum_probs=65.8

Q ss_pred             cceEEecccCCCcHHHHHHHhcccC--cEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYG--EIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfG--eI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      .+|||+|||.++++++|+++|++||  .|.+|++     +++++|||||+|.+.++|++|++.|||..+.|++|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  8988875     56778999999999999999999999999999999999998


Q ss_pred             CCch
Q 002974          436 PGGA  439 (861)
Q Consensus       436 pk~~  439 (861)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            8653

>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=99.50  E-value=5.5e-14  Score=128.60  Aligned_cols=80  Identities=20%  Similarity=0.303  Sum_probs=74.1

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ...++|||+|||..+++++|+++|++||.|..|++... +|||||+|.+.++|++|++.|+|..|.|++|+|.+++++..
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            45689999999999999999999999999999998643 89999999999999999999999999999999999998764


Q ss_pred             h
Q 002974          440 R  440 (861)
Q Consensus       440 r  440 (861)
                      .
T Consensus       102 ~  102 (109)
T 1x4g_A          102 M  102 (109)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.50  E-value=3.8e-14  Score=130.49  Aligned_cols=80  Identities=26%  Similarity=0.524  Sum_probs=73.2

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++.   +|||||+|.+.++|++|++.|+|..+.|+.|+|.|+.+
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            356678999999999999999999999999999999984   89999999999999999999999999999999999987


Q ss_pred             CCC
Q 002974          352 KDN  354 (861)
Q Consensus       352 k~~  354 (861)
                      +..
T Consensus       103 ~~~  105 (108)
T 2jvo_A          103 PAK  105 (108)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            644

>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=99.50  E-value=3.1e-14  Score=127.31  Aligned_cols=80  Identities=19%  Similarity=0.244  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .....++|||+|||.++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.|+|..|.|+.|+|.
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            345679999999999999999999999999886443     257789999999999999999999999999999999999


Q ss_pred             ecCCC
Q 002974          348 YSIPK  352 (861)
Q Consensus       348 ~a~~k  352 (861)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98753

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.50  E-value=3.3e-14  Score=132.52  Aligned_cols=79  Identities=11%  Similarity=0.100  Sum_probs=72.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCC-CEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFG-DIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG-~I~svki-tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ....++|||+|||+++++++|+++|++|| +|..+++ ..+++|||||+|.+.++|++|++.|||..|.|+.|+|.++..
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            34578999999999999999999999999 8999997 467899999999999999999999999999999999999864


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      .
T Consensus       105 ~  105 (111)
T 2jvr_A          105 P  105 (111)
T ss_dssp             -
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=99.50  E-value=2.5e-14  Score=128.72  Aligned_cols=76  Identities=14%  Similarity=0.224  Sum_probs=71.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ..++|||+|||..+++++|+++|++||.|++|++. +.+|||||+|.+.++|++|++.|||..+.|++|+|++++++
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            46799999999999999999999999999999976 67999999999999999999999999999999999999874

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.49  E-value=3.9e-14  Score=130.41  Aligned_cols=81  Identities=23%  Similarity=0.421  Sum_probs=73.2

Q ss_pred             CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       357 ~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ......++|||+|||..+++++|+++|++||.|+.|++.   +|||||+|.+.++|++|++.|||..+.|++|+|+++++
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            344567899999999999999999999999999999986   89999999999999999999999999999999999998


Q ss_pred             Cchh
Q 002974          437 GGAR  440 (861)
Q Consensus       437 k~~r  440 (861)
                      +..+
T Consensus       103 ~~~r  106 (108)
T 2jvo_A          103 PAKR  106 (108)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7643

>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=99.49  E-value=6.3e-14  Score=133.21  Aligned_cols=80  Identities=21%  Similarity=0.383  Sum_probs=74.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|+.|++.     ++.+|||||+|.+.++|++|++.|||..|.|++|+|++
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            3456899999999999999999999999999999873     56789999999999999999999999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      ++++.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            99875

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=4.3e-14  Score=126.66  Aligned_cols=80  Identities=16%  Similarity=0.198  Sum_probs=71.8

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ....++|||+|||..+++++|+++|++||.|....+.++.+|||||+|.+.++|++|++.|||..|.|++|+|++++++.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            34568999999999999999999999999996222356789999999999999999999999999999999999999875

>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=99.49  E-value=1.6e-13  Score=126.17  Aligned_cols=80  Identities=16%  Similarity=0.316  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCcccc--------C
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPL--------R  340 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L--------~  340 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..|        .
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            4557899999999999999999999999999999985    567899999999999999999999999999        5


Q ss_pred             cceeeeeecCCC
Q 002974          341 RRKLDIHYSIPK  352 (861)
Q Consensus       341 Gr~L~V~~a~~k  352 (861)
                      +++|.|.|+.++
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            778999998754

>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=99.49  E-value=7.9e-14  Score=128.41  Aligned_cols=81  Identities=16%  Similarity=0.304  Sum_probs=73.3

Q ss_pred             cccCCcceEEecccCCCcHHHHH---HHhcccCcEEEEEeCC--------CCccEEEEEECCHHHHHHHHHHhCCCeeCC
Q 002974          358 KDANQGTLVVFNLDSSVSTEELH---QIFGIYGEIREIRDTQ--------HKHNHKFIEFYDIRAAETALRTLNRSDVAG  426 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLr---elFskfGeI~sVritg--------ksKGfAFVeF~d~eaA~kAL~~LNG~~I~G  426 (861)
                      +....++|||+|||+.+++++|+   ++|++||+|.+|++..        +.+|||||+|.+.++|++|++.|||..|.|
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            34457899999999999999999   9999999999998732        345899999999999999999999999999


Q ss_pred             cEEEEEeccCCc
Q 002974          427 KQIKLEASRPGG  438 (861)
Q Consensus       427 r~IkVe~Akpk~  438 (861)
                      ++|+|++++++.
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            999999999875

>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=8.2e-14  Score=127.57  Aligned_cols=78  Identities=18%  Similarity=0.238  Sum_probs=72.5

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCC-----cEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG-----KQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G-----r~IkVe~A  434 (861)
                      ....+|||+|||+++++++|+++|++||+|+.|++...  |||||+|.+.++|++||+.||+..|.|     ++|+|+++
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            34689999999999999999999999999999998644  999999999999999999999999999     99999999


Q ss_pred             cCCch
Q 002974          435 RPGGA  439 (861)
Q Consensus       435 kpk~~  439 (861)
                      +++..
T Consensus        91 ~~~~~   95 (108)
T 1x4c_A           91 GPRSP   95 (108)
T ss_dssp             SCCSC
T ss_pred             CCCCC
Confidence            98763

>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=99.49  E-value=1e-13  Score=125.01  Aligned_cols=77  Identities=30%  Similarity=0.401  Sum_probs=72.0

Q ss_pred             ccCCcceEEecccC-CCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          359 DANQGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       359 ~~~~~tLfVgNLp~-svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ....++|||+|||. .+++++|+++|++||.|.+|++   .+|||||+|.+.++|++|++.|||..+.|++|+|++++++
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 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE---CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            34578999999998 9999999999999999999998   4899999999999999999999999999999999999876


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        96 ~   96 (97)
T 2xnq_A           96 A   96 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.6e-14  Score=129.74  Aligned_cols=82  Identities=22%  Similarity=0.374  Sum_probs=74.3

Q ss_pred             CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       357 ~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ......++|||+|||..+++++|+++|++||+|+.|++.   +..+|||||+|.+.++|++|++.|||..|.|++|+|++
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            344567899999999999999999999999999999874   34589999999999999999999999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      ++++.
T Consensus       104 a~~~~  108 (109)
T 2err_A          104 ATARV  108 (109)
T ss_dssp             CCCSC
T ss_pred             CCCCc
Confidence            98863

>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=99.49  E-value=3.7e-14  Score=134.02  Aligned_cols=81  Identities=17%  Similarity=0.210  Sum_probs=73.0

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCC--CeeCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR--SDVAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG--~~I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||+++++++|+++|++||+|++|++.. .||||||+|.+.++|++|++.|++  ..|.|++|+|.+++++
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 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEG-GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCC
Confidence            3467999999999999999999999999999999753 589999999999999999999984  6899999999999987


Q ss_pred             chhh
Q 002974          438 GARR  441 (861)
Q Consensus       438 ~~rr  441 (861)
                      ..+.
T Consensus       108 ~~~~  111 (119)
T 2ad9_A          108 ELKT  111 (119)
T ss_dssp             SCCC
T ss_pred             CCCc
Confidence            6443

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.49  E-value=6.4e-14  Score=129.58  Aligned_cols=77  Identities=17%  Similarity=0.344  Sum_probs=70.6

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||.++++++|+++|++||+|++|++.     ++.+|||||+|.+.++|++|++.|||..|.|++|+|++
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            4456899999999999999999999999999999873     45689999999999999999999999999999999999


Q ss_pred             cc
Q 002974          434 SR  435 (861)
Q Consensus       434 Ak  435 (861)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            75

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.49  E-value=2e-13  Score=127.68  Aligned_cols=83  Identities=24%  Similarity=0.414  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..+.|+.|+|.+
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            4567899999999999999999999999999999986    466899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++...
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=1.4e-13  Score=123.57  Aligned_cols=78  Identities=23%  Similarity=0.342  Sum_probs=72.3

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhccc--CcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIY--GEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskf--GeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ....++|||+|||..+++++|+++|++|  |.|..|++.   ++||||+|.+.++|++|++.||+..|.|++|+|+++++
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            3456899999999999999999999999  999999863   78999999999999999999999999999999999998


Q ss_pred             Cch
Q 002974          437 GGA  439 (861)
Q Consensus       437 k~~  439 (861)
                      +..
T Consensus        89 ~~~   91 (99)
T 2cpd_A           89 VDK   91 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            763

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.49  E-value=2.4e-14  Score=128.87  Aligned_cols=77  Identities=29%  Similarity=0.426  Sum_probs=72.2

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ++|||+|||.++++++|+++|++||+|..|++...++|||||+|.+.++|++|++.|++..+.|++|+|++++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            47999999999999999999999999999987655799999999999999999999999999999999999998763

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.49  E-value=7e-14  Score=128.64  Aligned_cols=82  Identities=16%  Similarity=0.395  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.+ +..+.|+.|+|.
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            4556899999999999999999999999999999986     4778999999999999999999976 599999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++...
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99877553

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=2.2e-14  Score=132.11  Aligned_cols=80  Identities=21%  Similarity=0.438  Sum_probs=73.1

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||.|..|++.     ++.+|||||+|.+.++|++|+ .||+..|.|+.|+|+++
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            346799999999999999999999999999999874     567899999999999999999 89999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus       102 ~~~~~~  107 (114)
T 2cq4_A          102 QAEKNR  107 (114)
T ss_dssp             HHHHHH
T ss_pred             CCCccC
Confidence            876543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.49  E-value=1.7e-14  Score=130.61  Aligned_cols=77  Identities=13%  Similarity=0.186  Sum_probs=71.9

Q ss_pred             CcceEEecccC------CCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCC-cEE
Q 002974          362 QGTLVVFNLDS------SVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAG-KQI  429 (861)
Q Consensus       362 ~~tLfVgNLp~------svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~G-r~I  429 (861)
                      .++|||+|||.      ++++++|+++|++||.|.+|++.     ++++|||||+|.+.++|++|++.|||..|.| ++|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            57899999999      99999999999999999999863     6789999999999999999999999999999 999


Q ss_pred             EEEeccCCc
Q 002974          430 KLEASRPGG  438 (861)
Q Consensus       430 kVe~Akpk~  438 (861)
                      +|.++.++.
T Consensus        86 ~V~~a~~~~   94 (100)
T 3ns6_A           86 FLYTMKDVE   94 (100)
T ss_dssp             EEEESHHHH
T ss_pred             EEEECchhh
Confidence            999998754

>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=99.49  E-value=1e-13  Score=133.74  Aligned_cols=80  Identities=23%  Similarity=0.427  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..|++...++|||||+|.+.++|++|++.|+|..|.|++|+|.|+.++
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            45678999999999999999999999999999999986668999999999999999999999999999999999999875

>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=99.49  E-value=8.9e-14  Score=146.35  Aligned_cols=80  Identities=21%  Similarity=0.417  Sum_probs=73.1

Q ss_pred             ccCCcceEEecccCCCcHHHHH----HHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          359 DANQGTLVVFNLDSSVSTEELH----QIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLr----elFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ....++|||+|||.++++++|+    ++|++||.|++|++  +++.+|||||+|.+.++|++|++.|||..|.|+.|+|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   85 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   85 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            3457899999999999999977    89999999999987  55778999999999999999999999999999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      +++.+.
T Consensus        86 ~a~~~~   91 (282)
T 3pgw_A           86 YAKTDS   91 (282)
T ss_pred             EeccCc
Confidence            997755

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=2.6e-14  Score=128.96  Aligned_cols=82  Identities=22%  Similarity=0.371  Sum_probs=74.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            44689999999999999999999999999999876     3455899999999999999999999999999999999999


Q ss_pred             cCCchhh
Q 002974          435 RPGGARR  441 (861)
Q Consensus       435 kpk~~rr  441 (861)
                      .++..+.
T Consensus        86 ~~~~~~~   92 (104)
T 1p1t_A           86 ASEKNKE   92 (104)
T ss_dssp             TCTTHHH
T ss_pred             CCccchh
Confidence            9887544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=7.9e-14  Score=128.74  Aligned_cols=81  Identities=22%  Similarity=0.294  Sum_probs=73.5

Q ss_pred             CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Q 002974          357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL  431 (861)
Q Consensus       357 ~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkV  431 (861)
                      ..+...++|||+|||..+++++|+++|++||+|+.|++.     ++.+|||||+|.+.++|++|++.|++ .|.|++|+|
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            345567899999999999999999999999999999873     45689999999999999999999998 899999999


Q ss_pred             EeccCCc
Q 002974          432 EASRPGG  438 (861)
Q Consensus       432 e~Akpk~  438 (861)
                      ++++++.
T Consensus        91 ~~a~~~~   97 (116)
T 2cqd_A           91 NLAYLGA   97 (116)
T ss_dssp             EESTTTC
T ss_pred             EEcccCC
Confidence            9998764

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.48  E-value=6.6e-14  Score=125.75  Aligned_cols=79  Identities=24%  Similarity=0.335  Sum_probs=73.5

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ....++|||+|||..+++++|+++|++||+|+.|++. +.+|||||+|.+.++|++|++.||+..|.|++|+|++++++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe-cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            3456899999999999999999999999999999975 468999999999999999999999999999999999999875

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.48  E-value=8.5e-14  Score=125.03  Aligned_cols=77  Identities=22%  Similarity=0.332  Sum_probs=70.5

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEE--------EEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~s--------Vri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                      ....++|||+|||..+++++|+++|++||.|.+        |++     +++.+|||||+|.+.++|++|++.|||..+.
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            445789999999999999999999999999988        765     3556899999999999999999999999999


Q ss_pred             CcEEEEEecc
Q 002974          426 GKQIKLEASR  435 (861)
Q Consensus       426 Gr~IkVe~Ak  435 (861)
                      |++|+|++|+
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

>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=99.48  E-value=1.2e-13  Score=133.80  Aligned_cols=83  Identities=25%  Similarity=0.464  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.
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            3456899999999999999999999999999999985     57799999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++..+
T Consensus       146 ~a~~~~~~  153 (158)
T 2kn4_A          146 MARYGRPP  153 (158)
T ss_dssp             EECCSSCC
T ss_pred             ECCCCCCC
Confidence            99876544

>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=99.48  E-value=8.2e-14  Score=122.01  Aligned_cols=76  Identities=29%  Similarity=0.431  Sum_probs=70.4

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+ .||+..+.|++|+|++++
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            3578999999999999999999999999999876     4556899999999999999999 899999999999999998


Q ss_pred             CC
Q 002974          436 PG  437 (861)
Q Consensus       436 pk  437 (861)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            75

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=6.2e-14  Score=128.69  Aligned_cols=83  Identities=20%  Similarity=0.350  Sum_probs=74.4

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEE--------EEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIR--------EIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~--------sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      .....++|||+|||..+++++|+++|++||.|.        .|++     +++.+|||||+|.+.++|++|++.||+..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999998        5765     345689999999999999999999999999


Q ss_pred             CCcEEEEEeccCCchh
Q 002974          425 AGKQIKLEASRPGGAR  440 (861)
Q Consensus       425 ~Gr~IkVe~Akpk~~r  440 (861)
                      .|++|+|++++++..+
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999987643

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=1.4e-13  Score=126.36  Aligned_cols=80  Identities=16%  Similarity=0.177  Sum_probs=72.5

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ....++|||+|||..+++++|+++|++||+|++|++    .++.++||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            345689999999999999999999999999999876    3345899999999999999999999999999999999999


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      +...
T Consensus        92 ~~~~   95 (114)
T 2do0_A           92 ERAL   95 (114)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            8654

>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=99.48  E-value=1.1e-13  Score=125.90  Aligned_cols=81  Identities=12%  Similarity=0.201  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE-EEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT-IYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~s-vki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .....++|||+|||+++++++|+++|++||.|.. |++    +++++|||||+|.+.++|++|++. ++..+.||.|.|.
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            4456899999999999999999999999999987 764    678999999999999999999986 9999999999999


Q ss_pred             ecCCCCC
Q 002974          348 YSIPKDN  354 (861)
Q Consensus       348 ~a~~k~~  354 (861)
                      ++.+++.
T Consensus        90 ~~~~~~~   96 (104)
T 1wg5_A           90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHH
Confidence            9876543

>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=99.48  E-value=2.3e-14  Score=127.20  Aligned_cols=77  Identities=18%  Similarity=0.226  Sum_probs=68.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..+.++|||+|||+++++++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|++..|.|++|+|.+
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            345799999999999999999999999999865442     567899999999999999999999999999999999998


Q ss_pred             cC
Q 002974          349 SI  350 (861)
Q Consensus       349 a~  350 (861)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>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=99.48  E-value=6.1e-14  Score=130.60  Aligned_cols=79  Identities=27%  Similarity=0.424  Sum_probs=73.0

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...++|||+|||.++++++|+++|++||.|+.|++    +++.+|||||+|.+.++|++|++.|||..|.|++|+|++++
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            34679999999999999999999999999999887    35568999999999999999999999999999999999998


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ++.
T Consensus        85 ~~~   87 (116)
T 2fy1_A           85 KPS   87 (116)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            765

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.48  E-value=3.3e-14  Score=136.07  Aligned_cols=86  Identities=26%  Similarity=0.461  Sum_probs=78.2

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCccee
Q 002974          270 HPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  344 (861)
Q Consensus       270 ~~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L  344 (861)
                      .+....+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|
T Consensus        40 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           40 PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3445667899999999999999999999999999999985     56789999999999999999999999999999999


Q ss_pred             eeeecCCCCCC
Q 002974          345 DIHYSIPKDNP  355 (861)
Q Consensus       345 ~V~~a~~k~~~  355 (861)
                      +|.|+.++..+
T Consensus       120 ~V~~a~~~~~~  130 (135)
T 2lea_A          120 RVQMARYGRPP  130 (135)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEECCCCCCC
Confidence            99999876554

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=6.3e-14  Score=128.41  Aligned_cols=78  Identities=13%  Similarity=0.312  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .+.+.++|||+|||+++|+++|+++|++||+|..|++    .+.++|||||+|.+.++|++|++ +++..+.|+.|.|.+
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            3456899999999999999999999999999999985    36789999999999999999998 999999999999998


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      +..
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.48  E-value=1.3e-13  Score=124.67  Aligned_cols=80  Identities=19%  Similarity=0.260  Sum_probs=72.2

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++|| |..|++     +++.+|||||+|.+.++|++|+ .||+..|.|++|+|++
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            44578999999999999999999999997 999876     3556899999999999999999 8999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9987643

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=6.2e-14  Score=126.67  Aligned_cols=82  Identities=22%  Similarity=0.254  Sum_probs=74.8

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcc-cCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCe-eCCcEEEEEe
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGI-YGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSD-VAGKQIKLEA  433 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFsk-fGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~-I~Gr~IkVe~  433 (861)
                      ....+|||+|||..+++++|+++|++ ||.|.+|++    +++++|||||+|.+.++|++|++.|++.. |.|++|+|++
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            45689999999999999999999999 999999887    45578999999999999999999999999 9999999999


Q ss_pred             ccCCchhh
Q 002974          434 SRPGGARR  441 (861)
Q Consensus       434 Akpk~~rr  441 (861)
                      +.++..+.
T Consensus        87 a~~~~~~~   94 (104)
T 2dhg_A           87 AIPKASRV   94 (104)
T ss_dssp             CCCCCSCC
T ss_pred             ccCCCcCC
Confidence            98876443

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=7.9e-14  Score=125.50  Aligned_cols=82  Identities=29%  Similarity=0.450  Sum_probs=72.9

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .....++|||+|||..+++++|+++|++||.|.-++. .++.+|||||+|.+.++|++|++.||+..|.|++|+|+++++
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            3456789999999999999999999999999854433 556799999999999999999999999999999999999998


Q ss_pred             Cch
Q 002974          437 GGA  439 (861)
Q Consensus       437 k~~  439 (861)
                      +..
T Consensus        91 ~~~   93 (101)
T 2fc9_A           91 RGS   93 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.4e-13  Score=123.99  Aligned_cols=84  Identities=21%  Similarity=0.370  Sum_probs=74.8

Q ss_pred             CcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       357 ~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ......++|||+|||..+++++|+++|+.|+.|.-+..  +++.+|||||+|.+.++|++|++.||+..|.|++|+|+++
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            34556789999999999999999999999987776653  5567899999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus        90 ~~~~~~   95 (102)
T 2fc8_A           90 KPKGEG   95 (102)
T ss_dssp             CCCCSS
T ss_pred             cCCCCC
Confidence            987644

>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=99.48  E-value=7.3e-14  Score=130.62  Aligned_cols=82  Identities=24%  Similarity=0.387  Sum_probs=74.5

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||.|..|.+     ++.++|||||+|.+.++|++|++.||+..|.|+.|+|++
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            345679999999999999999999999999999987     445589999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      +.++..+
T Consensus        99 a~~~~~~  105 (126)
T 3ex7_B           99 CFVRGPP  105 (126)
T ss_dssp             SEESSSC
T ss_pred             ecCCCCC
Confidence            9876643

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.48  E-value=5.5e-14  Score=138.08  Aligned_cols=78  Identities=14%  Similarity=0.267  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG--~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...++|||+|||+++++++|+++|++||  .|..|++     +++++|||||+|.+.++|++||+.|+|..|.|+.|+|.
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            3578999999999999999999999999  9999985     68899999999999999999999999999999999999


Q ss_pred             ecCCC
Q 002974          348 YSIPK  352 (861)
Q Consensus       348 ~a~~k  352 (861)
                      ++.++
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            99753

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.47  E-value=1.8e-14  Score=134.35  Aligned_cols=78  Identities=22%  Similarity=0.377  Sum_probs=71.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|+ .|||..|.|+.|+|+++
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            34679999999999999999999999999999876     4567999999999999999999 79999999999999999


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      ++..
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8754

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=9.6e-14  Score=132.25  Aligned_cols=82  Identities=15%  Similarity=0.267  Sum_probs=73.9

Q ss_pred             cCCcceEEecccCCCcHHHHH----HHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          360 ANQGTLVVFNLDSSVSTEELH----QIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLr----elFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ...++|||+|||+.+++++|+    ++|++||+|.+|.+  +++++|||||+|.+.++|.+|++.|||..|.|++|+|.|
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            346789999999999999876    69999999999887  357899999999999999999999999999999999999


Q ss_pred             ccCCchhh
Q 002974          434 SRPGGARR  441 (861)
Q Consensus       434 Akpk~~rr  441 (861)
                      ++.+....
T Consensus       107 a~~~~~~~  114 (127)
T 2a3j_A          107 SETPQSQV  114 (127)
T ss_dssp             CCCCCHHH
T ss_pred             ccCcchhc
Confidence            99876444

>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=99.47  E-value=1.3e-13  Score=133.95  Aligned_cols=81  Identities=23%  Similarity=0.318  Sum_probs=74.4

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||+|+.|++     ++..++||||+|.+.++|++||+.||+..|.|++|+|+++
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            45689999999999999999999999999999987     4567899999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus       117 ~~~~~~  122 (156)
T 1h2v_Z          117 AGFKEG  122 (156)
T ss_dssp             SCCCTT
T ss_pred             CCCCCc
Confidence            886543

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.47  E-value=7.6e-14  Score=128.97  Aligned_cols=77  Identities=19%  Similarity=0.259  Sum_probs=72.2

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+|||..+++++|+++|++||.|..|++. ..++||||+|.+.++|++|++.|||..|.|++|+|+|+....
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe-CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            45799999999999999999999999999999975 588999999999999999999999999999999999998654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.47  E-value=1e-13  Score=126.44  Aligned_cols=80  Identities=16%  Similarity=0.202  Sum_probs=72.3

Q ss_pred             ccCCcceEEecccCCC------cHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCc-E
Q 002974          359 DANQGTLVVFNLDSSV------STEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGK-Q  428 (861)
Q Consensus       359 ~~~~~tLfVgNLp~sv------TeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr-~  428 (861)
                      ....++|||+|||..+      ++++|+++|++||.|..|++.   ++++|||||+|.+.++|++|++.|||..|.|+ +
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      789999999999999999874   46689999999999999999999999999998 9


Q ss_pred             EEEEeccCCc
Q 002974          429 IKLEASRPGG  438 (861)
Q Consensus       429 IkVe~Akpk~  438 (861)
                      |+|.++....
T Consensus        92 l~V~~a~~~~  101 (105)
T 2nlw_A           92 FRVNLFTDFD  101 (105)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEEcchHh
Confidence            9999998653

>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=99.47  E-value=4.8e-14  Score=125.08  Aligned_cols=79  Identities=24%  Similarity=0.311  Sum_probs=71.3

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCc-EEEEEeCCCCccEEEEEECCHHHHHHHHHHhCC-CeeCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDTQHKHNHKFIEFYDIRAAETALRTLNR-SDVAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGe-I~sVritgksKGfAFVeF~d~eaA~kAL~~LNG-~~I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||..+++++|+++|++||. |..+.+  .++|||||+|.+.++|++|++.||| ..+.|++|+|++++++
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 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL--LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE--EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE--cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            35679999999999999999999999999 665655  4689999999999999999999999 9999999999999987


Q ss_pred             chh
Q 002974          438 GAR  440 (861)
Q Consensus       438 ~~r  440 (861)
                      ..+
T Consensus        84 ~~~   86 (93)
T 2cqh_A           84 KLR   86 (93)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            644

>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=99.47  E-value=1.5e-13  Score=124.77  Aligned_cols=76  Identities=20%  Similarity=0.361  Sum_probs=70.5

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...++|||+|||..+++++|+++|++||.|+.|++    +++.+|||||+|.+.++|++|++.||+..|.|++|+|+++.
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            45689999999999999999999999999999876    34568999999999999999999999999999999999985

>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=99.47  E-value=7.6e-14  Score=124.34  Aligned_cols=81  Identities=21%  Similarity=0.399  Sum_probs=73.9

Q ss_pred             cCCcceEEecccCCCcHHHHH----HHhcccCcEEEEEeC--CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          360 ANQGTLVVFNLDSSVSTEELH----QIFGIYGEIREIRDT--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLr----elFskfGeI~sVrit--gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ...++|||+|||..+++++|+    ++|++||.|..|++.  +..+|||||+|.+.++|++|++.|||..+.|++|+|++
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            356799999999999999999    999999999999874  35689999999999999999999999999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++...
T Consensus        86 a~~~~~~   92 (97)
T 1nu4_A           86 AKTDSDI   92 (97)
T ss_dssp             CSSCCTH
T ss_pred             ccCCCcc
Confidence            9987643

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=7.3e-14  Score=125.08  Aligned_cols=79  Identities=23%  Similarity=0.338  Sum_probs=72.5

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEE-EEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcE----E
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIR-EIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ----I  429 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~-sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~----I  429 (861)
                      ...++|||+|||..+++++|+++|++||+|. .|++     +++++|||||+|.+.++|++|++.|||..+.|+.    |
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            4568999999999999999999999999999 8876     3566899999999999999999999999999999    9


Q ss_pred             EEEeccCCc
Q 002974          430 KLEASRPGG  438 (861)
Q Consensus       430 kVe~Akpk~  438 (861)
                      +|.++++..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999998764

>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=99.46  E-value=9e-14  Score=127.82  Aligned_cols=81  Identities=25%  Similarity=0.312  Sum_probs=73.2

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcE----EEEEe-CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEI----REIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI----~sVri-tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||.|    ..+++ +++.+|||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            456899999999999999999999999998    45543 6788999999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            987644

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.46  E-value=5e-14  Score=119.87  Aligned_cols=70  Identities=19%  Similarity=0.427  Sum_probs=65.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ |++..+.|++|+|++|
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            5999999999999999999999999999985     57789999999999999999997 9999999999999875

>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=99.46  E-value=1.2e-13  Score=127.24  Aligned_cols=81  Identities=27%  Similarity=0.393  Sum_probs=74.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+|||..+++++|+++|++||.|..|++  .+..+|||||+|.+.++|.+|++.|||..+.|+.|+|.++.++.
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            4579999999999999999999999999999987  45668999999999999999999999999999999999998765


Q ss_pred             hhh
Q 002974          439 ARR  441 (861)
Q Consensus       439 ~rr  441 (861)
                      ..+
T Consensus        87 ~~~   89 (115)
T 3lqv_A           87 AFQ   89 (115)
T ss_dssp             HTT
T ss_pred             hhh
Confidence            443

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.46  E-value=2.5e-13  Score=126.99  Aligned_cols=79  Identities=16%  Similarity=0.283  Sum_probs=72.9

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...++|||+|||..+++++|+++|++||+|+.|++    +++.+|||||+|.+.++|++|++.|||..|.|++|+|+++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            45679999999999999999999999999999887    34578999999999999999999999999999999999998


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      +..
T Consensus       113 ~~~  115 (124)
T 2kt5_A          113 SQI  115 (124)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            764

>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=99.46  E-value=6.4e-14  Score=123.52  Aligned_cols=76  Identities=16%  Similarity=0.367  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      +..++|||+|||+++++++|+++|++| .|..+++. +++|||||+|.+.++|++|++.|+|..+.|++|+|.++..+
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            457899999999999999999999999 99999884 89999999999999999999999999999999999998654

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=4.7e-14  Score=129.87  Aligned_cols=78  Identities=18%  Similarity=0.407  Sum_probs=72.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      +...++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+ .|++..|.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            345799999999999999999999999999999986     3778999999999999999999 8999999999999999


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      +.++
T Consensus       101 a~~~  104 (114)
T 2cq4_A          101 SQAE  104 (114)
T ss_dssp             HHHH
T ss_pred             cCCC
Confidence            8754

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.46  E-value=8.3e-14  Score=136.82  Aligned_cols=81  Identities=10%  Similarity=0.148  Sum_probs=73.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccC--cEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYG--EIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfG--eI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ..++|||+|||+.+++++|+++|++||  +|.+|++     +++++|||||+|.+.++|++||+.|||..|.|++|+|.+
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            357999999999999999999999999  9999886     567799999999999999999999999999999999999


Q ss_pred             ccCCchhh
Q 002974          434 SRPGGARR  441 (861)
Q Consensus       434 Akpk~~rr  441 (861)
                      +.++..+.
T Consensus       134 a~~~~~~~  141 (156)
T 3n9u_C          134 ATRQNLSQ  141 (156)
T ss_dssp             CCHHHHHH
T ss_pred             cCCCcchh
Confidence            98865443

>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=99.46  E-value=2.5e-14  Score=125.92  Aligned_cols=76  Identities=24%  Similarity=0.441  Sum_probs=67.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.+ |++|++.|+|..+.|+.|+|.++.++
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             CC
Q 002974          353 DN  354 (861)
Q Consensus       353 ~~  354 (861)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=2.6e-13  Score=121.57  Aligned_cols=78  Identities=22%  Similarity=0.365  Sum_probs=71.8

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ...++|||+||  .+++++|+++|++||+|..|++ .+.+|||||+|.+.++|++|++.||+..|.|++|+|.+++++..
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i-~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEe-cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            45689999996  8999999999999999999997 47899999999999999999999999999999999999998764


Q ss_pred             h
Q 002974          440 R  440 (861)
Q Consensus       440 r  440 (861)
                      +
T Consensus        90 ~   90 (97)
T 1x5p_A           90 L   90 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.46  E-value=1.2e-13  Score=132.42  Aligned_cols=76  Identities=21%  Similarity=0.333  Sum_probs=71.4

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccE-EEEEECCHHHHHHHHHHhCCCeeCC--cEEEEEeccCCc
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNH-KFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPGG  438 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGf-AFVeF~d~eaA~kAL~~LNG~~I~G--r~IkVe~Akpk~  438 (861)
                      -.|||+||++.+|+++|+++|++||+|.+|++..+.+|| |||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
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            468899999999999999999999999999987677888 9999999999999999999999988  999999999875

>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=99.46  E-value=1.4e-13  Score=135.29  Aligned_cols=85  Identities=20%  Similarity=0.409  Sum_probs=75.7

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.+     ++.++|||||+|.+.++|++||+.|+|..|.|+.|.
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            445667899999999999999999999999999999985     567899999999999999999999999999999999


Q ss_pred             eeecCCCCCC
Q 002974          346 IHYSIPKDNP  355 (861)
Q Consensus       346 V~~a~~k~~~  355 (861)
                      |.|+.++...
T Consensus       146 V~~a~~~~~~  155 (165)
T 1rk8_A          146 VDWCFVKGPK  155 (165)
T ss_dssp             EEESEECC--
T ss_pred             EEEecCCCCC
Confidence            9999876543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.46  E-value=8e-14  Score=124.82  Aligned_cols=77  Identities=30%  Similarity=0.420  Sum_probs=71.5

Q ss_pred             cCCcceEEecccC-CCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          360 ANQGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       360 ~~~~tLfVgNLp~-svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ...++|||+|||. .+++++|+++|++||.|.+|++   .+|||||+|.+.++|++|++.||+..+.|++|+|++++++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE---ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            4567999999998 9999999999999999999997   48999999999999999999999999999999999998765


Q ss_pred             h
Q 002974          439 A  439 (861)
Q Consensus       439 ~  439 (861)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.46  E-value=1.8e-13  Score=119.70  Aligned_cols=75  Identities=23%  Similarity=0.370  Sum_probs=68.3

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||+.+++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++ +++..|.|++|+|++
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            456789999999999999999999999999999986     35668999999999999999997 588899999999987


Q ss_pred             c
Q 002974          434 S  434 (861)
Q Consensus       434 A  434 (861)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.3e-13  Score=125.53  Aligned_cols=80  Identities=21%  Similarity=0.250  Sum_probs=72.9

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCc-EEEEEeC------CCCccEEEEEECCHHHHHHHHHHhC--CCeeCCcEEE
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDT------QHKHNHKFIEFYDIRAAETALRTLN--RSDVAGKQIK  430 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGe-I~sVrit------gksKGfAFVeF~d~eaA~kAL~~LN--G~~I~Gr~Ik  430 (861)
                      ...++|||+|||..+++++|+++|++||. |.+|.+.      ++++|||||+|.+.++|++|++.|+  +..+.|++|+
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            34679999999999999999999999998 9999874      3678999999999999999999996  5899999999


Q ss_pred             EEeccCCch
Q 002974          431 LEASRPGGA  439 (861)
Q Consensus       431 Ve~Akpk~~  439 (861)
                      |++++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999998764

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=9.5e-14  Score=124.11  Aligned_cols=79  Identities=19%  Similarity=0.197  Sum_probs=70.3

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||..+++++|+++|++||.|..+++     +++.+|||||+|.+.++|++|++.||+..|.|++|+|+++
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            44678999999999999999999999999865332     4567899999999999999999999999999999999999


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      ..+.
T Consensus        93 ~~~~   96 (98)
T 2cqp_A           93 SGPS   96 (98)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            8653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.45  E-value=6.3e-14  Score=139.77  Aligned_cols=126  Identities=22%  Similarity=0.334  Sum_probs=99.2

Q ss_pred             CcceEEecccC-CCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCchh
Q 002974          362 QGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGAR  440 (861)
Q Consensus       362 ~~tLfVgNLp~-svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~r  440 (861)
                      .++|||+|||. .+++++|+++|++||.|.+|++....+|||||+|.+.++|++|++.|+|..+.|++|+|.+++++...
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~   82 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ   82 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcC
Confidence            57899999999 99999999999999999999987777999999999999999999999999999999999999865311


Q ss_pred             h-hchhhhh-------------------------hhccccCC-CCCCCCCCcccc----CCcc-cEEEEeC-CCCCccee
Q 002974          441 R-FMVQSEQ-------------------------EQDDLNLC-QIPFDDLSSGQM----VSSG-VITSTCM-DNGSIQVL  487 (861)
Q Consensus       441 r-l~qq~eq-------------------------~q~E~~vg-kNLp~s~tee~L----s~fG-~I~Sv~~-enG~srGF  487 (861)
                      . .....+.                         ......+. +||+.++++++|    ..|| .|..++. .+.+..||
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~af  162 (198)
T 1qm9_A           83 LPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMAL  162 (198)
T ss_dssp             CSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEE
T ss_pred             CCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEE
Confidence            1 0000000                         00011122 899999999998    8999 9988884 44444455

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.45  E-value=1.8e-13  Score=125.95  Aligned_cols=82  Identities=21%  Similarity=0.363  Sum_probs=70.8

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      .....++|||+|||..+++++|+++|++||+|.+|++.     +.++|||||+|.+.++|++|++.+ +..|.|+.|+|+
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            34557899999999999999999999999999999873     566899999999999999999976 599999999999


Q ss_pred             eccCCchh
Q 002974          433 ASRPGGAR  440 (861)
Q Consensus       433 ~Akpk~~r  440 (861)
                      ++.++..+
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99987643

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=1e-13  Score=125.61  Aligned_cols=82  Identities=27%  Similarity=0.417  Sum_probs=74.1

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      .....++|||+|||..+++++|+++|++||+|..|++     ++..+|||||+|.+.++|++||+. ++..|.|++|+|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            3456789999999999999999999999999999876     345689999999999999999998 9999999999999


Q ss_pred             eccCCchh
Q 002974          433 ASRPGGAR  440 (861)
Q Consensus       433 ~Akpk~~r  440 (861)
                      +++++..+
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99987644

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.3e-13  Score=127.28  Aligned_cols=81  Identities=17%  Similarity=0.431  Sum_probs=74.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++. ++..|.|+.|+|.+
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            345799999999999999999999999999999985     467899999999999999999987 99999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++...
T Consensus       103 a~~~~~~  109 (116)
T 1x4b_A          103 AVAREES  109 (116)
T ss_dssp             CSSCCCC
T ss_pred             CCCCccC
Confidence            9887654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=8.4e-14  Score=128.56  Aligned_cols=81  Identities=11%  Similarity=0.262  Sum_probs=73.1

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||.|..|++.     +..+|||||+|.+.++|++||+. ++..|.|++|+|++
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            3446899999999999999999999999999998862     45689999999999999999997 99999999999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      ++++..+
T Consensus       103 a~~~~~~  109 (116)
T 1x4b_A          103 AVAREES  109 (116)
T ss_dssp             CSSCCCC
T ss_pred             CCCCccC
Confidence            9987643

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.45  E-value=4e-14  Score=127.40  Aligned_cols=81  Identities=16%  Similarity=0.244  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ..+.++|||+|||.++++++|+++|++||.|..+.    .+++++|||||+|.+.++|++|++ |++..|.|+.|+|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            44689999999999999999999999999775521    257889999999999999999998 9999999999999999


Q ss_pred             CCCCCC
Q 002974          350 IPKDNP  355 (861)
Q Consensus       350 ~~k~~~  355 (861)
                      .++...
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=6.2e-14  Score=128.48  Aligned_cols=78  Identities=9%  Similarity=0.154  Sum_probs=71.3

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +...++|||+|||+++|+++|+++|++||+|.+|++.    +.++|||||+|.+.++|++|+. +++..|.|+.|+|.++
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            3456899999999999999999999999999999873    5678999999999999999999 9999999999999988


Q ss_pred             cCC
Q 002974          435 RPG  437 (861)
Q Consensus       435 kpk  437 (861)
                      ...
T Consensus        87 ~~~   89 (103)
T 1s79_A           87 DDY   89 (103)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            754

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=3e-13  Score=120.40  Aligned_cols=80  Identities=23%  Similarity=0.303  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-e-CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-T-ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-i-tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ....++|||+|||+++++++|+++|++||.|..|+ + ..+..+.|||+|.+.++|++|++.|+|..|.|++|+|.++.+
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            34579999999999999999999999999999994 4 444556699999999999999999999999999999999988


Q ss_pred             CC
Q 002974          352 KD  353 (861)
Q Consensus       352 k~  353 (861)
                      ++
T Consensus        92 ~~   93 (96)
T 2e44_A           92 EM   93 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            74

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.45  E-value=5e-14  Score=120.13  Aligned_cols=71  Identities=17%  Similarity=0.430  Sum_probs=66.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ++|||+|||.++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.++ ..+.|++|+|+++
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            58999999999999999999999999998875     47789999999999999999999999 9999999999987

>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=99.44  E-value=9e-14  Score=125.58  Aligned_cols=78  Identities=21%  Similarity=0.333  Sum_probs=69.2

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC------CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT------QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit------gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ....++|||+|||.++++++|+++|++|| |.+|++.      ++++|||||+|.+.++|++|+ .|||..|.|+.|+|+
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            34568999999999999999999999999 9999873      446899999999999999999 899999999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      +++++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998864

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=5.1e-13  Score=118.96  Aligned_cols=81  Identities=17%  Similarity=0.308  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      ....++|||+|||.++++++|+++|++||.|..|........||||+|.+.++|++|++ |++..|.|+.|.|.++.++.
T Consensus         5 ~~~~~~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            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            34578999999999999999999999999999985433222299999999999999999 99999999999999997665


Q ss_pred             CC
Q 002974          354 NP  355 (861)
Q Consensus       354 ~~  355 (861)
                      ..
T Consensus        84 ~~   85 (94)
T 2e5g_A           84 FQ   85 (94)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=4.2e-13  Score=119.46  Aligned_cols=79  Identities=15%  Similarity=0.140  Sum_probs=71.4

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEE-eC-CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVr-it-gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||+.+++++|+++|++||.|..|+ +. ....+.|||+|.+.++|++|++.|||..|.|++|+|+++.++
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 43 334566999999999999999999999999999999999987


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        93 ~   93 (96)
T 2e44_A           93 M   93 (96)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=3.5e-13  Score=123.83  Aligned_cols=80  Identities=16%  Similarity=0.266  Sum_probs=72.1

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCee--------CC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDV--------AG  426 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I--------~G  426 (861)
                      +...++|||+|||..+++++|+++|++||+|..|++    .+.++|||||+|.+.++|++|++.|||..|        .+
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            345689999999999999999999999999999886    345689999999999999999999999999        57


Q ss_pred             cEEEEEeccCCc
Q 002974          427 KQIKLEASRPGG  438 (861)
Q Consensus       427 r~IkVe~Akpk~  438 (861)
                      ++|+|.|++++.
T Consensus       102 ~~l~v~~a~p~~  113 (114)
T 1x5o_A          102 EPLLCKFSGPSS  113 (114)
T ss_dssp             SCBEEEECCCSC
T ss_pred             CceeEEccCCCC
Confidence            889999998763

>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=99.44  E-value=1.9e-13  Score=130.82  Aligned_cols=82  Identities=20%  Similarity=0.387  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--------E--EeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcce
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--------I--YTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK  343 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~s--------v--kitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~  343 (861)
                      ..++++|||+|||+++++++|+++|++||.|..        +  ..+++++|||||+|.+.++|++|++.|||..|.|+.
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            457899999999999999999999999998765        2  236899999999999999999999999999999999


Q ss_pred             eeeeecCCCCCC
Q 002974          344 LDIHYSIPKDNP  355 (861)
Q Consensus       344 L~V~~a~~k~~~  355 (861)
                      |.|.|+.+...+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999875443

>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=99.44  E-value=7.9e-14  Score=123.76  Aligned_cols=76  Identities=20%  Similarity=0.237  Sum_probs=67.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+++++|+++|++||.|..+.+     .++.+|||||+|.+.++|++|++.||+..|.|++|+|+++.
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            4579999999999999999999999999875433     45678999999999999999999999999999999999986


Q ss_pred             C
Q 002974          436 P  436 (861)
Q Consensus       436 p  436 (861)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.44  E-value=9.6e-14  Score=118.12  Aligned_cols=70  Identities=14%  Similarity=0.308  Sum_probs=65.4

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++ |++..+.|++|+|++|
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            5999999999999999999999999999876     45568999999999999999998 9999999999999875

>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=99.44  E-value=1.6e-13  Score=120.92  Aligned_cols=76  Identities=14%  Similarity=0.317  Sum_probs=71.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+|||+.+++++|+++|++| +|.+|++. +++|||||+|.+.++|++|++.|||..+.|++|+|+++..+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            45789999999999999999999999 99999875 789999999999999999999999999999999999997653

>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=2.7e-13  Score=126.41  Aligned_cols=78  Identities=19%  Similarity=0.364  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .+.++|||+|||.++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|+ .|+|..|.|+.|+|.++
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            34799999999999999999999999999999985     5788999999999999999999 79999999999999999


Q ss_pred             CCCC
Q 002974          350 IPKD  353 (861)
Q Consensus       350 ~~k~  353 (861)
                      .+..
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7643

>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=99.43  E-value=7.7e-14  Score=130.81  Aligned_cols=79  Identities=10%  Similarity=0.186  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE---E--eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI---Y--TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~sv---k--itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||+++++++|+++|++||.|..+   .  .+++++|||||+|.+.++|++||+ |++..|.|+.|.|.
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            44567999999999999999999999999987542   2  368899999999999999999999 99999999999999


Q ss_pred             ecCCC
Q 002974          348 YSIPK  352 (861)
Q Consensus       348 ~a~~k  352 (861)
                      ++.++
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98653

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.43  E-value=3.8e-13  Score=133.70  Aligned_cols=81  Identities=22%  Similarity=0.303  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHcCccccCc--ceeeeeecC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSI  350 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G--r~L~V~~a~  350 (861)
                      .....+|||+||++.+++++|+++|++||+|+.|++ +++.+|||||+|.+.++|++|++.|+|..|.|  ++|+|.|++
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            444677999999999999999999999999999997 35568899999999999999999999999965  999999999


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      ++..
T Consensus       123 ~~~l  126 (164)
T 1sjr_A          123 LTSL  126 (164)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            8754

>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=2.3e-13  Score=130.49  Aligned_cols=80  Identities=25%  Similarity=0.359  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccE-EEEEeCCHHHHHHHHHHcCccccCc--ceeeeeecCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIP  351 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGy-AFVeF~d~e~A~kALkaLnG~~L~G--r~L~V~~a~~  351 (861)
                      ..-.+|||+||++.+|+++|+++|++||+|..|++..+.+|| |||+|.+.++|++|++.|||..|.|  +.|+|+|+++
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            445677899999999999999999999999999975566788 9999999999999999999999988  9999999987


Q ss_pred             CCC
Q 002974          352 KDN  354 (861)
Q Consensus       352 k~~  354 (861)
                      +..
T Consensus       106 ~~l  108 (130)
T 3zzy_A          106 TSL  108 (130)
T ss_dssp             SSC
T ss_pred             Cce
Confidence            654

>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=99.43  E-value=1.1e-13  Score=129.34  Aligned_cols=78  Identities=18%  Similarity=0.163  Sum_probs=71.0

Q ss_pred             cCCcceEEecccCC-CcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCC--CeeCCcEEEEEeccC
Q 002974          360 ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR--SDVAGKQIKLEASRP  436 (861)
Q Consensus       360 ~~~~tLfVgNLp~s-vTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG--~~I~Gr~IkVe~Akp  436 (861)
                      ...++|||+|||++ +++++|+++|++||+|.+|++. +.||||||+|.+.++|++|++.|++  ..|.|++|+|.+++.
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 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            35679999999998 9999999999999999999975 5799999999999999999998864  569999999999987


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      +.
T Consensus       102 ~~  103 (112)
T 1x4f_A          102 YK  103 (112)
T ss_dssp             CS
T ss_pred             cc
Confidence            65

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=6e-14  Score=122.23  Aligned_cols=76  Identities=21%  Similarity=0.324  Sum_probs=69.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+++++|+++|++||+|..|++     ++..+|||||+|.+.++|++|++.|||..+.|+.|+|.++.
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            4579999999999999999999999999999986     34568999999999999999999999999999999987765


Q ss_pred             C
Q 002974          436 P  436 (861)
Q Consensus       436 p  436 (861)
                      .
T Consensus        84 s   84 (85)
T 1x4e_A           84 S   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.43  E-value=5.7e-14  Score=123.67  Aligned_cols=75  Identities=20%  Similarity=0.430  Sum_probs=67.3

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ++|||+|||..+++++|+++|++||+|.+|++.     ++++|||||+|.+.+ |++|++.|||..+.|++|+|++|.++
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            579999999999999999999999999999873     566899999999999 99999999999999999999999886


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.43  E-value=8.3e-14  Score=131.95  Aligned_cols=80  Identities=21%  Similarity=0.366  Sum_probs=72.7

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEE--EEe-----CCCCccEEEEEECCHHHHHHHHHHhCCC----eeCC
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--IRD-----TQHKHNHKFIEFYDIRAAETALRTLNRS----DVAG  426 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~s--Vri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~----~I~G  426 (861)
                      .+...++|||+|||+.+++++|+++|++||.|..  |++     ++++||||||+|.+. +|.+|++.|||.    .|.|
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            3456789999999999999999999999999966  765     466799999999999 999999999999    9999


Q ss_pred             cEEEEEeccCCc
Q 002974          427 KQIKLEASRPGG  438 (861)
Q Consensus       427 r~IkVe~Akpk~  438 (861)
                      ++|+|++++++.
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            999999998865

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.43  E-value=4.3e-13  Score=126.83  Aligned_cols=76  Identities=25%  Similarity=0.426  Sum_probs=69.8

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||+|+.|++.     ++.+|||||+|.+.++|++|++.|||..|.|++|+|++
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            4457899999999999999999999999999999873     45689999999999999999999999999999999998


Q ss_pred             c
Q 002974          434 S  434 (861)
Q Consensus       434 A  434 (861)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>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=99.43  E-value=6.9e-13  Score=119.71  Aligned_cols=79  Identities=16%  Similarity=0.345  Sum_probs=71.4

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||..+++++|+++|++||.|+.|++     +++++|||||+|.+.++|++|++  ++..|.|++|+|++
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            445689999999999999999999999999999876     35668999999999999999999  57899999999999


Q ss_pred             ccCCch
Q 002974          434 SRPGGA  439 (861)
Q Consensus       434 Akpk~~  439 (861)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            998763

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.43  E-value=1.2e-13  Score=119.65  Aligned_cols=69  Identities=17%  Similarity=0.262  Sum_probs=64.0

Q ss_pred             cceEEecccCCC------cHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCc-EEEE
Q 002974          363 GTLVVFNLDSSV------STEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGK-QIKL  431 (861)
Q Consensus       363 ~tLfVgNLp~sv------TeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr-~IkV  431 (861)
                      ++|||+|||..+      ++++|+++|++||+|.+|++.   ++++|||||+|.+.++|++|++.|||..+.|+ +|+|
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            689999999999      779999999999999999863   45689999999999999999999999999999 8876

>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=99.43  E-value=1.2e-13  Score=127.68  Aligned_cols=79  Identities=13%  Similarity=0.156  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCE-EEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI-RTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I-~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||+++++++|+++|++||.| ..|++    +++++|||||+|.+.++|++||+. ++..|.|+.|.|.
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            44568999999999999999999999999999 66664    577899999999999999999986 9999999999999


Q ss_pred             ecCCC
Q 002974          348 YSIPK  352 (861)
Q Consensus       348 ~a~~k  352 (861)
                      ++.++
T Consensus        90 ~a~~~   94 (114)
T 2cpy_A           90 VVTLE   94 (114)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=3.6e-13  Score=118.95  Aligned_cols=77  Identities=18%  Similarity=0.255  Sum_probs=70.7

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ....+|||+|||.++++++|+++|++| .|..|++    .++++|||||+|.+.++|++|++ ||+..|.|+.|+|.++.
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            456899999999999999999999999 8988876    45568999999999999999999 99999999999999998


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ++.
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            764

>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=99.42  E-value=3.5e-13  Score=126.48  Aligned_cols=79  Identities=14%  Similarity=0.292  Sum_probs=71.4

Q ss_pred             CCCCCcEEEE--cCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCcccc-----Ccceee
Q 002974          273 GEHPSRTLFV--RNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL-----RRRKLD  345 (861)
Q Consensus       273 ~~~~srtLfV--gNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L-----~Gr~L~  345 (861)
                      ...++++|||  +||+.++++++|+++|++||.|..|.+. ..||||||+|.+.++|++|++.|||+.+     .|+.|.
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~-~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~   99 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   99 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEE
Confidence            3457899999  7799999999999999999999999973 4689999999999999999999999988     689999


Q ss_pred             eeecCCC
Q 002974          346 IHYSIPK  352 (861)
Q Consensus       346 V~~a~~k  352 (861)
                      |.|+...
T Consensus       100 v~~a~~~  106 (114)
T 2cq2_A          100 LNFVEKV  106 (114)
T ss_dssp             EEEESCC
T ss_pred             EEecccC
Confidence            9998754

>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=99.42  E-value=3.2e-13  Score=117.68  Aligned_cols=73  Identities=18%  Similarity=0.375  Sum_probs=68.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcC----C-------CEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcc
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQF----G-------DIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRR  342 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqf----G-------~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr  342 (861)
                      .++.++|||+|||+++++++|+++|++|    |       .|..+++ .+.+|||||+|.+.++|++|+ .|+|..+.|+
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~-~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~   80 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQ   80 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE-CSSSSEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEe-cCCCcEEEEEcCCHHHHHHHH-hcCCCEECCe
Confidence            3568999999999999999999999999    8       9999998 456999999999999999999 9999999999


Q ss_pred             eeeeee
Q 002974          343 KLDIHY  348 (861)
Q Consensus       343 ~L~V~~  348 (861)
                      .|+|+.
T Consensus        81 ~l~V~r   86 (87)
T 2hzc_A           81 SLKIRR   86 (87)
T ss_dssp             ECEEEC
T ss_pred             EEEEeC
Confidence            999974

>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=99.42  E-value=3.1e-13  Score=120.23  Aligned_cols=78  Identities=22%  Similarity=0.467  Sum_probs=63.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccc--cCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP--LRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~--L~Gr~L~V~~a~  350 (861)
                      ...+..+|||+|||+++++++|+++|++||.|.+|++...+||||||+|.+.++|++    +++..  +.|+.|.|.++.
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            456789999999999999999999999999999999877799999999999999984    34444  569999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      ++..
T Consensus        83 ~k~~   86 (89)
T 3d2w_A           83 PKHN   86 (89)
T ss_dssp             ----
T ss_pred             CCCc
Confidence            7653

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.41  E-value=3.1e-13  Score=134.32  Aligned_cols=77  Identities=21%  Similarity=0.320  Sum_probs=70.4

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-CCCccEEEEEECCHHHHHHHHHHhCCCeeCC--cEEEEEeccCCc
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPGG  438 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-gksKGfAFVeF~d~eaA~kAL~~LNG~~I~G--r~IkVe~Akpk~  438 (861)
                      ..+|||+||++.+++++|+++|++||+|++|++. .++++||||+|.+.++|++|++.|||..|.|  ++|+|+|++++.
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            4579999999999999999999999999999874 3457899999999999999999999999965  999999999874

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.41  E-value=1e-13  Score=124.93  Aligned_cols=81  Identities=20%  Similarity=0.481  Sum_probs=72.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ....+.++|||+|||.++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++  ++..+.|+.|.|.
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~   81 (102)
T 2xs2_A            4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLG   81 (102)
T ss_dssp             CCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEE
Confidence            34556899999999999999999999999999999986    56789999999999999999998  9999999999999


Q ss_pred             ecCCCCC
Q 002974          348 YSIPKDN  354 (861)
Q Consensus       348 ~a~~k~~  354 (861)
                      ++.++..
T Consensus        82 ~a~~~~~   88 (102)
T 2xs2_A           82 PAIRKQN   88 (102)
T ss_dssp             EEEECC-
T ss_pred             ECCcCcc
Confidence            9986654

>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=99.41  E-value=3.3e-13  Score=123.11  Aligned_cols=80  Identities=9%  Similarity=0.206  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ...+.++|||+|||+++++++|+++|++||.| .|++    +++++|||||+|.+.++|++||+ ++++.|.||.|.|.+
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-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            44568999999999999999999999999955 7764    67889999999999999999995 899999999999999


Q ss_pred             cCCCCC
Q 002974          349 SIPKDN  354 (861)
Q Consensus       349 a~~k~~  354 (861)
                      +.+...
T Consensus        89 ~~~~~~   94 (102)
T 1wez_A           89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            876543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.41  E-value=1.5e-13  Score=117.16  Aligned_cols=71  Identities=21%  Similarity=0.384  Sum_probs=66.0

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ++|||+|||.++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.++ ..+.|++|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            47999999999999999999999999999876     35568999999999999999999999 9999999999987

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.41  E-value=4.7e-13  Score=127.24  Aligned_cols=74  Identities=22%  Similarity=0.299  Sum_probs=68.2

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccE-EEEEECCHHHHHHHHHHhCCCeeCC--cEEEEEeccCCc
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNH-KFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPGG  438 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGf-AFVeF~d~eaA~kAL~~LNG~~I~G--r~IkVe~Akpk~  438 (861)
                      .|||+||++.+++++|+++|++||+|++|++..+ .|| |||+|.+.++|.+|++.|||..|.|  +.|+|.+++++.
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            4789999999999999999999999999988644 586 9999999999999999999999987  699999999875

>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=99.41  E-value=5.1e-13  Score=121.61  Aligned_cols=78  Identities=22%  Similarity=0.290  Sum_probs=71.2

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEE-EEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~s-Vri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ....+|||+|||+.+++++|+++|++||.|.. |++    +++++|||||+|.+.++|++||+. ++..|.|+.|+|.++
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            45689999999999999999999999999987 765    467789999999999999999997 999999999999998


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      .+++
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7665

>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=99.41  E-value=6e-13  Score=118.34  Aligned_cols=77  Identities=22%  Similarity=0.382  Sum_probs=64.1

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCe--eCCcEEEEEeccC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD--VAGKQIKLEASRP  436 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~--I~Gr~IkVe~Akp  436 (861)
                      .....+|||+|||+++|+++|+++|++||+|.+|++..++||||||+|.+.++|++    |++..  +.|++|+|.++.+
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            34568999999999999999999999999999999887789999999999999983    56665  4599999999998


Q ss_pred             Cch
Q 002974          437 GGA  439 (861)
Q Consensus       437 k~~  439 (861)
                      +..
T Consensus        84 k~~   86 (89)
T 3d2w_A           84 KHN   86 (89)
T ss_dssp             ---
T ss_pred             CCc
Confidence            753

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.40  E-value=1e-13  Score=124.68  Aligned_cols=80  Identities=23%  Similarity=0.271  Sum_probs=70.9

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEE----EeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI----RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sV----ritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ....+|||+|||..+++++|+++|++||.|..+    ..+++++|||||+|.+.++|++|++ ||+..|.|++|+|.+++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            356799999999999999999999999987651    1246789999999999999999999 99999999999999999


Q ss_pred             CCchh
Q 002974          436 PGGAR  440 (861)
Q Consensus       436 pk~~r  440 (861)
                      ++..+
T Consensus        94 ~~~~~   98 (101)
T 1fj7_A           94 GRDGT   98 (101)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=6.5e-13  Score=120.53  Aligned_cols=76  Identities=17%  Similarity=0.321  Sum_probs=67.7

Q ss_pred             CCCcE-EEEcCCCCCCcHHH----HHHHhhcC-CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          275 HPSRT-LFVRNINSNVEDSE----LKALFEQF-GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       275 ~~srt-LfVgNLP~~vTEed----L~elFsqf-G~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .|+.| |||+|||.++++++    |+++|++| |+|..|  ++   |+|||+|.+.++|++|++.|+|..+.||+|+|.|
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            45666 99999999999988    55899999 599998  33   9999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      ++.+.+-
T Consensus        81 A~~~sd~   87 (96)
T 2diu_A           81 TPKNREL   87 (96)
T ss_dssp             SCCSCCC
T ss_pred             cCCCcce
Confidence            9876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.11  E-value=2.2e-14  Score=132.63  Aligned_cols=83  Identities=22%  Similarity=0.370  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE--------EEe-----CCCcccEEEEEeCCHHHHHHHHHHcCcccc
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRT--------IYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPL  339 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~s--------vki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L  339 (861)
                      ...+.++|||+|||.++++++|+++|++||.|..        |++     +++++|||||+|.+.++|++|++.|++..+
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            3567899999999999999999999999999988        653     467899999999999999999999999999


Q ss_pred             CcceeeeeecCCCCCC
Q 002974          340 RRRKLDIHYSIPKDNP  355 (861)
Q Consensus       340 ~Gr~L~V~~a~~k~~~  355 (861)
                      .|++|+|.++.++...
T Consensus        83 ~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           83 SGNPIKVSFATRRADF   98 (116)
Confidence            9999999999877554

>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=99.40  E-value=2.2e-13  Score=126.06  Aligned_cols=82  Identities=11%  Similarity=0.140  Sum_probs=72.8

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcE-EEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEI-REIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI-~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....++|||+|||+++++++|+++|++||.| ..|++    +++.+|||||+|.+.++|++||+. |+..|.|+.|+|.+
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            3456899999999999999999999999999 67776    356799999999999999999996 99999999999999


Q ss_pred             ccCCchhh
Q 002974          434 SRPGGARR  441 (861)
Q Consensus       434 Akpk~~rr  441 (861)
                      +.++..++
T Consensus        91 a~~~~~~~   98 (114)
T 2cpy_A           91 VTLEDMRE   98 (114)
T ss_dssp             ECHHHHHH
T ss_pred             CCHHHHHH
Confidence            98766443

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.40  E-value=3.5e-13  Score=125.77  Aligned_cols=77  Identities=8%  Similarity=0.114  Sum_probs=70.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~---I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ....++|||+|||+++++++|+++|++||.   |..|++    .++++|||||+|.+.++|++|++ ++++.|.||.|+|
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            456899999999999999999999999998   777764    47789999999999999999998 9999999999999


Q ss_pred             eecCC
Q 002974          347 HYSIP  351 (861)
Q Consensus       347 ~~a~~  351 (861)
                      .++..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98854

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.40  E-value=1.8e-13  Score=131.89  Aligned_cols=78  Identities=14%  Similarity=0.134  Sum_probs=70.3

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCc---EEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGE---IREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGe---I~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ....+|||+|||+++|+++|+++|++||.   |.+|++    .++++|||||+|.+.++|++||+ ||+..|.|+.|+|.
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            45678999999999999999999999999   777665    35678999999999999999999 99999999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      ++.+++
T Consensus       121 ~a~~~e  126 (136)
T 2hgl_A          121 KSHRTE  126 (136)
T ss_dssp             ECCHHH
T ss_pred             ECChHH
Confidence            997654

>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=99.40  E-value=2.9e-13  Score=118.95  Aligned_cols=79  Identities=22%  Similarity=0.449  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      .++++|||+|||.++++++|+++|++||.|..|++...++|||||+|.+.++|++|+.  ....+.|++|+|.++.++..
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            4579999999999999999999999999999999877789999999999999986543  23456899999999988765


Q ss_pred             C
Q 002974          355 P  355 (861)
Q Consensus       355 ~  355 (861)
                      .
T Consensus        81 ~   81 (88)
T 1wf0_A           81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.39  E-value=1.7e-13  Score=116.41  Aligned_cols=70  Identities=20%  Similarity=0.476  Sum_probs=65.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++ +++..+.|+.|.|+++
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            6999999999999999999999999999985     46789999999999999999998 5899999999999875

>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=99.39  E-value=6.2e-13  Score=123.45  Aligned_cols=76  Identities=18%  Similarity=0.264  Sum_probs=66.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcE-----EEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ-----IKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~-----IkVe~Ak  435 (861)
                      ...+|||+|||+++++++|+++|++||+|+.|.+...  |||||+|.+.++|++||+.||+..|.|++     |+|..+.
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            4579999999999999999999999999999998644  99999999999999999999999999998     7887777


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ++.
T Consensus        93 ~~~   95 (115)
T 3beg_B           93 PRS   95 (115)
T ss_dssp             ---
T ss_pred             CCC
Confidence            654

>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=99.39  E-value=7.1e-13  Score=126.90  Aligned_cols=81  Identities=25%  Similarity=0.351  Sum_probs=72.1

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEE--------E--EeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------I--RDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~s--------V--ritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                      ...++|||+|||+.+++++|+++|++||.|..        |  ..+++.+|||||+|.+.++|.+|++.|||..|.|+.|
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            34679999999999999999999999998765        3  2367889999999999999999999999999999999


Q ss_pred             EEEeccCCchh
Q 002974          430 KLEASRPGGAR  440 (861)
Q Consensus       430 kVe~Akpk~~r  440 (861)
                      +|.++++...+
T Consensus       123 ~V~~a~~~~~~  133 (143)
T 3egn_A          123 VVQFARSARPK  133 (143)
T ss_dssp             EEEECCCSCC-
T ss_pred             EEEECCCCCCc
Confidence            99999876544

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.39  E-value=7.4e-13  Score=117.93  Aligned_cols=77  Identities=16%  Similarity=0.307  Sum_probs=68.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+|||..+++++|+++|++||.|.+|........||||+|.+.++|++|++ ||+..|.|+.|+|+++.++.
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            457999999999999999999999999999984432222299999999999999999 99999999999999987765

>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=5.9e-13  Score=123.61  Aligned_cols=77  Identities=14%  Similarity=0.235  Sum_probs=65.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcce-----eeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK-----LDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~-----L~V~~  348 (861)
                      ....++|||+|||+++++++|+++|++||+|..|++...  |||||+|.+.++|++||+.|||+.|.|++     |+|..
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~   90 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   90 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEecc
Confidence            356799999999999999999999999999999998433  99999999999999999999999999999     55555


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      +.++
T Consensus        91 ~~~~   94 (115)
T 3beg_B           91 DGPR   94 (115)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            5443

>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=99.38  E-value=3.2e-13  Score=130.18  Aligned_cols=78  Identities=8%  Similarity=0.089  Sum_probs=70.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~---I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      .....++|||+|||+++|+++|+++|++||.   |..|++    .++++|||||+|.+.++|++|++ |+++.|.||.|+
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            3456899999999999999999999999998   666664    47889999999999999999999 999999999999


Q ss_pred             eeecCC
Q 002974          346 IHYSIP  351 (861)
Q Consensus       346 V~~a~~  351 (861)
                      |.++.+
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            998853

>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=99.38  E-value=5.1e-13  Score=138.96  Aligned_cols=76  Identities=17%  Similarity=0.262  Sum_probs=70.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCC--CEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFG--DIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG--~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..++|||+|||+++|+++|+++|++||  .|..|++     ++++||||||+|.+.++|++||+.|+++.|.|+.|+|.+
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            578999999999999999999999999  9999985     678999999999999999999999999999999999999


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.38  E-value=3.2e-13  Score=126.10  Aligned_cols=78  Identities=14%  Similarity=0.155  Sum_probs=70.2

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCc---EEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGE---IREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGe---I~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ....+|||+|||+++|+++|+++|+.||.   |..|++    .++++|||||+|.+.++|++||+ ||+..|.|+.|+|.
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            45678999999999999999999999998   777765    35678999999999999999999 99999999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      ++.+++
T Consensus        94 ~a~~~~   99 (118)
T 2db1_A           94 KSHRTE   99 (118)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            997554

>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=99.37  E-value=2.8e-13  Score=123.96  Aligned_cols=79  Identities=10%  Similarity=0.053  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCC---EEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGD---IRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~---I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      .....++|||+|||+++++++|+++|++||.   |..|++    .++++|||||+|.+.++|++|++ +++..+.||.|+
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            3456899999999999999999999999998   788875    36789999999999999999998 999999999999


Q ss_pred             eeecCCC
Q 002974          346 IHYSIPK  352 (861)
Q Consensus       346 V~~a~~k  352 (861)
                      |.++.++
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998643

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.37  E-value=9.1e-13  Score=131.91  Aligned_cols=80  Identities=25%  Similarity=0.446  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ...+.++|||+|||+.+++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|+|..|.|+.|+|.|
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            4456899999999999999999999999999999986    367899999999999999999999999999999999999


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      +...
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            9754

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=1.8e-13  Score=128.30  Aligned_cols=79  Identities=11%  Similarity=0.140  Sum_probs=70.3

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEE-E----eCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-R----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sV-r----itgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ....+|||+|||+.+++++|+++|++||.|..+ .    .+++.+|||||+|.+.++|++||+ ||+..|.|+.|+|.++
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            346799999999999999999999999998652 2    256679999999999999999999 9999999999999999


Q ss_pred             cCCch
Q 002974          435 RPGGA  439 (861)
Q Consensus       435 kpk~~  439 (861)
                      .++..
T Consensus       102 ~~~~~  106 (124)
T 1wel_A          102 TKKGM  106 (124)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            87653

>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=8.6e-13  Score=123.82  Aligned_cols=78  Identities=19%  Similarity=0.193  Sum_probs=70.3

Q ss_pred             cCCcceEE--ecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCee-----CCcEEEEE
Q 002974          360 ANQGTLVV--FNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV-----AGKQIKLE  432 (861)
Q Consensus       360 ~~~~tLfV--gNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I-----~Gr~IkVe  432 (861)
                      ...++|||  +||++.+++++|+++|++||+|.+|.+. ..||||||+|.+.++|++|++.|||+++     .|++|.|.
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 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN  101 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEE
Confidence            34678999  6699999999999999999999999875 4689999999999999999999999998     68999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      +++...
T Consensus       102 ~a~~~p  107 (114)
T 2cq2_A          102 FVEKVQ  107 (114)
T ss_dssp             EESCCC
T ss_pred             ecccCc
Confidence            987543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.37  E-value=1.9e-12  Score=123.10  Aligned_cols=76  Identities=20%  Similarity=0.273  Sum_probs=68.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccE-EEEEeCCHHHHHHHHHHcCccccCc--ceeeeeecCCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGF-VMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIPKDN  354 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGy-AFVeF~d~e~A~kALkaLnG~~L~G--r~L~V~~a~~k~~  354 (861)
                      ..|||+||++.+++++|+++|++||.|..|++..+ .|| |||+|.+.++|++|++.|||..|.|  +.|+|.|++++..
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            44679999999999999999999999999987433 486 9999999999999999999999987  6999999987754

>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=99.36  E-value=2.3e-13  Score=131.61  Aligned_cols=121  Identities=10%  Similarity=0.050  Sum_probs=69.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEE
Q 002974          314 RGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR  393 (861)
Q Consensus       314 rGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVr  393 (861)
                      +|+|+.+|..++.+..|+..+... ..|....-....  ...........+|||+|||+++|+++|+++|++|| |++|+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~--~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~   76 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGD--SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVH   76 (139)
T ss_dssp             -----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEE
T ss_pred             CCcccccccCccccchhcccchhc-cCCCCCCCCCCC--cccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEE
Confidence            367888888888877777654432 222222111111  01112234567999999999999999999999999 66887


Q ss_pred             eC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          394 DT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       394 it----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      +.    ++++|||||+|.+.++|++|| .+|+..|.|+.|+|.++.++..
T Consensus        77 i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           77 IEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             EEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            63    567899999999999999999 6999999999999999987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.04  E-value=6.7e-14  Score=129.41  Aligned_cols=80  Identities=21%  Similarity=0.311  Sum_probs=72.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEE--------EEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--------IRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG  426 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~s--------Vri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G  426 (861)
                      ...++|||+|||..+++++|+++|++||.|..        |++     +++.+|||||+|.+.++|++|++.||+..|.|
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            45689999999999999999999999999988        654     34568999999999999999999999999999


Q ss_pred             cEEEEEeccCCch
Q 002974          427 KQIKLEASRPGGA  439 (861)
Q Consensus       427 r~IkVe~Akpk~~  439 (861)
                      ++|+|++++++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999988753

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=1.1e-12  Score=121.72  Aligned_cols=76  Identities=7%  Similarity=0.177  Sum_probs=68.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ....++|||+|||+++++++|+++|++| .|..|++    .++++|||||+|.+.++|++|+ .+++..|.||.|.|..+
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            3456899999999999999999999999 8888885    4678999999999999999999 69999999999999877


Q ss_pred             CC
Q 002974          350 IP  351 (861)
Q Consensus       350 ~~  351 (861)
                      .+
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            53

>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=99.35  E-value=9.5e-13  Score=120.06  Aligned_cols=77  Identities=10%  Similarity=0.174  Sum_probs=68.8

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ....+|||+|||+++++++|+++|++||.| +|++    +++++|||||+|.+.++|++||+ +|+..|.|+.|+|.++.
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 7765    45678999999999999999995 89999999999999988


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      +..
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.35  E-value=3.8e-13  Score=123.02  Aligned_cols=79  Identities=13%  Similarity=0.075  Sum_probs=71.2

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCc---EEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGE---IREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL  431 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGe---I~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkV  431 (861)
                      .....+|||+|||+++++++|+++|+.||.   |..|++.    ++++|||||+|.+.++|++||+ +|+..|.|+.|+|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            345678999999999999999999999998   8888763    5678999999999999999999 9999999999999


Q ss_pred             EeccCCc
Q 002974          432 EASRPGG  438 (861)
Q Consensus       432 e~Akpk~  438 (861)
                      .++.++.
T Consensus        87 ~~a~~~~   93 (107)
T 2lmi_A           87 YEINNED   93 (107)
T ss_dssp             EECCHHH
T ss_pred             EECCHHH
Confidence            9998765

>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=99.35  E-value=5.4e-13  Score=138.77  Aligned_cols=78  Identities=14%  Similarity=0.161  Sum_probs=71.6

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccC--cEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYG--EIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfG--eI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ..++|||+||++.+|+++|+++|++||  +|++|++     ++++||||||+|.+.++|++||+.||+..|.|++|+|.+
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  9999886     566799999999999999999999999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      +++..
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            98765

>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=99.35  E-value=5.5e-13  Score=117.16  Aligned_cols=77  Identities=16%  Similarity=0.301  Sum_probs=67.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ..++|||+|||..+++++|+++|++||+|.+|++...++|||||+|.+.++|++|+.  ....+.|++|+|.+++++..
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCCCC
Confidence            357999999999999999999999999999999877789999999999999986533  13355899999999998764

>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=99.34  E-value=2.8e-12  Score=129.93  Aligned_cols=115  Identities=13%  Similarity=0.149  Sum_probs=90.3

Q ss_pred             CHHHHHHHHHHc--CccccCcceeeeeecCCCCCCCC-----cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC
Q 002974          323 DIRAARNAMKAL--QNKPLRRRKLDIHYSIPKDNPSE-----KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT  395 (861)
Q Consensus       323 d~e~A~kALkaL--nG~~L~Gr~L~V~~a~~k~~~~~-----k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit  395 (861)
                      +.+.+..|++..  ....+.+...+|.....+..+..     .....++|||+|||..+++++|+++|++||.|..|++.
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            667888888877  55566666666665532222211     22346899999999999999999999999999999863


Q ss_pred             ----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          396 ----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       396 ----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                          +..+|||||+|.+.++|++|+..+ +..+.|++|+|.+++.-.
T Consensus       143 ~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          143 RTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDYF  188 (193)
T ss_dssp             ECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC-
T ss_pred             ECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHHH
Confidence                567899999999999999999865 459999999999987643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=1.9e-12  Score=117.48  Aligned_cols=73  Identities=22%  Similarity=0.331  Sum_probs=65.9

Q ss_pred             CCcceEEecccCCCcHHH----HHHHhccc-CcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEE----LHQIFGIY-GEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeed----LrelFskf-GeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..+.|||+|||+.+++++    |+++|++| |+|.+|  ++   |+|||+|.+.++|.+|++.|+|..+.||+|+|.+|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~   82 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTP   82 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecC
Confidence            344599999999999988    55899999 599998  33   999999999999999999999999999999999999


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      .+.
T Consensus        83 ~~s   85 (96)
T 2diu_A           83 KNR   85 (96)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            875

>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=99.34  E-value=4.2e-13  Score=113.93  Aligned_cols=70  Identities=17%  Similarity=0.348  Sum_probs=64.7

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeC-----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVrit-----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +|||+|||.++++++|+++|++||+|..|++.     +.++|||||+|.+.++|++|++ +++..+.|++|+|++|
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            69999999999999999999999999998763     5568999999999999999999 5899999999999875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.33  E-value=2.2e-12  Score=135.56  Aligned_cols=103  Identities=17%  Similarity=0.185  Sum_probs=78.3

Q ss_pred             ccccCcceeeeeecCCCCCCCCcccCCcceEEecccCCC---------cHHHHHHHhcccCcEEEEEeCCCCccEEEEEE
Q 002974          336 NKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSV---------STEELHQIFGIYGEIREIRDTQHKHNHKFIEF  406 (861)
Q Consensus       336 G~~L~Gr~L~V~~a~~k~~~~~k~~~~~tLfVgNLp~sv---------TeedLrelFskfGeI~sVritgksKGfAFVeF  406 (861)
                      ...+.|+.....+..........+...++|||+||+..+         ++++|+++|++||+|++|++. ..||||||+|
T Consensus       108 ~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~-~~kG~AFV~F  186 (240)
T 3u1l_A          108 VLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-ESKNCGFVKF  186 (240)
T ss_dssp             SBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEE-GGGTEEEEEE
T ss_pred             CcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEE-CCCCEEEEEe
Confidence            344556655444443322222234567899999999998         799999999999999999976 4799999999


Q ss_pred             CCHHHHHHHHHHhCCCee------------CCcEEEEEeccCCch
Q 002974          407 YDIRAAETALRTLNRSDV------------AGKQIKLEASRPGGA  439 (861)
Q Consensus       407 ~d~eaA~kAL~~LNG~~I------------~Gr~IkVe~Akpk~~  439 (861)
                      .+.++|+.|+++|+|..|            .|+.|.|.||+.+..
T Consensus       187 ~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          187 KYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             SSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             CCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCC
Confidence            999999999999999999            899999999987653

>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=99.33  E-value=2.4e-12  Score=112.13  Aligned_cols=71  Identities=18%  Similarity=0.363  Sum_probs=66.2

Q ss_pred             CCcceEEecccCCCcHHHHHHHhccc----C-------cEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIY----G-------EIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskf----G-------eI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                      ..++|||+|||..+++++|+++|++|    |       .|.++++. ..+|||||+|.+.++|++|+ .|||..+.|++|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~-~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l   82 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEC-SSSSEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEec-CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            46799999999999999999999999    8       99999975 46999999999999999999 999999999999


Q ss_pred             EEEe
Q 002974          430 KLEA  433 (861)
Q Consensus       430 kVe~  433 (861)
                      +|+.
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9974

>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=99.33  E-value=7.3e-13  Score=128.15  Aligned_cols=80  Identities=9%  Similarity=0.190  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .....++|||+|||+++|+++|+++|++|| |..|++    +++++|||||+|.+.++|++|| .+++..|.||.|.|.+
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 7999999999999999


Q ss_pred             cCCCCC
Q 002974          349 SIPKDN  354 (861)
Q Consensus       349 a~~k~~  354 (861)
                      +.++..
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.32  E-value=1.7e-12  Score=123.69  Aligned_cols=77  Identities=14%  Similarity=0.207  Sum_probs=68.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEE--EEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIR--TIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~--svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      .....++|||+|||+++++++|+++|++| .|.  .|++    .++++|||||+|.+.++|++|++ +++..|.||.|.|
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            44568899999999999999999999999 676  7875    47789999999999999999998 5789999999999


Q ss_pred             eecCC
Q 002974          347 HYSIP  351 (861)
Q Consensus       347 ~~a~~  351 (861)
                      .++.+
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88854

>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=1e-12  Score=118.40  Aligned_cols=78  Identities=21%  Similarity=0.380  Sum_probs=71.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ....++|||+|||..+++++|+++|++||.|..|++    +++.+|||||+|.+.++|++|++  ++..+.|++|.|.++
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            345689999999999999999999999999999886    34578999999999999999999  999999999999999


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      .++.
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            8765

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=2.2e-12  Score=119.67  Aligned_cols=74  Identities=11%  Similarity=0.160  Sum_probs=67.5

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ..+|||+|||+++++++|+++|+.| .|..|++.    ++++|||||+|.+.++|++|| .+|+..|.||.|+|..+.++
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            4689999999999999999999999 88888873    567899999999999999999 59999999999999888654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.31  E-value=2.1e-12  Score=135.59  Aligned_cols=81  Identities=21%  Similarity=0.380  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCC---------cHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCcccc-----
Q 002974          274 EHPSRTLFVRNINSNV---------EDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL-----  339 (861)
Q Consensus       274 ~~~srtLfVgNLP~~v---------TEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L-----  339 (861)
                      ....++|||+||+..+         +|++|+++|++||+|..|++ ..+||||||+|.+.++|+.|+++|+|+.|     
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            4568999999999998         79999999999999999997 46799999999999999999999999999     


Q ss_pred             -------CcceeeeeecCCCCCC
Q 002974          340 -------RRRKLDIHYSIPKDNP  355 (861)
Q Consensus       340 -------~Gr~L~V~~a~~k~~~  355 (861)
                             .|+.|.|.|+..+.++
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC-----
T ss_pred             ccccccCCCCEEEEEEccCCCCH
Confidence                   8999999999876554

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=4e-12  Score=117.57  Aligned_cols=73  Identities=16%  Similarity=0.318  Sum_probs=61.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----C---CCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----A---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----t---gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      ....++|||+|||+++++++|+++|++||.|. +.+     +   ++++|||||+|.+.++|++|++.|++  +.|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEE
Confidence            35689999999999999999999999999999 653     2   58899999999999999999999843  5666666


Q ss_pred             eeec
Q 002974          346 IHYS  349 (861)
Q Consensus       346 V~~a  349 (861)
                      +..+
T Consensus        82 ~~~~   85 (114)
T 2dnl_A           82 CVSS   85 (114)
T ss_dssp             EECC
T ss_pred             eccC
Confidence            6544

>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=99.30  E-value=1.1e-11  Score=114.46  Aligned_cols=82  Identities=16%  Similarity=0.292  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCCCCc-----------HHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHcCccccC
Q 002974          273 GEHPSRTLFVRNINSNVE-----------DSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPLR  340 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vT-----------EedL~elFsqfG~I~svki-tgksrGyAFVeF~d~e~A~kALkaLnG~~L~  340 (861)
                      ...++++|+|+||....+           +++|+++|++||.|..|.+ ...++|||||+|.+.++|++|++.|+|..+.
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            556799999999954433           6899999999999999986 4568999999999999999999999999999


Q ss_pred             cceeeeeecCCCCC
Q 002974          341 RRKLDIHYSIPKDN  354 (861)
Q Consensus       341 Gr~L~V~~a~~k~~  354 (861)
                      |++|+|.++.++..
T Consensus        91 gr~l~v~~a~~~~~  104 (112)
T 2dit_A           91 GRQITAQAWDGTTD  104 (112)
T ss_dssp             TEECEEEECCSCCC
T ss_pred             CcEEEEEEeCCCCC
Confidence            99999999987654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.29  E-value=1.4e-12  Score=123.65  Aligned_cols=76  Identities=18%  Similarity=0.231  Sum_probs=67.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCE----EEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDI----RTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I----~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      .+.++|||+|||+++|+++|+++|++||.|    ..|++    +++++|||||+|.+.++|++|++. +++.|.||.|.|
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    34442    678999999999999999999985 999999999999


Q ss_pred             eecCC
Q 002974          347 HYSIP  351 (861)
Q Consensus       347 ~~a~~  351 (861)
                      ..+.+
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87753

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.29  E-value=4.1e-12  Score=127.19  Aligned_cols=79  Identities=16%  Similarity=0.277  Sum_probs=72.9

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...++|||+|||..+++++|+++|++||+|+.|.+.    +.++|||||+|.+.++|++|++.||+..|.|++|+|+++.
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            346799999999999999999999999999999874    5578999999999999999999999999999999999998


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            754

>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=99.28  E-value=5.9e-12  Score=142.72  Aligned_cols=81  Identities=27%  Similarity=0.434  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..+.++|||+|||..+|+++|+++|++||.|..|++     +++++|||||+|.+.++|++||+.|||+.|.|+.|.|.|
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            346789999999999999999999999999999986     577899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002974          349 SIPKDN  354 (861)
Q Consensus       349 a~~k~~  354 (861)
                      +.++..
T Consensus       179 a~~~~~  184 (437)
T 3pgw_S          179 ERGRTV  184 (437)
T ss_pred             eCCCCC
Confidence            987543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.27  E-value=1.5e-12  Score=123.48  Aligned_cols=80  Identities=23%  Similarity=0.222  Sum_probs=69.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcE----EEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEI----REIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI----~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ...+|||+|||+++|+++|+++|++||.|    ..|++    +++++|||||+|.+.++|++||+. |+..|.||.|+|.
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            45789999999999999999999999975    45554    466789999999999999999995 9999999999999


Q ss_pred             eccCCchhh
Q 002974          433 ASRPGGARR  441 (861)
Q Consensus       433 ~Akpk~~rr  441 (861)
                      .+.+++.++
T Consensus       101 ~a~~~e~~~  109 (123)
T 2dha_A          101 RSTAAEVQQ  109 (123)
T ss_dssp             EECHHHHHH
T ss_pred             ECCHHHHHH
Confidence            987655333

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=1.1e-11  Score=114.63  Aligned_cols=75  Identities=13%  Similarity=0.155  Sum_probs=63.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC--------CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT--------QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit--------gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ..++|||+|||+++++++|+++|++||+|. +.+.        ++++|||||+|.+.++|++||+.|+  .++|+.|.+.
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 6542        4679999999999999999999984  4777777777


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      .+.+..
T Consensus        84 ~~~~~~   89 (114)
T 2dnl_A           84 SSPTIK   89 (114)
T ss_dssp             CCSSSC
T ss_pred             cCCCcC
Confidence            665443

>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=99.25  E-value=4.6e-12  Score=120.66  Aligned_cols=77  Identities=25%  Similarity=0.275  Sum_probs=67.5

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEE--EEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIR--EIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~--sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ....+|||+|||+++|+++|+++|++| .|+  .|++    .++++|||||+|.+.++|++||+ +++..|.||.|+|.+
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 566  7876    35678999999999999999999 578999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      +.+++
T Consensus       118 a~~~e  122 (126)
T 2hgm_A          118 SSQEE  122 (126)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            86543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.23  E-value=2.8e-11  Score=111.37  Aligned_cols=78  Identities=14%  Similarity=0.241  Sum_probs=68.6

Q ss_pred             CCCCcEEEEcCCCC-----CCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHcCccccCcc
Q 002974          274 EHPSRTLFVRNINS-----NVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRR  342 (861)
Q Consensus       274 ~~~srtLfVgNLP~-----~vTEedL~elFsqfG~I~svki------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr  342 (861)
                      ..++++|+|+||..     +-++++|+++|++||.|..|++      +++++|||||+|.+.++|++|++.|||..+.||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            35789999999963     2368999999999999999985      146799999999999999999999999999999


Q ss_pred             eeeeeecCC
Q 002974          343 KLDIHYSIP  351 (861)
Q Consensus       343 ~L~V~~a~~  351 (861)
                      .|.|.++.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999854

>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=99.22  E-value=4.1e-11  Score=110.51  Aligned_cols=80  Identities=20%  Similarity=0.282  Sum_probs=69.6

Q ss_pred             ccCCcceEEecccCCCc-----------HHHHHHHhcccCcEEEEEe-CCCCccEEEEEECCHHHHHHHHHHhCCCeeCC
Q 002974          359 DANQGTLVVFNLDSSVS-----------TEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG  426 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svT-----------eedLrelFskfGeI~sVri-tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G  426 (861)
                      ....++|+|.||....+           +++|+++|++||+|.+|.+ ...++|||||+|.+.++|++|++.|||..|.|
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            44578999999944332           5899999999999999876 34578999999999999999999999999999


Q ss_pred             cEEEEEeccCCc
Q 002974          427 KQIKLEASRPGG  438 (861)
Q Consensus       427 r~IkVe~Akpk~  438 (861)
                      ++|+|.++.++.
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            999999998865

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.21  E-value=4.1e-11  Score=110.34  Aligned_cols=77  Identities=17%  Similarity=0.158  Sum_probs=67.3

Q ss_pred             cCCcceEEecccC-----CCcHHHHHHHhcccCcEEEEEeC------CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcE
Q 002974          360 ANQGTLVVFNLDS-----SVSTEELHQIFGIYGEIREIRDT------QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQ  428 (861)
Q Consensus       360 ~~~~tLfVgNLp~-----svTeedLrelFskfGeI~sVrit------gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~  428 (861)
                      ...++|+|.||..     +-++++|+++|++||+|.+|++.      ++++|||||+|.+.++|.+|++.|||+.+.||+
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            3467899999963     23689999999999999999863      356899999999999999999999999999999


Q ss_pred             EEEEeccC
Q 002974          429 IKLEASRP  436 (861)
Q Consensus       429 IkVe~Akp  436 (861)
                      |+|.++.+
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

>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=99.19  E-value=3.5e-11  Score=121.90  Aligned_cols=76  Identities=13%  Similarity=0.305  Sum_probs=68.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ..++|||+|||+++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.+ +..+.|+.|.|.++..
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            4689999999999999999999999999999985    4778999999999999999999755 5689999999998764


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      -
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.17  E-value=2.3e-11  Score=116.40  Aligned_cols=80  Identities=18%  Similarity=0.265  Sum_probs=69.5

Q ss_pred             cceEEecc----cCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECC----H-HH---HHHHHH--HhCCCe
Q 002974          363 GTLVVFNL----DSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYD----I-RA---AETALR--TLNRSD  423 (861)
Q Consensus       363 ~tLfVgNL----p~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d----~-ea---A~kAL~--~LNG~~  423 (861)
                      ++|||+||    |+.+++++|+++|++||+|.+|++     ++.++|||||+|.|    . ++   |.+|+.  .|+|..
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    999999999999999999999875     67889999999996    3 22   899988  789999


Q ss_pred             eCCcEEEEEeccCCchhhh
Q 002974          424 VAGKQIKLEASRPGGARRF  442 (861)
Q Consensus       424 I~Gr~IkVe~Akpk~~rrl  442 (861)
                      |.|++|+|.+-+.....++
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            9999999999887765443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.13  E-value=3.5e-11  Score=115.18  Aligned_cols=73  Identities=18%  Similarity=0.277  Sum_probs=65.0

Q ss_pred             cEEEEcCC----CCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCC----HHH----HHHHHH--HcCccc
Q 002974          278 RTLFVRNI----NSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYD----IRA----ARNAMK--ALQNKP  338 (861)
Q Consensus       278 rtLfVgNL----P~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d----~e~----A~kALk--aLnG~~  338 (861)
                      ..|||+||    |+.+++.+|+++|++||+|.+|.+     |+.++|||||+|.+    +++    |.+|++  .|+|..
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    999999999999999999999984     78999999999996    322    888988  789999


Q ss_pred             cCcceeeeeecC
Q 002974          339 LRRRKLDIHYSI  350 (861)
Q Consensus       339 L~Gr~L~V~~a~  350 (861)
                      |.|++|+|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999998753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=1.4e-10  Score=106.19  Aligned_cols=66  Identities=20%  Similarity=0.287  Sum_probs=60.0

Q ss_pred             CCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          372 SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       372 ~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ..+++++|+++|++||+|.+|++.++++|||||+|.+.++|++|++.++  .+.|++|+|.|++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCCC
Confidence            5789999999999999999999988899999999999999999999744  47899999999987753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.10  E-value=4.5e-10  Score=102.76  Aligned_cols=76  Identities=16%  Similarity=0.259  Sum_probs=64.6

Q ss_pred             CcEEEEcCCC-------CCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          277 SRTLFVRNIN-------SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       277 srtLfVgNLP-------~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .++|-|.-..       ..+++++|+++|++||+|..|++.++++|||||+|.+.++|++|++.+++  +.+++|+|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEc
Confidence            4455555443       56899999999999999999998789999999999999999999998555  67999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .++..
T Consensus        88 ~~~~~   92 (100)
T 2d9o_A           88 EGQPQ   92 (100)
T ss_dssp             SCCCC
T ss_pred             cCCCC
Confidence            87643

>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=99.10  E-value=2.3e-10  Score=105.16  Aligned_cols=77  Identities=17%  Similarity=0.316  Sum_probs=66.2

Q ss_pred             CCcceEEecc--cCCCc--------HHHHHHHhcccCcEEEEEeCC-------CCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          361 NQGTLVVFNL--DSSVS--------TEELHQIFGIYGEIREIRDTQ-------HKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       361 ~~~tLfVgNL--p~svT--------eedLrelFskfGeI~sVritg-------ksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      +.+.|.+.|+  +..+.        +++|++.|++||+|++|++..       +++|+|||+|.+.++|.+|++.|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4678899998  43443        379999999999999998742       458999999999999999999999999


Q ss_pred             eCCcEEEEEeccCC
Q 002974          424 VAGKQIKLEASRPG  437 (861)
Q Consensus       424 I~Gr~IkVe~Akpk  437 (861)
                      +.||+|+|.++...
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999998753

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.08  E-value=2e-10  Score=105.63  Aligned_cols=78  Identities=17%  Similarity=0.367  Sum_probs=67.6

Q ss_pred             CCCCcEEEEcCC--CCCCc--------HHHHHHHhhcCCCEEEEEeC-------CCcccEEEEEeCCHHHHHHHHHHcCc
Q 002974          274 EHPSRTLFVRNI--NSNVE--------DSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAMKALQN  336 (861)
Q Consensus       274 ~~~srtLfVgNL--P~~vT--------EedL~elFsqfG~I~svkit-------gksrGyAFVeF~d~e~A~kALkaLnG  336 (861)
                      ..|++.|.|.|+  |.++.        +++|++.|++||.|..|++.       .+++|||||+|.+.++|++|++.|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            357999999998  44443        36899999999999999962       25689999999999999999999999


Q ss_pred             cccCcceeeeeecCC
Q 002974          337 KPLRRRKLDIHYSIP  351 (861)
Q Consensus       337 ~~L~Gr~L~V~~a~~  351 (861)
                      +.+.||.|+|.|+..
T Consensus        82 ~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           82 RKFANRVVVTKYCDP   96 (105)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEeCCCEEEEEEeCH
Confidence            999999999998753

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.05  E-value=2.6e-10  Score=125.63  Aligned_cols=77  Identities=16%  Similarity=0.311  Sum_probs=67.7

Q ss_pred             CCCCCcEEEEcC--CCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccC---cc--eee
Q 002974          273 GEHPSRTLFVRN--INSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR---RR--KLD  345 (861)
Q Consensus       273 ~~~~srtLfVgN--LP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~---Gr--~L~  345 (861)
                      ...++++|||+|  |+..+||++|+++|++||+|..|++. .+||||||+|.+.++|++|++.|||+.+.   |+  .|+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~-~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC-TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            356899999999  57899999999999999999999874 47999999999999999999999999873   44  577


Q ss_pred             eeecC
Q 002974          346 IHYSI  350 (861)
Q Consensus       346 V~~a~  350 (861)
                      |.|+.
T Consensus        93 ~~~~~   97 (345)
T 3tht_A           93 LNFVE   97 (345)
T ss_dssp             EEECS
T ss_pred             EEEee
Confidence            78774

>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=99.04  E-value=1.4e-10  Score=106.36  Aligned_cols=68  Identities=29%  Similarity=0.399  Sum_probs=60.0

Q ss_pred             EecccCCCcHHHHHHHh------------cccCcEEEEEeC----CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          367 VFNLDSSVSTEELHQIF------------GIYGEIREIRDT----QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       367 VgNLp~svTeedLrelF------------skfGeI~sVrit----gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      +.||+..+++++|++.|            ++||+|.+|++.    ++++|||||+|.+.++|++|++.|||+.+.||+|+
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            66788888888777666            999999999974    34589999999999999999999999999999999


Q ss_pred             EEec
Q 002974          431 LEAS  434 (861)
Q Consensus       431 Ve~A  434 (861)
                      |+++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.02  E-value=1.2e-10  Score=106.79  Aligned_cols=68  Identities=19%  Similarity=0.347  Sum_probs=59.1

Q ss_pred             EcCCCCCCcHHHHHHHh------------hcCCCEEEEEeC----CCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          282 VRNINSNVEDSELKALF------------EQFGDIRTIYTA----CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       282 VgNLP~~vTEedL~elF------------sqfG~I~svkit----gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      +.+|+..+++++|++.|            ++||+|..|++.    ++++|||||+|.+.++|++|++.|||+.+.||+|+
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            45666777777777666            999999999973    45799999999999999999999999999999999


Q ss_pred             eeec
Q 002974          346 IHYS  349 (861)
Q Consensus       346 V~~a  349 (861)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.00  E-value=6e-10  Score=122.73  Aligned_cols=76  Identities=22%  Similarity=0.300  Sum_probs=66.4

Q ss_pred             ccCCcceEEec--ccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeC---Cc--EEEE
Q 002974          359 DANQGTLVVFN--LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA---GK--QIKL  431 (861)
Q Consensus       359 ~~~~~tLfVgN--Lp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~---Gr--~IkV  431 (861)
                      .....+|||+|  |+..+|+++|+++|++||+|++|.+. ..||||||+|.+.++|++|+++|||+++.   |+  .|.|
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 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECC-TTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEe-CCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEE
Confidence            34567999999  67899999999999999999999875 47999999999999999999999999883   45  6788


Q ss_pred             Eecc
Q 002974          432 EASR  435 (861)
Q Consensus       432 e~Ak  435 (861)
                      .+++
T Consensus        94 ~~~~   97 (345)
T 3tht_A           94 NFVE   97 (345)
T ss_dssp             EECS
T ss_pred             EEee
Confidence            8774

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.93  E-value=1.7e-09  Score=101.70  Aligned_cols=76  Identities=18%  Similarity=0.257  Sum_probs=64.9

Q ss_pred             CCcceEEeccc--CCC---cHHHHHHHhcccCcEEEEEeC---------CCCccEEEEEECCHHHHHHHHHHhCCCeeCC
Q 002974          361 NQGTLVVFNLD--SSV---STEELHQIFGIYGEIREIRDT---------QHKHNHKFIEFYDIRAAETALRTLNRSDVAG  426 (861)
Q Consensus       361 ~~~tLfVgNLp--~sv---TeedLrelFskfGeI~sVrit---------gksKGfAFVeF~d~eaA~kAL~~LNG~~I~G  426 (861)
                      ..++|++.|+-  .++   .+++|++.|++||+|.+|++.         ++.+|++||+|.+.++|.+|++.|||+.+.|
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            46789999983  222   368999999999999998762         2346999999999999999999999999999


Q ss_pred             cEEEEEeccC
Q 002974          427 KQIKLEASRP  436 (861)
Q Consensus       427 r~IkVe~Akp  436 (861)
                      |.|+|.++..
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

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.92  E-value=1.8e-09  Score=101.58  Aligned_cols=76  Identities=14%  Similarity=0.228  Sum_probs=66.1

Q ss_pred             CCCcEEEEcCCCC--CC---cHHHHHHHhhcCCCEEEEEeC---------CCcccEEEEEeCCHHHHHHHHHHcCccccC
Q 002974          275 HPSRTLFVRNINS--NV---EDSELKALFEQFGDIRTIYTA---------CKHRGFVMISYYDIRAARNAMKALQNKPLR  340 (861)
Q Consensus       275 ~~srtLfVgNLP~--~v---TEedL~elFsqfG~I~svkit---------gksrGyAFVeF~d~e~A~kALkaLnG~~L~  340 (861)
                      .++++|+|+|+-.  ++   -++||++.|++||+|..|++.         ++++|+|||+|.+.++|++|++.|||..+.
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            3799999999932  22   368999999999999999851         246799999999999999999999999999


Q ss_pred             cceeeeeecC
Q 002974          341 RRKLDIHYSI  350 (861)
Q Consensus       341 Gr~L~V~~a~  350 (861)
                      ||.|.|.|+.
T Consensus        98 GR~i~v~~~~  107 (118)
T 3ue2_A           98 GRKVVAEVYD  107 (118)
T ss_dssp             TEECEEEEEC
T ss_pred             CcEEEEEEcC
Confidence            9999999875

>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=98.90  E-value=3e-09  Score=99.54  Aligned_cols=77  Identities=16%  Similarity=0.131  Sum_probs=64.8

Q ss_pred             CCcceEEecccC--CC--------cHHHHHHHhcccCcEEEEEeCCC-CccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          361 NQGTLVVFNLDS--SV--------STEELHQIFGIYGEIREIRDTQH-KHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       361 ~~~tLfVgNLp~--sv--------TeedLrelFskfGeI~sVritgk-sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                      ..+.|.+.|+=.  +.        .+++|++.|++||.|++|.+... .+|++||+|.+.++|.+|++.|||+.+.||.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            456788888832  21        24689999999999999987433 48999999999999999999999999999999


Q ss_pred             EEEeccCC
Q 002974          430 KLEASRPG  437 (861)
Q Consensus       430 kVe~Akpk  437 (861)
                      +|.++...
T Consensus        86 ~v~~~~~~   93 (114)
T 3s6e_A           86 TAAYVPLP   93 (114)
T ss_dssp             EEEEECHH
T ss_pred             EEEEEcHH
Confidence            99998643

>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=98.88  E-value=3.8e-09  Score=98.86  Aligned_cols=77  Identities=17%  Similarity=0.214  Sum_probs=65.9

Q ss_pred             CCCCcEEEEcCCCCCC----------cHHHHHHHhhcCCCEEEEEeCC-CcccEEEEEeCCHHHHHHHHHHcCccccCcc
Q 002974          274 EHPSRTLFVRNINSNV----------EDSELKALFEQFGDIRTIYTAC-KHRGFVMISYYDIRAARNAMKALQNKPLRRR  342 (861)
Q Consensus       274 ~~~srtLfVgNLP~~v----------TEedL~elFsqfG~I~svkitg-ksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr  342 (861)
                      ..+++.|.+.|+=..-          -++||++.|++||.|..|++.. ..+|||||+|.+.++|++|++.|||..+.||
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            3578899999983221          1468899999999999999743 3589999999999999999999999999999


Q ss_pred             eeeeeecC
Q 002974          343 KLDIHYSI  350 (861)
Q Consensus       343 ~L~V~~a~  350 (861)
                      .|+|.|+.
T Consensus        84 ~i~v~~~~   91 (114)
T 3s6e_A           84 MITAAYVP   91 (114)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEEc
Confidence            99999985

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.67  E-value=6.3e-08  Score=87.21  Aligned_cols=75  Identities=27%  Similarity=0.419  Sum_probs=63.9

Q ss_pred             cCCcceEEecccC----CCcH----HHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Q 002974          360 ANQGTLVVFNLDS----SVST----EELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL  431 (861)
Q Consensus       360 ~~~~tLfVgNLp~----svTe----edLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkV  431 (861)
                      ....||+|.-.+.    .+-+    .+|.+.|++||+|..+++...   .+||+|.+.++|.+|++ |||..+.||.|+|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d---~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV   80 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED---KMWVTFLEGSSALNVLS-LNGKELLNRTITI   80 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS---SEEEEESSHHHHHHGGG-GTTCEETTEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC---CEEEEECChHHHHHHHh-cCCeEeCCeEEEE
Confidence            4567889988762    3434    679999999999999998653   39999999999999999 9999999999999


Q ss_pred             EeccCCc
Q 002974          432 EASRPGG  438 (861)
Q Consensus       432 e~Akpk~  438 (861)
                      +++.+.-
T Consensus        81 ~lkt~dW   87 (91)
T 2dnr_A           81 ALKSPSG   87 (91)
T ss_dssp             EECCCSS
T ss_pred             EeCCCCc
Confidence            9998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.64  E-value=6.5e-08  Score=91.62  Aligned_cols=80  Identities=19%  Similarity=0.162  Sum_probs=69.8

Q ss_pred             CCcceEEecccCC-CcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECC-HHHHHHHHHHhC--CCeeCCcEEEEEeccC
Q 002974          361 NQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYD-IRAAETALRTLN--RSDVAGKQIKLEASRP  436 (861)
Q Consensus       361 ~~~tLfVgNLp~s-vTeedLrelFskfGeI~sVritgksKGfAFVeF~d-~eaA~kAL~~LN--G~~I~Gr~IkVe~Akp  436 (861)
                      ....|||+||+.. +++++|+++|++||+|..|.+.. ....|||+|.+ .++|+.|++.||  +..|.|..++++...-
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~-g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~G   95 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   95 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEec-CCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCC
Confidence            3568999999999 99999999999999999999753 34479999999 899999999995  6789999999998876


Q ss_pred             Cchhh
Q 002974          437 GGARR  441 (861)
Q Consensus       437 k~~rr  441 (861)
                      ..++.
T Consensus        96 eeE~~  100 (121)
T 1owx_A           96 EVEKE  100 (121)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66655

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.53  E-value=2.8e-07  Score=87.27  Aligned_cols=76  Identities=18%  Similarity=0.174  Sum_probs=64.8

Q ss_pred             CCCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCC-HHHHHHHHHHcC--ccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYD-IRAARNAMKALQ--NKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~-vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d-~e~A~kALkaLn--G~~L~Gr~L~V~~  348 (861)
                      .-.+.+.|||+||+.+ +++++|+++|++||+|..|.+. ...-.|||+|.+ .++|.+|++.|+  +..|.|..+++..
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 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEe-cCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            3456899999999999 9999999999999999999973 233379999999 899999999994  6778888777765


Q ss_pred             c
Q 002974          349 S  349 (861)
Q Consensus       349 a  349 (861)
                      .
T Consensus        93 L   93 (121)
T 1owx_A           93 L   93 (121)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.44  E-value=3.8e-07  Score=82.15  Aligned_cols=74  Identities=24%  Similarity=0.338  Sum_probs=62.1

Q ss_pred             CCCcEEEEcCCC----CCCcH----HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          275 HPSRTLFVRNIN----SNVED----SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       275 ~~srtLfVgNLP----~~vTE----edL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      .|..||+|.-.+    .++-+    .+|.+.|.+||+|..+++-.   +.+||+|.+.++|.+|++ |+|..+.||.|+|
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            456788888776    23333    67899999999999999733   339999999999999998 9999999999999


Q ss_pred             eecCCC
Q 002974          347 HYSIPK  352 (861)
Q Consensus       347 ~~a~~k  352 (861)
                      +++.+.
T Consensus        81 ~lkt~d   86 (91)
T 2dnr_A           81 ALKSPS   86 (91)
T ss_dssp             EECCCS
T ss_pred             EeCCCC
Confidence            998764

>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=98.37  E-value=2.7e-07  Score=83.62  Aligned_cols=74  Identities=26%  Similarity=0.355  Sum_probs=62.3

Q ss_pred             ccCCcceEEecccCC-----CcH----HHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          359 DANQGTLVVFNLDSS-----VST----EELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       359 ~~~~~tLfVgNLp~s-----vTe----edLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                      .....||+|.-++..     +-+    .+|.+.|++||+|..+++....   +||+|.+.++|.+||+ |||..+.||.|
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            345789999988643     323    6699999999999999986443   9999999999999999 99999999999


Q ss_pred             EEEeccC
Q 002974          430 KLEASRP  436 (861)
Q Consensus       430 kVe~Akp  436 (861)
                      +|++..+
T Consensus        88 ~V~~k~~   94 (95)
T 1ufw_A           88 KISGPSS   94 (95)
T ss_dssp             EEECCCC
T ss_pred             EEeccCC
Confidence            9987654

>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=98.33  E-value=6.9e-07  Score=91.22  Aligned_cols=63  Identities=19%  Similarity=0.226  Sum_probs=57.0

Q ss_pred             CcHHHHHHHhcccCcEEEEEeC----C-----CCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          374 VSTEELHQIFGIYGEIREIRDT----Q-----HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       374 vTeedLrelFskfGeI~sVrit----g-----ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      -.+++|++.|++||+|.+|.+.    .     +.+|++||+|.+.++|.+|++.|||+.++||.|+|.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4568999999999999998862    2     6789999999999999999999999999999999999863

>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=98.25  E-value=1.5e-06  Score=88.72  Aligned_cols=62  Identities=13%  Similarity=0.155  Sum_probs=56.6

Q ss_pred             CcHHHHHHHhhcCCCEEEEEe---------CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          289 VEDSELKALFEQFGDIRTIYT---------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       289 vTEedL~elFsqfG~I~svki---------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      -.+++|++.|++||.|..+++         ++.++|++||+|.+.++|++|++.|+|..+.||.|.+.|+.
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            357899999999999999986         23789999999999999999999999999999999999874

>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=98.12  E-value=2.6e-06  Score=77.24  Aligned_cols=72  Identities=14%  Similarity=0.218  Sum_probs=60.1

Q ss_pred             CCCcEEEEcCCCCC-----C-cH---HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          275 HPSRTLFVRNINSN-----V-ED---SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       275 ~~srtLfVgNLP~~-----v-TE---edL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      .|..||+|.-++..     + ++   .+|.+.|.+||+|..+++-..   -+||+|.+.++|.+||+ |+|+.+.||.|+
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 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG---QMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT---EEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC---cEEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            46789999988743     2 22   568899999999999996322   29999999999999998 999999999999


Q ss_pred             eeecC
Q 002974          346 IHYSI  350 (861)
Q Consensus       346 V~~a~  350 (861)
                      |++-.
T Consensus        89 V~~k~   93 (95)
T 1ufw_A           89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EeccC
Confidence            98754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.88  E-value=2.9e-05  Score=72.09  Aligned_cols=73  Identities=27%  Similarity=0.274  Sum_probs=65.7

Q ss_pred             CCcceEEecccCCCcHHHHHHHhccc-----CcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIY-----GEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskf-----GeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ..++|-+-|||..+++..|+.+..+|     |.|+.|.+.+.. +=|+|+|.|...|.+|.-+|+|.+|.||+|+|.-.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-CceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            46899999999999999999999999     999998876554 45999999999999999999999999999998643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.42  E-value=0.00092  Score=61.42  Aligned_cols=89  Identities=17%  Similarity=0.206  Sum_probs=74.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhc-----CCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQ-----FGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsq-----fG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...++|.|.|||+.+.++.|.-+|+.     =|+|..+....   +-|+|+|.+.+.|++.++ -....|++..|.|...
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            34689999999999999999999997     26899998744   789999999999999996 4467889999999776


Q ss_pred             CCCCCCCCcccCCcceEEecccCCCc
Q 002974          350 IPKDNPSEKDANQGTLVVFNLDSSVS  375 (861)
Q Consensus       350 ~~k~~~~~k~~~~~tLfVgNLp~svT  375 (861)
                      .+++        .++|++.+|++.++
T Consensus        82 ~~~~--------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           82 PPRA--------PARLLLQGLPPGTS   99 (104)
T ss_dssp             CCCC--------CCCCCCCSCCCCCC
T ss_pred             CCCC--------cceEeeecCCCCCC
Confidence            5543        36899999998764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.38  E-value=0.00034  Score=64.98  Aligned_cols=72  Identities=14%  Similarity=0.171  Sum_probs=64.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcC-----CCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQF-----GDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqf-----G~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...++|-+=|||..++++.|+.+.+.+     |.|+.+.+- ...+=|+|+|.|...|-+|.-+|+|..|.||+|++.
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            457899999999999999999999999     999999873 344569999999999999998999999999999984

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.11  E-value=0.0017  Score=59.68  Aligned_cols=76  Identities=21%  Similarity=0.234  Sum_probs=66.6

Q ss_pred             CcceEEecccCCCcHHHHHHHhcc-----cCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGI-----YGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFsk-----fGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ..+|.|.|||+.++++.|.-+|+.     =|+|..+...+   +-|+|+|.+.+.|++.|+ -....+.+..|.|.+.-+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLA-QADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEEECCC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhc-CCcceecCeEEEEEcCCC
Confidence            468999999999999999999987     26899998765   779999999999999998 237789999999999988


Q ss_pred             Cchhh
Q 002974          437 GGARR  441 (861)
Q Consensus       437 k~~rr  441 (861)
                      +..++
T Consensus        84 ~~~~r   88 (104)
T 2dhx_A           84 RAPAR   88 (104)
T ss_dssp             CCCCC
T ss_pred             CCcce
Confidence            88766

>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=0.0016  Score=59.88  Aligned_cols=76  Identities=18%  Similarity=0.233  Sum_probs=63.0

Q ss_pred             CcceEEecccCCC-c----HHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSV-S----TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~sv-T----eedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|+|.||+.++ .    .+.++++|..|+++........-+ =..|.|.+.++|.+|...|++..+.|++|+|.++++
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            3689999998866 2    257789999999888766543223 468999999999999999999999999999999986


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      -.
T Consensus        84 ~~   85 (104)
T 1wey_A           84 LH   85 (104)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=96.70  E-value=0.0018  Score=59.58  Aligned_cols=75  Identities=17%  Similarity=0.223  Sum_probs=63.8

Q ss_pred             CcEEEEcCCCCCC-c----HHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          277 SRTLFVRNINSNV-E----DSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       277 srtLfVgNLP~~v-T----EedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      .++|+|.||+.++ +    .+.++++|.+|+++..... -++-.-..|.|.+.++|.+|...|++..+.|++|+|-++.+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~-lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEE-ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceee-cCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            5789999998876 2    2578899999998877664 35555679999999999999999999999999999999875


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      .
T Consensus        84 ~   84 (104)
T 1wey_A           84 L   84 (104)
T ss_dssp             S
T ss_pred             C
Confidence            4

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.48  E-value=0.0078  Score=56.71  Aligned_cols=77  Identities=16%  Similarity=0.144  Sum_probs=63.9

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCC-cEEEEEeccCC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG-KQIKLEASRPG  437 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G-r~IkVe~Akpk  437 (861)
                      ....+.|.|.+.|... -..|.+.|++||+|.+... ....++-.|+|.+..+|++||. .||..|.| ..|=|.+...+
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~d~   97 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   97 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECCCH
Confidence            3456789999999885 5667789999999999886 4567899999999999999999 69999985 77888887654


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        98 ~   98 (119)
T 1wwh_A           98 N   98 (119)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=95.38  E-value=0.05  Score=49.57  Aligned_cols=55  Identities=20%  Similarity=0.317  Sum_probs=45.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ  335 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLn  335 (861)
                      .+.++| ++|+.+...||.++|+.||.|.--.+   .---|||.|.+++.|..|++.+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wi---dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWI---DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEE---ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEE---cCCeEEEEecCHHHHHHHHHhcc
Confidence            566777 99999999999999999996544444   23479999999999999998764

>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=95.23  E-value=0.037  Score=49.78  Aligned_cols=64  Identities=5%  Similarity=0.050  Sum_probs=53.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CCC------cccEEEEEeCCHHHHHHHHHHcCccccCc
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACK------HRGFVMISYYDIRAARNAMKALQNKPLRR  341 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-tgk------srGyAFVeF~d~e~A~kALkaLnG~~L~G  341 (861)
                      ++|.|++||+..||+++.+.+..+..+...+. .++      .-.-|||.|.+.+++....+.++|..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            57999999999999999999999988766552 222      22479999999999999999999988653

>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=94.67  E-value=0.088  Score=49.59  Aligned_cols=72  Identities=15%  Similarity=0.167  Sum_probs=59.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCc-ceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR-RKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~G-r~L~V~~a  349 (861)
                      ...+.|-|=+.|+.. ...+...|++||+|.+... .....+..|.|.+..+|++||. .||+.|.| -.|-|.+.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~-~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc-CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            347888998998884 6778889999999999887 3456799999999999999996 79998874 55666654

>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=94.59  E-value=0.16  Score=45.65  Aligned_cols=63  Identities=11%  Similarity=0.098  Sum_probs=52.1

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-CCC------CccEEEEEECCHHHHHHHHHHhCCCeeC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQH------KHNHKFIEFYDIRAAETALRTLNRSDVA  425 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-tgk------sKGfAFVeF~d~eaA~kAL~~LNG~~I~  425 (861)
                      ++|.|++||+.+|++++.+.++...++..... .++      .-.-|||.|.+.+++..-.+.++|..+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            47999999999999999999999988766543 121      1235999999999999999999999774

>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=94.17  E-value=0.13  Score=46.80  Aligned_cols=52  Identities=25%  Similarity=0.380  Sum_probs=42.4

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcE--EEEEeCCCCccEEEEEECCHHHHHHHHHHhC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEI--REIRDTQHKHNHKFIEFYDIRAAETALRTLN  420 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI--~sVritgksKGfAFVeF~d~eaA~kAL~~LN  420 (861)
                      ..++| ++|+++...||.++|+.||.|  ..|..     ..|||.|.+++.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~I~WidD-----TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDD-----TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEET-----TEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEEEEEEcC-----CeEEEEecCHHHHHHHHHhcc
Confidence            34555 999999999999999999843  34442     369999999999999999763

>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=93.70  E-value=0.065  Score=48.93  Aligned_cols=54  Identities=20%  Similarity=0.327  Sum_probs=44.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ  335 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLn  335 (861)
                      +.++| ++|+.+...||.++|+.||.|.--.+   .-.-|||.|.+++.|..|+..+.
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            45666 99999999999999999996554445   23479999999999999998764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.25  E-value=0.073  Score=50.92  Aligned_cols=73  Identities=16%  Similarity=0.203  Sum_probs=57.1

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEE-EEe----------------CC--CCccEEEEEECCHHHHHHHHHHhCCC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRD----------------TQ--HKHNHKFIEFYDIRAAETALRTLNRS  422 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~s-Vri----------------tg--ksKGfAFVeF~d~eaA~kAL~~LNG~  422 (861)
                      ...|.|.+.|+..+. .+.+.|++||.|.+ +..                .+  ...++..|+|.+..+|.+||+ -||+
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            456888999776654 45678999999977 211                11  135678999999999999999 6999


Q ss_pred             eeCCcEEEEEeccC
Q 002974          423 DVAGKQIKLEASRP  436 (861)
Q Consensus       423 ~I~Gr~IkVe~Akp  436 (861)
                      .|.|..|=|.+..+
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            99999999998863

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.79  E-value=0.04  Score=62.91  Aligned_cols=58  Identities=12%  Similarity=0.300  Sum_probs=44.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHH
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK  332 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALk  332 (861)
                      ++..|+|||. .|..+++.+|.++|++||+|..+.......-||.|+|.+.++++.++.
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            3458999997 799999999999999999999998755555699999999999997765

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.65  E-value=0.049  Score=62.21  Aligned_cols=56  Identities=13%  Similarity=0.145  Sum_probs=44.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHH
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR  417 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~  417 (861)
                      ..+.|+|. .+..+++.+|.++|++||.|..+........||.|+|.+.+++.+++.
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            35789997 799999999999999999999998776667799999999999997765

>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=91.92  E-value=0.091  Score=48.00  Aligned_cols=53  Identities=23%  Similarity=0.360  Sum_probs=42.6

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhC
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN  420 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LN  420 (861)
                      .++| ++|+++...||.++|+.||.| .|+...  -..|||.|.+++.|..|+..+.
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            4555 999999999999999999843 333321  3479999999999999999775

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=91.33  E-value=0.19  Score=45.72  Aligned_cols=66  Identities=8%  Similarity=0.040  Sum_probs=51.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eCCC------cccEEEEEeCCHHHHHHHHHHcCccccCc
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-TACK------HRGFVMISYYDIRAARNAMKALQNKPLRR  341 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-itgk------srGyAFVeF~d~e~A~kALkaLnG~~L~G  341 (861)
                      .+-+|.|+.||+..||+++.+.+..+=++...+ +.++      .-.-|||.|.+.++.....+..+|..+.+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            467899999999999999988887765553332 1111      12369999999999999999999988653

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=89.72  E-value=0.58  Score=42.53  Aligned_cols=72  Identities=10%  Similarity=0.040  Sum_probs=53.4

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-CCC----C--ccEEEEEECCHHHHHHHHHHhCCCeeCC-----cEEE
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQH----K--HNHKFIEFYDIRAAETALRTLNRSDVAG-----KQIK  430 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-tgk----s--KGfAFVeF~d~eaA~kAL~~LNG~~I~G-----r~Ik  430 (861)
                      -+|.|+.||+.+|++++.+.++..-++..... .++    .  -.-|||.|.+.++...-.+..+|..+-+     .+..
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            47999999999999999998888666543221 111    1  1248999999999999999999997742     3445


Q ss_pred             EEec
Q 002974          431 LEAS  434 (861)
Q Consensus       431 Ve~A  434 (861)
                      |++|
T Consensus        90 VE~A   93 (97)
T 2l08_A           90 VEFA   93 (97)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            5555

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=88.49  E-value=0.43  Score=45.61  Aligned_cols=71  Identities=15%  Similarity=0.196  Sum_probs=52.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eC-----------------C-CcccEEEEEeCCHHHHHHHHHHcCcc
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIY-TA-----------------C-KHRGFVMISYYDIRAARNAMKALQNK  337 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svk-it-----------------g-ksrGyAFVeF~d~e~A~kALkaLnG~  337 (861)
                      ...|.|=+.|++ ....+.+.|++||.|.+-. .+                 . ...++..|+|.+..+|++||. .||+
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            445666667544 4556778899999997732 11                 0 135688999999999999996 8999


Q ss_pred             ccCcceeeeeec
Q 002974          338 PLRRRKLDIHYS  349 (861)
Q Consensus       338 ~L~Gr~L~V~~a  349 (861)
                      .|.|..|-|.+.
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            999887777665

---

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	861
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-13
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-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
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-07
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-13
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-12
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	2e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	9e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-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
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-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 {	7e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	9e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-11
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	6e-10
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	4e-06
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
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	3e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-10
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	7e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-07
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	1e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-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	5e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-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
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-07
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
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	9e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-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 (	2e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-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	4e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	5e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	6e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	6e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-05
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
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	6e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.002
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	7e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	6e-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	1e-06
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
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-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
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	5e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-05
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	0.001
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-05
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	0.002
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	8e-04
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	9e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.3 bits (182), Expect = 1e-16
 Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK--HRGFVMISYYDIRAARNAMKA 333
            +R L++RN+   +   E+  +F ++G IR I        RG   + Y DI  A+NA   
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 334 LQNKPLRRRKLDIHYSIPKDNPSEKDANQ 362
           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 = 63.5 bits (154), Expect = 8e-13
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHN--HKFIEFYDIRAAETALRTLNR 421
            L + NL   ++ EE++ IFG YG IR+IR           ++ + DI  A+ A   L+ 
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 422 SDVAGKQIKLEASRPGGARRFMVQSEQEQD 451
            +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 = 75.4 bits (184), Expect = 3e-16
 Identities = 31/171 (18%), Positives = 55/171 (32%), Gaps = 12/171 (7%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAM 331
            R LF+  ++    D  L++ FEQ+G +            + RGF  ++Y  +     AM
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 332 KAL-QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIR 390
            A       R  +     S               + V  +        L   F  YG+I 
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125

Query: 391 EIRDTQHKHNHK-----FIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
            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 = 7e-14
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDI--------RTIYTACKHRGFVMISYYDIRAARNAM 331
           LF++N+N +  +  LK +F + G I        +         GF  + Y     A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 332 KALQNKPLRRRKLDIHYSIPKDNPS 356
           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 = 6e-10
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK--------FIEFYDIRAAETAL 416
           L + NL+ S + E L  +F   G I+    ++ K+           F+E+     A+ AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 417 RTLNRSDVAGKQIKLEASRPG 437
           + 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 = 65.4 bits (159), Expect = 1e-13
 Identities = 20/81 (24%), Positives = 38/81 (46%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
            +RTL  +N++ N+ + ELK +FE   +IR +    K +G   I +     A   ++  Q
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74

Query: 336 NKPLRRRKLDIHYSIPKDNPS 356
              +  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 = 62.8 bits (152), Expect = 1e-12
 Identities = 22/87 (25%), Positives = 38/87 (43%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAET 414
            S+K     TL+  NL  +++ +EL ++F    EIR +          +IEF     AE 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARR 441
            L     +++ G+ + L  +   G  R
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGEKGGTR 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 = 64.3 bits (156), Expect = 2e-13
 Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 9/93 (9%)

Query: 279 TLFVRNINSNVEDSELKALFEQFG-------DIRTIYTACKHRGFVMISYYDIRAARNAM 331
            LF+  I    +  E+     +            +     K+RGF  + Y   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 332 KALQNKPLRR--RKLDIHYSIPKDNPSEKDANQ 362
           + 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 = 46.2 bits (109), Expect = 6e-07
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYG----EIREIRDTQHKHNHK---FIEFYDIRAAETAL 416
            L +  +      EE+ +          ++        K  ++   F+E+   RAA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 417 RTLNRSDV--AGKQIKLEASRP 436
           R L    +   G QI ++ + P
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEP 84

>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 = 2e-13
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNA 330
            S TL+V N++    + ++  LF + GDI+ I            GF  + YY    A NA
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 331 MKALQNKPLRRRKLDIHYSIPK 352
           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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
           TL V NL    + E+++++F   G+I++I     K         F+E+Y    AE A+R 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           +N + +  + I+ +        R
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEGR 91

>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 = 62.8 bits (152), Expect = 8e-13
 Identities = 23/89 (25%), Positives = 47/89 (52%), Gaps = 6/89 (6%)

Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIR--TIYTACKHRGFVMISYYDIRAARN 329
           P+ T+++ N+N  ++  ELK    A+F +FG I    +  + K RG   + + ++ +A N
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPSEK 358
           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 = 1e-07
 Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 364 TLVVFNLDSSVSTEELHQ----IFGIYGEIREIRDTQHKHN--HKFIEFYDIRAAETALR 417
           T+ + NL+  +  +EL +    IF  +G+I +I  ++        F+ F ++ +A  ALR
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 418 TLNRSDVAGKQIKLEASRP 436
           ++       K ++++ ++ 
Sbjct: 65  SMQGFPFYDKPMRIQYAKT 83

>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 = 61.9 bits (150), Expect = 2e-12
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC------KHRGFVMISYYDIRAA 327
           +  +  + VRNI       E++ LF  FG+++T+           HRGF  + +   + A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 328 RNAMKALQN-KPLRRRKLDIHYSIPKD 353
           + 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 = 56.5 bits (136), Expect = 1e-10
 Identities = 18/94 (19%), Positives = 42/94 (44%), Gaps = 13/94 (13%)

Query: 350 IPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE------IREIRDTQHKHNHKF 403
           +PK   + K      ++V N+    +  E+ ++F  +GE       +++  T       F
Sbjct: 2   VPKKQTTSK------ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 55

Query: 404 IEFYDIRAAETALRTL-NRSDVAGKQIKLEASRP 436
           ++F   + A+ A   L + + + G+++ LE +  
Sbjct: 56  VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 89

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
            + L+VRN+  +  +  ++  F             K R +  + + +   A  AMKAL  
Sbjct: 8   VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 337 KPLRRRKLDIHYSIPKDNPS 356
           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 = 50.8 bits (121), Expect = 1e-08
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            L V NL  S S E + + F         R  +   ++ F+ F +   A  A++ LN   
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER-VKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 424 VAGKQIKLEASRP 436
           + G  I++  ++P
Sbjct: 69  LDGSPIEVTLAKP 81

>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 = 61.6 bits (149), Expect = 2e-12
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKHNHKFIEFYDIRAAE 413
           E D    TL V NL   V+   + Q+F   G  +  +   +      + F+EFY+ R A 
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 414 TALRTLNRSDVAGKQIKLEASRPGGARR 441
            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 = 60.1 bits (145), Expect = 7e-12
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYY---DIRAARNA 330
           +   RTL+V N++ +V +  +  LF Q G  ++     +H       +    + R A  A
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAA 64

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           + A+  + +  +++ ++++    +
Sbjct: 65  LAAMNGRKILGKEVKVNWATTPSS 88

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNA 330
             R L+V  +   V+D  L A F  FGDI  I         KHRGF  + +     A  A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 331 MKALQNKPLRRRKLDIHYSIPK 352
           +  +    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 = 55.4 bits (133), Expect = 3e-10
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L V  L   V  + LH  F  +G+I +I      +T+      F+EF     A  A+  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 419 LNRSDVAGKQIKLEASRP 436
           +N S++ G+ I++  ++P
Sbjct: 67  MNESELFGRTIRVNLAKP 84

>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 = 61.4 bits (149), Expect = 2e-12
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 276 PSRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
            +  +F+ N+N+  V+ S+++A+F ++G I        H+GF  + Y + R AR A+   
Sbjct: 14  MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNARAAVAGE 70

Query: 335 QNKPLRRRKLDIHYSIPKDNP 355
             + +  + 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 = 56.8 bits (137), Expect = 1e-10
 Identities = 15/89 (16%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTE-ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 412
             ++  +    + + NL++ V  + ++  IF  YG+I             F+++ + R A
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---VHKGFAFVQYVNERNA 63

Query: 413 ETALRTLNRSDVAGKQIKLEASRPGGARR 441
             A+   +   +AG+ + +  +      R
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>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 = 3e-12
 Identities = 13/76 (17%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKA 333
           +L+V +++ +V ++ L   F   G I +I         +  G+  +++     A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 334 LQNKPLRRRKLDIHYS 349
           +    ++ + + 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 = 7e-12
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 418
           +L V +L   V+   L++ F   G I  IR      T+    + ++ F     AE AL T
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 419 LNRSDVAGKQIKLEASR 435
           +N   + GK +++  S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 418
            L+V  L   ++  EL+ +F   G I   R      T + + + F++F     ++ A++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 419 LNRSDVAGKQIKLEASRPG 437
           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 = 58.5 bits (141), Expect = 2e-11
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-----FVMISYYDIRAARNAM 331
           +  L V  +  ++ D EL ALF   G I T      ++      +  + +     ++ A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 332 KALQNKPLRRRKLDIHYSIP 351
           K L    +R ++L + Y+ P
Sbjct: 62  KVLNGITVRNKRLKVSYARP 81

>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 = 60.8 bits (147), Expect = 5e-12
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
            + T++   I S + D  ++  F  FG I  I      +G+  + +    +A +A+ ++ 
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVN 75

Query: 336 NKPLRRRKLDIHYSIPKDNPS 356
              +    +  ++     + +
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 = 60.0 bits (145), Expect = 9e-12
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 353 DNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAA 412
           D  ++      T+    + S ++ + + Q F  +G+I EIR    +  + F+ F    +A
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR-VFPEKGYSFVRFSTHESA 67

Query: 413 ETALRTLNRSDVAGKQIKLEASRP 436
             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 = 60.4 bits (146), Expect = 5e-12
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIF---GIYGEIREIRDTQHKHNHKFIEFYDIRA 411
           PS + +  G + + NLD S+  + L+  F   G     + + D      + F+ F    A
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA 60

Query: 412 AETALRTLNRSDVAGKQIKLEASRP 436
           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 = 57.4 bits (138), Expect = 5e-11
 Identities = 13/79 (16%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFG---DIRTIYTACKHRGFVMISYYDIRAARNAMKA 333
              +F++N++ ++++  L   F  FG     + +      +G+  + +    AA  A++ 
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 334 LQNKPLRRRKLDIHYSIPK 352
           +    L  RK+ +     +
Sbjct: 68  MNGMLLNDRKVFVGRFKSR 86

>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 = 59.6 bits (144), Expect = 7e-12
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAAETALRT 418
           G L+V NLD  VS  ++ ++F  +G +++       +        + F     A  A++ 
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 419 LNRSDVAGKQIKLE 432
            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 = 54.2 bits (130), Expect = 5e-10
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI----YTACKHRGFVMISYYDIRAARNAMKALQ 335
           L V N++  V D++++ LF +FG ++        + +  G   + +     A  AMK   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 336 NKPLRRRKLDIHYS 349
             PL  R ++I   
Sbjct: 63  GVPLDGRPMNIQLV 76

>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 = 7e-12
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIR------TIYTACKHRGFVMISYYDIRAARNAMKA 333
           +F+ N++  +++  L   F  FG I               +G+  I++    A+  A++A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 334 LQNKPLRRRKLDIHYSIPKDN 354
           +  + 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: 365 LVVFNLDSSVSTEELHQIFGIYGEIRE------IRDTQHKHNHKFIEFYDIRAAETALRT 418
           + + NLD  +  + L+  F  +G I +        DT +   + FI F    A++ A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 419 LNRSDVAGKQIKLEASRPGGAR 440
           +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 = 60.0 bits (145), Expect = 7e-12
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           G   S  +FV     ++ + EL+  F Q+GD+  ++     R F  +++ D + A++   
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 333 ALQNKPLRRRKLDIHYSIPKDNPS 356
             ++  ++   + 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 = 52.7 bits (126), Expect = 3e-09
 Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            + V      ++ +EL + F  YG++ ++   +      F+ F D + A++         
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLI 64

Query: 424 VAGKQIKLEASRPGGARR 441
           + 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 = 9e-12
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 327
           GE  + +     LFV N+  ++ + E++ LFE++G    ++   K +GF  I       A
Sbjct: 1   GEKTFTQR--SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLA 57

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
             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 = 5e-10
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETAL 416
           +    +  L V NL   ++ EE+ ++F  YG+  E+          FI       AE A 
Sbjct: 3   KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAK 61

Query: 417 RTLNRSDVAGKQIKLEASRPGGA 439
             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 = 60.4 bits (146), Expect = 9e-12
 Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 9/102 (8%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDI-RTIYTACKHRGFVMISYYDIRAARNAM 331
           G+ P   + V N+   V    L  +F +FG + + I     ++   ++ Y D  +A++A 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 62

Query: 332 KALQNKPL--RRRKLDIHYS------IPKDNPSEKDANQGTL 365
            +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 = 49.2 bits (117), Expect = 6e-08
 Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKH-NHKFIEFYDIRAAETALRTLNRSD 423
           ++V NL   V+ + LHQIF  +G + +I      +     +++ D  +A+ A  +L+  +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 424 V--AGKQIKLEASRP 436
           +  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 = 59.7 bits (144), Expect = 1e-11
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 5/84 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGD-----IRTIYTACKHRGFVMISYYDIRAARNA 330
              T++V  ++  V +  L  LF Q G      +       +H+G+  + +     A  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           +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 = 57.7 bits (139), Expect = 5e-11
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDI 409
           P  +     T+ V  LD  VS   L ++F   G +          T     + F+EF   
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 410 RAAETALRTLNRSDVAGKQIKLEASRP 436
             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 = 59.3 bits (143), Expect = 1e-11
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDI 409
           P+ +  +  T+ V NL       +L ++F  +G I        + T       FI F+  
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 410 RAAETALRTLNRSDVAGKQIKLEASRP 436
             A  A+  ++        + +E ++P
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKP 87

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 3e-11
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAARNA 330
            + T+ V N++ +  +++L+ LF  FG I  IY A      + +GF  IS++    A  A
Sbjct: 7   DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 66

Query: 331 MKALQNKPLRRRKLDIHYSIPKDN 354
           +  +         L++ ++ P  N
Sbjct: 67  IAGVSGFGYDHLILNVEWAKPSTN 90

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 1e-10
 Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK---HRGFVMISYYDIRAARN 329
            +   + L V NI     D +L+ +F QFG I  +         +GF  +++ +   A  
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 330 AMKALQNKPLRRRKLDIHYSIPKDNPS 356
           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 = 54.7 bits (131), Expect = 6e-10
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRDTQHKHNHKFIEFYDIRAA 412
           SE  +    L V N+       +L Q+FG +G+I +   I + +      F+ F +   A
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 64

Query: 413 ETALRTLNRSDVAGKQIKLEASRP 436
           + A   L+ + V G++I++  +  
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNATA 88

>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: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK- 337
            L++ N++  V   +L+ LF                G+  + Y D   A  A++ L  K 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 338 PLRRRKLDIHYSIPKDNPS 356
            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 = 4e-06
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLN-RS 422
            L + NL  +V+ ++L Q+FG        +       + F+++ D   A  A+ TL+ + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG-YAFVDYPDQNWAIRAIETLSGKV 61

Query: 423 DVAGKQIKLEASRPGGAR 440
           ++ GK ++++ S     R
Sbjct: 62  ELHGKIMEVDYSVSKKLR 79

>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: 277 SRTLFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAM 331
              L+V N+   + D +L  +F ++G I            + RG   + Y     A+ A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 332 KALQNKPL--RRRKLDIHY 348
            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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIR-----EIRDTQHKHNHKFIEFYDIRAAETALRT 418
            L V NL  +++ ++L  IFG YG I        + T       F+ +     A+ A+  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 419 LNRSDVAGKQIKLE 432
           LN     G    L 
Sbjct: 68  LNNVIPEGGSQPLS 81

>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: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNA 330
               LFV +I+   ++ E++  F  +G+I+ I+          +G+ ++ Y   + A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 331 MKALQNKPLRRRKLDIHYSIPK 352
            +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 = 3e-09
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIR-----EIRDTQHKHNHKFIEFYDIRAAETALRT 418
            L V ++      +E+ + F  YGEI+       R T     +  +E+   + A  A   
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 419 LNRSDVAGKQIKLEASRPGG 438
           LN +++ G+ I+++     G
Sbjct: 69  LNGAEIMGQTIQVDWCFVKG 88

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 2e-10
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 351 PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIE 405
           P DN S ++ +  T+    L + +   +L   F   G++R++R     +++      ++E
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 406 FYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 54.7 bits (131), Expect = 8e-10
 Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAAR 328
           E  +RT+F   + + +   +L+  F   G +R +         + +G   + + +I++  
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDN 354
            A+  L  + L    + +  S  + N
Sbjct: 75  LAIG-LTGQRLLGVPIIVQASQAEKN 99

>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: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAM 331
           +  LF+  + + + D ++K L   FG ++             +G+    Y DI     A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 332 KALQNKPLRRRKLDIHYSIPKDNPS 356
             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 = 54.3 bits (130), Expect = 7e-10
 Identities = 12/79 (15%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 419
           L +  L + ++ +++ ++   +G ++     +           F E+ DI   + A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 420 NRSDVAGKQIKLEASRPGG 438
           N   +  K++ ++ +  G 
Sbjct: 64  NGMQLGDKKLLVQRASVGA 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 = 56.3 bits (135), Expect = 2e-10
 Identities = 25/103 (24%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI-----RTIYTACKHRGFVMISYYDIR 325
           P  +   R++FV NI     + +LK +F + G +            K +G+    Y D  
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 326 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSE-KDANQGTLVV 367
            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 = 47.1 bits (111), Expect = 4e-07
 Identities = 19/93 (20%), Positives = 41/93 (44%), Gaps = 6/93 (6%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNH-----KFIEFYD 408
           +P+  D +  ++ V N+    + E+L  IF   G +   R    +         F E+ D
Sbjct: 1   DPA-VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 409 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
              A +A+R LN  + +G+ ++++ +     + 
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>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 = 55.5 bits (133), Expect = 3e-10
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRT 418
            L+V  L  +++ EE   +FG  GEI   +      T     + F+ + D + AE A+ T
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 419 LNRSDVAGKQIKLEASRP 436
           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 = 1e-09
 Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 277 SRT-LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNA 330
           S+T L V  +  N+   E ++LF   G+I +             G+  ++Y D + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 331 MKALQNKPLRRRKLDIHYSIP 351
           +  L    L+ + + + Y+ P
Sbjct: 61  INTLNGLRLQTKTIKVSYARP 81

>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 = 55.8 bits (134), Expect = 3e-10
 Identities = 13/83 (15%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNA 330
             R LF+  ++    +  L+  +EQ+G +              RGF  +++  +     A
Sbjct: 19  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 331 MKALQNKPLRRRKLDIHYSIPKD 353
           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 = 8e-09
 Identities = 10/93 (10%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI-----REIRDTQHKHNHKF 403
           ++P +    +      L +  L    + E L   +  +G++          ++      F
Sbjct: 7   TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           + F  +   + A+       + G+ ++ + +  
Sbjct: 67  VTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA 98

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 3e-10
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-----FVMISYYDIRAARNA 330
           P+  L V  ++    + +L+ +F ++G I  +      +      F  + + ++  A+ A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 331 MKALQNKPLRRRKLDI 346
            +      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 = 54.7 bits (131), Expect = 5e-10
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L VF L    +  +L ++F  YG I ++     + ++      F+ F ++  A+ A   
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 419 LNRSDVAGKQIK 430
            N  ++ G++I+
Sbjct: 71  ANGMELDGRRIR 82

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.9 bits (134), Expect = 3e-10
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 5/96 (5%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAA 327
           G   S  LFVRN++    + +L+ LF  +G +  ++          +GF  +++     A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQG 363
             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 = 51.3 bits (122), Expect = 1e-08
 Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK-----HNHKFIEFYDIR 410
           S   +  G L V NL  + S E+L ++F  YG + E+               F+ F    
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 411 AAETALRTLNRSDVAGKQIKLEASRP 436
            A  A   ++     G+ + +  S  
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTI 87

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 3e-10
 Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 4/93 (4%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA--CKHRGFVMI 319
           S G V+   P G      ++V N+  ++   +++ +F ++G IR I          F  +
Sbjct: 1   SGGGVI-RGPAGN-NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFV 58

Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 352
            + 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 = 52.0 bits (124), Expect = 6e-09
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALRT 418
           N   + V NL   + T+++  +F  YG IR+I  ++ +      F+EF D R AE A+  
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 419 LNRSDVAGKQIKLEASRPGGAR 440
            +  D  G ++++E  R G   
Sbjct: 73  RDGYDYDGYRLRVEFPRSGRGT 94

>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 = 55.5 bits (133), Expect = 3e-10
 Identities = 30/96 (31%), Positives = 44/96 (45%), Gaps = 3/96 (3%)

Query: 262 SAGSVVGEHPYGEH-PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMIS 320
           S+GS  G+  YG+  P+  L+V  +  N   + L   F++FG IRTI    K   F  I 
Sbjct: 2   SSGSS-GKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQ 59

Query: 321 YYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
           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 = 1e-04
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            L V  L  + S   L + F  +G IR I       +  +I++  + AA+ A   +    
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 424 VAG--KQIKLEASRPG 437
           + G  ++++++ ++ G
Sbjct: 78  LGGPDRRLRVDFAKSG 93

>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 = 54.0 bits (129), Expect = 6e-10
 Identities = 13/79 (16%), Positives = 23/79 (29%), Gaps = 5/79 (6%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAMK 332
            TL++ N   +     ++ L +    +              R F  I       AR  ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 333 ALQNKPLRRRKLDIHYSIP 351
            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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
           TL + N   S +   +  +      +           +      +I+      A   +  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 419 LNRSDVAGKQIKLEASRP 436
           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 = 54.4 bits (130), Expect = 1e-09
 Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 6/90 (6%)

Query: 273 GEHPSRTLFVRNINSNVEDS-----ELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 327
           G   S  L     N +V        + ++LF  +    T     K    V I++ +  +A
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTF-QYFKSFKRVRINFSNPLSA 59

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNPSE 357
            +A   L       +++ ++++      S 
Sbjct: 60  ADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 13/88 (14%), Positives = 26/88 (29%), Gaps = 7/88 (7%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAA 327
               +  L V  +     + +LK  F  FG++  +           +GF  + + +    
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKDNP 355
              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 = 47.7 bits (113), Expect = 2e-07
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            L+V  L    + ++L + F  +GE+  +       T H     F+ F +       +  
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 419 LNRSDVAGKQIKLEASRPGGAR 440
            +  D  G+    +      ++
Sbjct: 70  RHMID--GRWCDCKLPNSKQSQ 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: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMK 332
             L+V  +   +   EL+ LF Q+G I T            RG   I +     A  A+K
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 333 ALQNKPL--RRRKLDIHYS 349
            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: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDIR 410
           S +DAN   L V  L  +++ +EL Q+F  YG I        + T       FI F    
Sbjct: 3   SIRDAN---LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 59

Query: 411 AAETALRTLNRSDVAGKQIKLE 432
            AE A++ LN    +G    + 
Sbjct: 60  EAEEAIKGLNGQKPSGATEPIT 81

>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 = 53.3 bits (127), Expect = 3e-09
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAAR-----NA 330
           P++ L+++N++  V + +L +LF +F + +      +     M     I          A
Sbjct: 17  PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 76

Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPS 356
           +  +    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 = 44.8 bits (105), Expect = 2e-06
 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 5/93 (5%)

Query: 349 SIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKF 403
            IP  +          L + NL   V+  +L  +F  + E +         T       F
Sbjct: 5   KIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF 64

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           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 = 53.2 bits (127), Expect = 3e-09
 Identities = 18/104 (17%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 256 VSNQGVSAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---- 311
           ++ Q + A     E P        LF+ ++     D +L  +F  FG++ +         
Sbjct: 1   LTQQSIGAAGSQKEGP----EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 56

Query: 312 -KHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
              + 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 = 50.9 bits (121), Expect = 2e-08
 Identities = 17/93 (18%), Positives = 45/93 (48%), Gaps = 6/93 (6%)

Query: 355 PSEKDANQGT-LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYD 408
            S+K+  +G  L +++L      ++L Q+F  +G +   +    K  +      F+ + +
Sbjct: 10  GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 69

Query: 409 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
             +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 = 52.9 bits (126), Expect = 3e-09
 Identities = 19/95 (20%), Positives = 38/95 (40%), Gaps = 13/95 (13%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTA-------------CKHRGFV 317
           P  +  +  ++V+ +N +V   +L   F+Q G ++                   K +G  
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK 352
            +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 = 51.7 bits (123), Expect = 9e-09
 Identities = 16/93 (17%), Positives = 38/93 (40%), Gaps = 13/93 (13%)

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-------------RDTQHKHNHKF 403
           ++D++   + V  L+ SV+ ++L   F   G ++               ++T        
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 404 IEFYDIRAAETALRTLNRSDVAGKQIKLEASRP 436
           + + 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 = 51.3 bits (122), Expect = 1e-08
 Identities = 19/102 (18%), Positives = 43/102 (42%), Gaps = 5/102 (4%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISY 321
           S+GS    H      S  + VR +  +V +++L    E+FG I  +      +   ++ +
Sbjct: 2   SSGSSGSHHKVS--VSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEF 58

Query: 322 YDIRAARNAMKALQNKP--LRRRKLDIHYSIPKDNPSEKDAN 361
            +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 = 3e-04
 Identities = 17/90 (18%), Positives = 30/90 (33%), Gaps = 3/90 (3%)

Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 413
               K +    + V  L  SV   +L +    +G I  +           +EF +I +A+
Sbjct: 7   GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVM-MMPFKRQALVEFENIDSAK 65

Query: 414 TALRTLNRSD--VAGKQIKLEASRPGGARR 441
             +         +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 = 50.5 bits (120), Expect = 2e-08
 Identities = 11/80 (13%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           G   S  + V+N+  +    E+  L + +          +++    ++  +   A+NA++
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYV--DRNKRTAFVTLLNGEQAQNAIQ 58

Query: 333 ALQNKPLRRRKLDIHYSIPK 352
                  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 = 42.4 bits (99), Expect = 1e-05
 Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            ++V NL    + +E+H +   Y    +           F+   +   A+ A++  ++  
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYD--LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64

Query: 424 VAGKQIKLEASRP 436
             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 = 50.6 bits (120), Expect = 2e-08
 Identities = 19/97 (19%), Positives = 41/97 (42%), Gaps = 11/97 (11%)

Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIR 325
           P      +T+F+RN++ + E+  L  + +QFGD++ +           +G     +    
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 326 AARNAMKALQ------NKPLRRRKLDIHYSIPKDNPS 356
           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 = 4e-06
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 12/91 (13%)

Query: 358 KDANQG-TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRA 411
            D  +G T+ + NL      E L ++   +G+++ +      DT+H     F +F    A
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 412 AETALRTLNRS------DVAGKQIKLEASRP 436
           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 = 49.2 bits (117), Expect = 4e-08
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMKAL 334
           +F+  ++       L+  F QFG+++             RGF  +++ D       +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 335 QNKPLRRRKLDI 346
               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 = 4e-08
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHN-----HKFIEFYDIRAAETALRTL 419
           + +  L    + E L + FG +GE++E    +           F+ F D    +  L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 420 NRSDVAGKQIK 430
           +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 = 49.3 bits (117), Expect = 4e-08
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
              TL+V   +  +  + L+  F  FG+I  +           ++Y  + +A  A+  L 
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESADQAVAELN 60

Query: 336 NKPLRRRKLDIHYSIPK 352
              +   +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: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
           TL V+  D  ++   L   F  +G I ++       N  F+ +  + +A+ A+  LN + 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQ 63

Query: 424 VAGKQIKLEASRP 436
           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 = 50.7 bits (120), Expect = 5e-08
 Identities = 27/128 (21%), Positives = 55/128 (42%), Gaps = 13/128 (10%)

Query: 318 MISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTE 377
           ++S YD       ++ LQ +  +          P     E D  +  L+V  + ++V   
Sbjct: 6   LVSQYDPYGQTAQLQQLQQQQQQHIP-------PTQMNPEPDVLR-NLMVNYIPTTVDEV 57

Query: 378 ELHQIFGIYGEIREIRDTQHKHN-----HKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
           +L Q+F  YG I  ++    +       + F++F    +A+ A+  LN  ++  K++K+ 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 433 ASRPGGAR 440
            +  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 = 48.7 bits (115), Expect = 2e-07
 Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG-----FVMISYYDIRAARNA 330
             R L V  I + V++ +L+ LFE++G I ++   C         +  + +    +A+ A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 331 MKALQNKPLRRRKLDIHYSIPKD 353
           +  L    +  ++L +  +    
Sbjct: 101 IAGLNGFNILNKRLKVALAASGH 123

>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 = 49.3 bits (117), Expect = 5e-08
 Identities = 18/100 (18%), Positives = 39/100 (39%), Gaps = 8/100 (8%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGD-----IRTIYTACKHRGF 316
           S+GS     P  + P  T F+ N+  +V +  +K  F           R      + +GF
Sbjct: 2   SSGSSGSRLP--KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGF 59

Query: 317 VMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
               + 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 = 39.3 bits (91), Expect = 2e-04
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGE-----IREIRDTQHKHNHKFIEFYDIRAAETALRT 418
           T  + NL   V+ E + + F           RE  + +      + EF D+ +  +AL +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 419 LNRSDVAGKQIKLEASRPGGARR 441
           LN   +  K+I+++ +     + 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>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 = 48.9 bits (116), Expect = 6e-08
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 276 PSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
             R + + +         +L  L E FG I              I       A+ A+   
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYY 65

Query: 335 QNKP--LRRRKLDIHYS 349
              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 = 6e-04
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 364 TLVVFNLDSSVSTE-ELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLN 420
            + + +     +   +L Q+   +G I       +K N  FIE      A+ A+   T  
Sbjct: 10  VVHIMDFQRGKNLRYQLLQLVEPFGVISNHL-ILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 421 RSDVAGKQIKLEASRP 436
            + V GK +++  S+ 
Sbjct: 69  PALVFGKPVRVHLSQK 84

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 47.9 bits (113), Expect = 1e-07
 Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 1/75 (1%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           P++ LF+ N+     +  L  LF QF   + +           + +     +  A +ALQ
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQ 66

Query: 336 NKPL-RRRKLDIHYS 349
              +     + 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 = 1e-07
 Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 5/83 (6%)

Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDI-----RTIYTACKHRGFVMISYYDIRAARNAM 331
              LFV  ++ +  +  L+ +F ++G I            + RGF  +++ +I  A++AM
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 332 KALQNKPLRRRKLDIHYSIPKDN 354
            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 = 44.0 bits (103), Expect = 3e-06
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 5/87 (5%)

Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAET 414
           +++G L V  L    + + L Q+F  YG+I E+   + +   +     F+ F +I  A+ 
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 415 ALRTLNRSDVAGKQIKLEASRPGGARR 441
           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 = 2e-07
 Identities = 15/83 (18%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 277 SRTLFVRNINSNV-EDSELKALFEQFGDIRTIYTA------CKHRGFVMISYYDIRAARN 329
            R + +RN+++ + +++ L+  FE FG I  I           +     + + +  +A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 330 AMKALQNKPLRRRKLDIHYSIPK 352
           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 = 2e-07
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDI-RTIYTACKHRGFVMISYYDIRAARNAMKAL 334
           PS TL + NI  +V + +LK LF   G + +      K R   +I    +  A  A+  L
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 335 QNKPLRR-RKLDIHYS 349
            N  L     L + +S
Sbjct: 69  HNHDLGENHHLRVSFS 84

>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 = 46.8 bits (110), Expect = 3e-07
 Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           PSR L +R +   V ++E+ AL   FG +  I    K +    +      AA   +    
Sbjct: 7   PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM-LKGKNQAFLELATEEAAITMVNYYS 65

Query: 336 NKP--LRRRKLDIHYSIPK 352
                LR + + I YS  K
Sbjct: 66  AVTPHLRNQPIYIQYSNHK 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 = 3e-07
 Identities = 10/71 (14%), Positives = 26/71 (36%), Gaps = 6/71 (8%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAETALRTL 419
           + V  L  + + E++   F  +G++ +        T       F+ F      E     +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 420 NRSDVAGKQIK 430
           +  ++  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 = 6e-06
 Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIR-----TIYTACKHRGFVMISYYDIRAARNAMKAL 334
           +FV  ++ N    ++K  FEQFG +         T  +HRGF  +++          + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 335 QNKPLRRRKLDI 346
               +  + ++ 
Sbjct: 61  HFHEINNKMVEC 72

>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 = 46.7 bits (110), Expect = 4e-07
 Identities = 11/82 (13%), Positives = 27/82 (32%), Gaps = 4/82 (4%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGD----IRTIYTACKHRGFVMISYYDIRAARN 329
           E     L++ N+  ++++ EL+ + + FG          ++   RG              
Sbjct: 15  EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 330 AMKALQNKPLRRRKLDIHYSIP 351
            +     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 = 42.5 bits (99), Expect = 1e-05
 Identities = 12/84 (14%), Positives = 27/84 (32%), Gaps = 4/84 (4%)

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHK----HNHKFIEFYDIRAA 412
           +++ +   L + NL  S+  +EL  +   +G++   R  +          F         
Sbjct: 13  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 72

Query: 413 ETALRTLNRSDVAGKQIKLEASRP 436
           E  +   N   +         + P
Sbjct: 73  EAVIGHFNGKFIKTPPGVSAPTEP 96

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 5e-07
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 277 SRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
           +  L V N+N   V    L  LF  +GD++ +      +   ++   D   A+ AM  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 336 NKPLRRRKLDIHYSIPKDNPSEKDANQGT 364
              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 = 44.8 bits (105), Expect = 3e-06
 Identities = 20/79 (25%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 364 TLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 422
            L+V NL+   V+ + L  +FG+YG+++ ++   +K  +  ++  D   A+ A+  LN  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 63

Query: 423 DVAGKQIKLEASRPGGARR 441
            + GK I++  S+    + 
Sbjct: 64  KLHGKPIRITLSKHQNVQL 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 6e-07
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMK 332
           R LF+  ++    D  L++ FEQ+G +              RGF  ++Y  +     AM 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 333 ALQNKPLRRRKLDI 346
           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 = 5e-05
 Identities = 11/72 (15%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDIRAAETALRT 418
            L +  L    + E L   F  +G + +       +T+      F+ +  +   + A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66

Query: 419 LNRSDVAGKQIK 430
                V G+ ++
Sbjct: 67  ARPHKVDGRVVE 78

>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 = 46.3 bits (109), Expect = 6e-07
 Identities = 11/80 (13%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 275 HPSRTLFVR--NINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
           + +++L V    + + V  ++L  + E+ G +  +     ++ +    Y     ++ A  
Sbjct: 16  YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYV 74

Query: 333 ALQNKPL---RRRKLDIHYS 349
            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 = 42.4 bits (99), Expect = 1e-05
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 8/75 (10%)

Query: 364 TLVVF--NLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNR 421
           +LVV    L + VS  +L  +    G +  +        + F  +     ++ A  TLN 
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM-PPNKPYSFARYRTTEESKRAYVTLN- 77

Query: 422 SDVAGKQIKLEASRP 436
               GK++  +  + 
Sbjct: 78  ----GKEVVDDLGQK 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 = 46.3 bits (109), Expect = 6e-07
 Identities = 16/91 (17%), Positives = 28/91 (30%), Gaps = 4/91 (4%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISY 321
           S+GS  G  P        + V  +  +    +LK    + GD+          G V    
Sbjct: 2   SSGSSGG--PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYL- 58

Query: 322 YDIRAARNAMKALQNKPLRRRKLDIHYSIPK 352
                   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 = 36.3 bits (83), Expect = 0.002
 Identities = 15/78 (19%), Positives = 27/78 (34%), Gaps = 2/78 (2%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
            ++V  L  S S ++L       G++        K     +E+      E ALR L+ + 
Sbjct: 17  RVLVSGLPPSGSWQDLKDHMREAGDVC--YADVQKDGMGMVEYLRKEDMEYALRKLDDTK 74

Query: 424 VAGKQIKLEASRPGGARR 441
               + +    R    R 
Sbjct: 75  FRSHEGETSYIRVYPERS 92

>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 = 7e-07
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 5/71 (7%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIRE-----IRDTQHKHNHKFIEFYDIRAAETALRTL 419
           L +  L    + ++L ++   YG+I        + T     + F++F    AA+ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 420 NRSDVAGKQIK 430
             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 = 6e-06
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDI-----RTIYTACKHRGFVMISYYDIRAARNAMKAL 334
           L++R +     D +L  L + +G I         T  K +G+  + +    AA+ A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 335 QNKPLRRRKL 344
           +   ++ +  
Sbjct: 61  KASGVQAQMA 70

>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: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYD 408
           + S+KD     + V  L    +   L + F  +G+I E      +   K     F+   D
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 409 IRAAETALRTLNRSDVAGKQIKLEASRPGGARR 441
             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 = 1e-06
 Identities = 22/93 (23%), Positives = 36/93 (38%), Gaps = 6/93 (6%)

Query: 270 HPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDI 324
               +     +FV  +  +  D+ L+  FE FGDI            K RG+  ++  D 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 325 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPSE 357
            AA  A K   N  +  RK +++ +     P  
Sbjct: 63  AAAERACKDP-NPIIDGRKANVNLAYLGAKPRS 94

>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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK-----HRGFVMISYYDIRAARNAMKAL 334
           +FV  ++ +  + +++  F  FG++ +I           RGF  I++ +    +  M+  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 335 QNKPLRRRKLDI 346
           +   +   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: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRTL 419
           + V  L      E++ + FG +GE+  I        +K     FI F +    +  +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 420 NRSDVAGKQIK 430
              +V   + +
Sbjct: 61  KYHNVGLSKCE 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 = 44.6 bits (105), Expect = 1e-06
 Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
           + +  L    + ++L   F  +GE+ +        T       F+ F +  + +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 420 NRSDVAGKQIK 430
               + 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 = 1e-05
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTA-----CKHRGFVMISYYDIRAARNAMKAL 334
           +F+  ++ +    +LK  F +FG++            + RGF  + + +  +    M   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 335 QNKPLRRRKLDI 346
           +   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 = 45.2 bits (106), Expect = 2e-06
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYD-IRAARNAMKALQN 336
              F  +++      +L  LF   G+I+ I          +I + +  + A    K   N
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-GAKEGIILFKEKAKEALGKAKDANN 70

Query: 337 KPLRRRKLDIHYSIPKD 353
             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 = 39.4 bits (91), Expect = 2e-04
 Identities = 14/88 (15%), Positives = 30/88 (34%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
                +LD     E+LH +F  +GEI+ I   +       +     + A    +  N  +
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 424 VAGKQIKLEASRPGGARRFMVQSEQEQD 451
           +  +  ++      G        +  +D
Sbjct: 73  LQLRNKEVTWEVLEGEVEKEALKKIIED 100

>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 = 44.0 bits (103), Expect = 4e-06
 Identities = 13/86 (15%), Positives = 26/86 (30%), Gaps = 13/86 (15%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI----------YTACKHRGFVMISYYDIRAA 327
           R L+V NI   + +  +   F     +  +              + + F  + +  +   
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 328 RNAMKALQNKPLRRRKLDIHYSIPKD 353
             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 = 38.2 bits (88), Expect = 4e-04
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 13/87 (14%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR----------DTQHKHNHKFIEFYDIRAAE 413
            L V N+   ++ E +   F     +  +                 N  F+EF  +    
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 414 TALRTLNRSDVAGKQIKLEASRPGGAR 440
            A+   +     G+ +K+   RP   +
Sbjct: 63  QAMA-FDGIIFQGQSLKI--RRPHDYQ 86

>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 = 43.9 bits (103), Expect = 4e-06
 Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 348 YSIPKDNPSEKDANQGT---LVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHN 400
           Y  P+++    D  +     + +         E   ++   YGE+ E+        H   
Sbjct: 10  YRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG 69

Query: 401 HKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS 434
           + +++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: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAMKALQ 335
           + ++       +     + E++G++  +             V + +     A  A+  L 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 336 NKPLRRRKLDIHYS 349
           N+    + +    S
Sbjct: 90  NRWFNGQPIHAELS 103

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 5e-06
 Identities = 10/91 (10%), Positives = 29/91 (31%), Gaps = 12/91 (13%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFG-DIRTIYTAC-----------KHRGFVMISYYD 323
             R + ++N+   ++  +   +  +   D+R   +                G   +S+ D
Sbjct: 7   HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRD 66

Query: 324 IRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
              A   ++ L  +    R++         +
Sbjct: 67  PEEADYCIQTLDGRWFGGRQITAQAWDGTTD 97

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.4 bits (102), Expect = 7e-06
 Identities = 14/101 (13%), Positives = 34/101 (33%), Gaps = 18/101 (17%)

Query: 276 PSRTLFVRNI------NSNVEDSELK-ALFEQFGDIRTIYTACKHR----------GFVM 318
           P+  L + N+        + E  E+   + ++      + +    R          G + 
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 319 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKD 359
           + +  +   + AM+ L  +    R +   Y    D+   +D
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYC-DPDSYHRRD 102

>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 = 7e-06
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 4/77 (5%)

Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISY----YDIRAARNAMKA 333
           + +FV  I  + E+  L+  FEQ+G I  I             +    +D   + + +  
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 334 LQNKPLRRRKLDIHYSI 350
            +   +     ++  ++
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 = 37.4 bits (86), Expect = 5e-04
 Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 6/72 (8%)

Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
            + V  +        L   F  YG+I  I     R +  K    F+ F D  + +  +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI- 62

Query: 419 LNRSDVAGKQIK 430
                V G   +
Sbjct: 63  QKYHTVNGHNCE 74

>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: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARNAM 331
               LF+ N+N N   +ELK    +      +       G    F  + +        A+
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71

Query: 332 KALQNKPLRRRKLDIHYSIPK 352
           + L    +   ++ +     +
Sbjct: 72  E-LTGLKVFGNEIKLEKPKGR 91

>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: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG----FVMISYYDIRAARN 329
           +  +R+++++   ++    ++K   E  G +  I             + + +  I +A+ 
Sbjct: 3   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 62

Query: 330 AMKALQNKPLRRRKLDIHYS 349
            ++    +  +   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 = 0.001
 Identities = 7/80 (8%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR----DTQHKHNHKFIEFYDIRAA 412
           + D    ++ +    +  + +++ +     G++  I+      +      F+ F  I +A
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 413 ETALRTLNRSDVAGKQIKLE 432
           +  +            + + 
Sbjct: 61  KKFVE-TPGQKYKETDLLIL 79

>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 = 40.7 bits (94), Expect = 7e-05
 Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 4/90 (4%)

Query: 276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ 335
               +  +N+ +    +E++  F +FG +  +          ++ + +   AR A + L 
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-GGITAIVEFLEPLEARKAFRHLA 67

Query: 336 NKPLRRRKLDIHYS---IPKDNPSEKDANQ 362
                   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: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVMISYYDIRAA 327
           G+     + V+N+   V   E+   F  +  I        +      G  M+++     A
Sbjct: 5   GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 64

Query: 328 RNAMKALQNKPLRRRKLDI 346
             A+  L ++P+  RK+ +
Sbjct: 65  TAAVIDLNDRPIGSRKVKL 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 5/83 (6%)

Query: 355 PSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDI 409
            S        + V N+  +VS +E+   F  Y  I         +         + F   
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 410 RAAETALRTLNRSDVAGKQIKLE 432
             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 = 37.1 bits (85), Expect = 8e-04
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 11/78 (14%)

Query: 278 RTLFVRNINSNVEDSELKALFE---QFGDIRTIYTA--------CKHRGFVMISYYDIRA 326
             +FV  ++  + D E+    E   +FG I  +                   ++Y     
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 327 ARNAMKALQNKPLRRRKL 344
           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 = 37.3 bits (85), Expect = 9e-04
 Identities = 8/83 (9%), Positives = 20/83 (24%), Gaps = 2/83 (2%)

Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKA 333
           +   R + + N+  +           +       Y   + +    I       A   +  
Sbjct: 15  QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDH 74

Query: 334 LQNKP--LRRRKLDIHYSIPKDN 354
              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 = 36.3 bits (83), Expect = 0.002
 Identities = 11/96 (11%), Positives = 30/96 (31%), Gaps = 6/96 (6%)

Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVM 318
           S+GS      +       + +R +     ++++   F     +R         +  G   
Sbjct: 2   SSGS--SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEAD 59

Query: 319 ISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN 354
           + +     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	861
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.94
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.66
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.66
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.66
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.65
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.65
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.63
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.63
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.63
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.63
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.63
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.63
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.63
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.62
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.62
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.62
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.61
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.61
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.61
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.61
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.61
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.6
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.6
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.6
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.6
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.6
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.6
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.6
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.6
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.6
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.6
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.6
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.59
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.59
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.59
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.59
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.58
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.58
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.58
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.58
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.58
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.58
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.58
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.58
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.57
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.57
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.57
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.57
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.57
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.57
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.57
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.57
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.57
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.57
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.56
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.56
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.56
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.56
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.56
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.56
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.56
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.55
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.55
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.55
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.55
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.55
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.54
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.54
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.54
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.54
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.54
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.54
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.54
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.54
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.54
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.54
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.53
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.53
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.53
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.53
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.53
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.53
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.53
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.53
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.52
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.52
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.52
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.52
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.51
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.51
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.51
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.5
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.5
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.5
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.5
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.5
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.5
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.5
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.49
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.49
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.49
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.48
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.48
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.48
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.48
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.47
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.47
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.46
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.46
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.46
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.45
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.45
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.45
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.45
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.44
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.44
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.44
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.43
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.43
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.43
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.43
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.42
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.41
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.41
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.39
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.39
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.38
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.38
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.36
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.35
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.35
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.33
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.33
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.33
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.31
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.24
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.23
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.21
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.2
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.2
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.19
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.17
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.15
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	99.15
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.13
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.13
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.09
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.92
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.88
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.57
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.04
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.02
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.73
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	94.99
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	94.61
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	83.39
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	83.1

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=9.7e-27  Score=228.54  Aligned_cols=163  Identities=18%  Similarity=0.342  Sum_probs=142.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..|+|||+|||+++|+++|+++|++||.|..+++     ++.++|||||+|.+.++|++|++ +.+..+.++.+.+.+..
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            3589999999999999999999999999999984     67899999999999999999997 56667788888887776


Q ss_pred             CCCCC--CCcccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          351 PKDNP--SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       351 ~k~~~--~~k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      ++...  .......++|||+|||..+|+++|+++|+.||.|..+.+     ++.++|||||+|.+.++|.+|++ +++..
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            55432  223455689999999999999999999999999999875     35678999999999999999997 79999


Q ss_pred             eCCcEEEEEeccCCchh
Q 002974          424 VAGKQIKLEASRPGGAR  440 (861)
Q Consensus       424 I~Gr~IkVe~Akpk~~r  440 (861)
                      +.|++|+|.+|.++.++
T Consensus       163 ~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         163 VNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             ETTEEEEEEECCCHHHH
T ss_pred             ECCEEEEEEecCCcccc
Confidence            99999999999987544

>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=99.66  E-value=9.7e-17  Score=138.41  Aligned_cols=75  Identities=25%  Similarity=0.474  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      .++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|||..+.|++|+|+|++|
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            578999999999999999999999999999985     578899999999999999999999999999999999999976

>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=99.66  E-value=1.9e-16  Score=140.52  Aligned_cols=80  Identities=18%  Similarity=0.325  Sum_probs=74.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ....++|||+|||.++|+++|+++|++||.|..|++     ++.++|||||+|.+.++|++|++.|+|..|.|++|+|+|
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            345789999999999999999999999999999985     578999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 002974          349 SIPKD  353 (861)
Q Consensus       349 a~~k~  353 (861)
                      |.++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98765

>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=99.66  E-value=1.3e-16  Score=140.16  Aligned_cols=80  Identities=20%  Similarity=0.415  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|||..+.|+.|+|+
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            3456789999999999999999999999999999985     57889999999999999999999999999999999999


Q ss_pred             ecCCC
Q 002974          348 YSIPK  352 (861)
Q Consensus       348 ~a~~k  352 (861)
                      |+.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99765

>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=99.65  E-value=1.5e-16  Score=137.19  Aligned_cols=76  Identities=28%  Similarity=0.414  Sum_probs=71.0

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||+|||.++++++|+++|++||.|++|++     .++.+|||||+|.+.++|++|++.|||..+.|++|+|+||+|
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            468999999999999999999999999999986     345689999999999999999999999999999999999987


Q ss_pred             C
Q 002974          437 G  437 (861)
Q Consensus       437 k  437 (861)
                      +
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.8e-16  Score=139.59  Aligned_cols=80  Identities=24%  Similarity=0.471  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..+.++|||+|||.++++++|+++|++||+|..|++     ++.++|||||+|.+.++|++|++.|+|..+.|+.|+|.|
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            456789999999999999999999999999999985     578999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 002974          349 SIPKD  353 (861)
Q Consensus       349 a~~k~  353 (861)
                      ++|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98764

>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=99.64  E-value=2.5e-16  Score=135.65  Aligned_cols=75  Identities=23%  Similarity=0.496  Sum_probs=70.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      .++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|.|++|
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            367999999999999999999999999999985     578999999999999999999999999999999999999976

>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=99.64  E-value=5e-16  Score=138.91  Aligned_cols=82  Identities=23%  Similarity=0.389  Sum_probs=75.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ...+++|||+|||+++++++|+++|++||.|..|++     +++++|||||+|.+.++|++|++.|+++.|.|+.|+|.+
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            345789999999999999999999999999999985     578899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T d1whwa_          85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             CCCCCcc
Confidence            9887654

>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=99.63  E-value=3.4e-16  Score=134.78  Aligned_cols=75  Identities=32%  Similarity=0.495  Sum_probs=70.2

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||+|||.++++++|+++|++||+|.+|++     .++.+|||||+|.+.++|++|++.|||..+.|++|+|++|+|
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            467999999999999999999999999999886     356689999999999999999999999999999999999987

>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=99.63  E-value=4.8e-16  Score=137.87  Aligned_cols=78  Identities=27%  Similarity=0.439  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +.+++|||+|||+++|+++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|+.|+|.|+
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            46899999999999999999999999999999985     5788999999999999999999999999999999999998


Q ss_pred             CCC
Q 002974          350 IPK  352 (861)
Q Consensus       350 ~~k  352 (861)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.63  E-value=1.9e-16  Score=139.15  Aligned_cols=79  Identities=29%  Similarity=0.486  Sum_probs=73.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|.|+.
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            4689999999999999999999999999999985     57899999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      ++..
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=3.6e-16  Score=137.66  Aligned_cols=80  Identities=21%  Similarity=0.321  Sum_probs=73.6

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      .....+|||+|||.++++++|+++|++||+|.+|++     ++.++|||||+|.+.++|++|++.|||..+.|++|+|+|
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            345678999999999999999999999999999876     456789999999999999999999999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      |+|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            99874

>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=99.63  E-value=2e-16  Score=144.63  Aligned_cols=103  Identities=26%  Similarity=0.402  Sum_probs=86.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ...+++|||+|||.++++++|+++|++||.|..|++  ++.++|||||+|.+.++|+.|++.|+|+.|.|+.|+|.++.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            346899999999999999999999999999999986  677899999999999999999999999999999999999864


Q ss_pred             CCCCCCcccCCcceEEecccCCCcHHHHHHHhcccCc
Q 002974          352 KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE  388 (861)
Q Consensus       352 k~~~~~k~~~~~tLfVgNLp~svTeedLrelFskfGe  388 (861)
                      +....            .......++++..+.++||.
T Consensus        84 ~~~~~------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          84 NRAFQ------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHHTT------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             Cchhh------------hhHHHHHHHHHHHHHHHhCC
Confidence            32211            11122356778888888874

>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=99.63  E-value=6.2e-16  Score=137.37  Aligned_cols=80  Identities=26%  Similarity=0.530  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHc-CccccCcceeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKAL-QNKPLRRRKLDI  346 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki------tgksrGyAFVeF~d~e~A~kALkaL-nG~~L~Gr~L~V  346 (861)
                      ..++++|||+|||.++++++|+++|++||.|..|++      +++++|||||+|.+.++|++|++.| ++..+.|++|+|
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            456789999999999999999999999999999985      4678999999999999999999998 899999999999


Q ss_pred             eecCCCC
Q 002974          347 HYSIPKD  353 (861)
Q Consensus       347 ~~a~~k~  353 (861)
                      .|+.++.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998654

>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=99.63  E-value=4e-16  Score=136.91  Aligned_cols=80  Identities=23%  Similarity=0.352  Sum_probs=72.7

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      .....+|||+|||..+++++|+++|++||+|++|++     +++++|||||+|.+.++|++|++.|||..+.|++|+|+|
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            345678999999999999999999999999999876     356789999999999999999999999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      |.+++
T Consensus        84 a~~kG   88 (88)
T d1rk8a_          84 CFVKG   88 (88)
T ss_dssp             SEECC
T ss_pred             ecCCC
Confidence            98764

>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=99.63  E-value=4e-16  Score=140.64  Aligned_cols=80  Identities=18%  Similarity=0.376  Sum_probs=74.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .+.++|||+|||+++++++|+++|++||.|..+++     ++.+||||||+|.+.++|++|++.|+|..|.|++|+|+|+
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            35688999999999999999999999999988874     5788999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .++.+
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            88765

>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=99.62  E-value=6.3e-16  Score=136.06  Aligned_cols=82  Identities=18%  Similarity=0.443  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ++.+.++|||+|||.++++++|+++|++||+|..|++   ....+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+
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            3456789999999999999999999999999999985   3456899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            86543

>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=99.62  E-value=3.2e-16  Score=137.67  Aligned_cols=79  Identities=27%  Similarity=0.439  Sum_probs=73.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||+++++++|+++|++||+|++|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|++|+
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            3579999999999999999999999999999986     46778999999999999999999999999999999999999


Q ss_pred             CCch
Q 002974          436 PGGA  439 (861)
Q Consensus       436 pk~~  439 (861)
                      |+..
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8753

>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=99.62  E-value=1.2e-15  Score=135.05  Aligned_cols=82  Identities=22%  Similarity=0.405  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .....++|||+|||+++++++|+++|++||+|..|++   ...++|||||+|.+.++|++|++.|+|..+.|++|+|.|+
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            3455788999999999999999999999999999985   4557899999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            87643

>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=99.61  E-value=8.7e-16  Score=145.17  Aligned_cols=82  Identities=21%  Similarity=0.427  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ....++|||+|||+++++++|+++|++||+|.+|++     ++++||||||+|.+.++|++|++.|||..|.|++|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999885     578999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +.++..+
T Consensus       119 a~~~~~~  125 (139)
T d1u6fa1         119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             cCCCCCC
Confidence            9876654

>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=99.61  E-value=3.2e-16  Score=139.55  Aligned_cols=82  Identities=24%  Similarity=0.400  Sum_probs=77.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ..++.++|||+|||+++++++|+++|++||.|..++.+++++|||||+|.+.++|++|++.|+|..|.|++|+|.|+.++
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            34568999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             CC
Q 002974          353 DN  354 (861)
Q Consensus       353 ~~  354 (861)
                      ..
T Consensus        92 ~~   93 (96)
T d1fjca_          92 GG   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.61  E-value=5.2e-16  Score=136.21  Aligned_cols=79  Identities=22%  Similarity=0.488  Sum_probs=73.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      +.++|||+|||+++++++|+++|++||.|..+.+     ++.++|||||+|.+.++|++|++.|+|..|.|++|+|+++.
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            4788999999999999999999999999999873     57899999999999999999999999999999999999998


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      ++.+
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.61  E-value=1.1e-15  Score=132.63  Aligned_cols=78  Identities=18%  Similarity=0.350  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccC-cceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR-RRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~-Gr~L~V~~a~  350 (861)
                      ...|+++|||+|||.++++++|+++|++||.|..|++....+|||||+|.+.++|++|++.|+|..+. |+.|+|.|++
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            45678999999999999999999999999999999987778899999999999999999999999884 7899999986

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=8.9e-16  Score=136.08  Aligned_cols=78  Identities=23%  Similarity=0.333  Sum_probs=72.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+|+++|+++|++||.|.+|++     ++.++|||||+|.+.++|++|++.|||..|.|++|+|++|+
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            3578999999999999999999999999999986     45678999999999999999999999999999999999999


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            875

>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=99.61  E-value=4.3e-16  Score=134.13  Aligned_cols=75  Identities=17%  Similarity=0.228  Sum_probs=67.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      .+||||+|||+++|+++|+++|++||.|..+.+     +++++|||||+|.+.++|++|++.|||+.+.|++|+|+++.|
T Consensus         1 d~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           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            379999999999999999999999999977653     578999999999999999999999999999999999999976

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.1e-15  Score=134.42  Aligned_cols=82  Identities=27%  Similarity=0.404  Sum_probs=73.7

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      +...++|||+|||..+++++|+++|++||+|..|++.   ...++||||+|.+.++|++|++.|||..+.|+.|+|.||+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            3456799999999999999999999999999999862   3458899999999999999999999999999999999998


Q ss_pred             CCchh
Q 002974          436 PGGAR  440 (861)
Q Consensus       436 pk~~r  440 (861)
                      ++..+
T Consensus        85 ~~~~~   89 (90)
T d2cqia1          85 TPSSQ   89 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            76543

>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=99.60  E-value=7.2e-16  Score=132.79  Aligned_cols=72  Identities=18%  Similarity=0.379  Sum_probs=68.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      +|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..+.||+|+|.|+.
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            6999999999999999999999999999985     57889999999999999999999999999999999999985

>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=99.60  E-value=6.7e-16  Score=139.97  Aligned_cols=79  Identities=13%  Similarity=0.270  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ..+..++|||+|||+++++++|+++|++||+|..|.+ .+.+|||||+|.+.++|++|++.|||..|.|+.|.|.|+...
T Consensus         6 ~~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_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            3456789999999999999999999999999999998 578999999999999999999999999999999999998654

>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=99.60  E-value=7.1e-16  Score=134.53  Aligned_cols=76  Identities=21%  Similarity=0.429  Sum_probs=71.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .+|||+|||+++|+++|+++|++||+|..|++     +++++|||||+|.++++|++|++.|+|..|.|++|.|.|+.+.
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            47999999999999999999999999999985     5789999999999999999999999999999999999999765


Q ss_pred             C
Q 002974          353 D  353 (861)
Q Consensus       353 ~  353 (861)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=7.1e-16  Score=135.41  Aligned_cols=78  Identities=18%  Similarity=0.380  Sum_probs=72.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      ..+|||+|||+++++++|+++|++||.|..+++   ...++|||||+|.+.++|++|++.|+|+.|.|++|+|.++.++.
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   35578999999999999999999999999999999999998765


Q ss_pred             C
Q 002974          354 N  354 (861)
Q Consensus       354 ~  354 (861)
                      +
T Consensus        88 ~   88 (89)
T d1cvja2          88 E   88 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.6e-15  Score=134.70  Aligned_cols=79  Identities=16%  Similarity=0.338  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      ..++++|||+|||+++++++|+++|++||.|..+++  +...++||||+|.+.++|++|++.|||+.|.|++|+|+|+++
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            456789999999999999999999999999999986  467889999999999999999999999999999999999976


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.60  E-value=7.4e-16  Score=134.20  Aligned_cols=78  Identities=22%  Similarity=0.337  Sum_probs=72.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      ..++|||+|||+++++++|+++|++||.|..+++ .+++|||||+|.+.++|++|++.|||..|.|+.|+|+|++|++.
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            3589999999999999999999999999888877 67899999999999999999999999999999999999988765

>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=99.60  E-value=1.6e-15  Score=134.47  Aligned_cols=83  Identities=22%  Similarity=0.459  Sum_probs=74.4

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcC------ccccC
Q 002974          272 YGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQ------NKPLR  340 (861)
Q Consensus       272 ~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLn------G~~L~  340 (861)
                      .+..+.++|||+|||+++++++|+++|++||+|..+.+     ++.++|||||+|.+.++|++|++.|+      |..+.
T Consensus         3 ~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~   82 (98)
T d1x4ha1           3 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   82 (98)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             cCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEEC
Confidence            35566899999999999999999999999999999884     46789999999999999999999886      67789


Q ss_pred             cceeeeeecCCCCC
Q 002974          341 RRKLDIHYSIPKDN  354 (861)
Q Consensus       341 Gr~L~V~~a~~k~~  354 (861)
                      ||.|+|.|+.++.+
T Consensus        83 gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          83 GRQLKVDLAVTRDE   96 (98)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCCc
Confidence            99999999987654

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=9.3e-16  Score=138.20  Aligned_cols=81  Identities=17%  Similarity=0.365  Sum_probs=74.1

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||+++++++|+++|++||.|.++++     ++..||||||+|.+.++|++||+.|||..|.|++|+|+|+
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            34578999999999999999999999999998875     4567899999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..+
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            998754

>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=99.60  E-value=2.8e-16  Score=141.60  Aligned_cols=81  Identities=23%  Similarity=0.431  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .+++.++|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++|++.|+|..|.|+.|+|+
T Consensus         4 ~~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             SHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3455789999999999999999999999999999884     57889999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 002974          348 YSIPKD  353 (861)
Q Consensus       348 ~a~~k~  353 (861)
                      |+.++.
T Consensus        84 ~a~~~~   89 (104)
T d1p1ta_          84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             ECCCCC
Confidence            997653

>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=3.8e-16  Score=137.22  Aligned_cols=80  Identities=21%  Similarity=0.352  Sum_probs=72.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeC---CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT---QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVrit---gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ...+|||+|||+++++++|+++|++||.|.+|++.   ..++|||||+|.+.++|++|++.|||..|.|++|+|++++++
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            34689999999999999999999999999999873   335799999999999999999999999999999999999987


Q ss_pred             chh
Q 002974          438 GAR  440 (861)
Q Consensus       438 ~~r  440 (861)
                      .+|
T Consensus        87 ~~R   89 (89)
T d1cvja2          87 KER   89 (89)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            643

>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=99.60  E-value=2.3e-15  Score=133.33  Aligned_cols=81  Identities=21%  Similarity=0.362  Sum_probs=73.6

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe---CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD---TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri---tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      .....++|||+|||+++++++|+++|++||+|++|++   ...++|||||+|.+.++|++|++.||+..+.|++|+|++|
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            3445678999999999999999999999999999986   3345899999999999999999999999999999999999


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      +++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            9875

>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=99.60  E-value=9.8e-16  Score=132.58  Aligned_cols=73  Identities=19%  Similarity=0.428  Sum_probs=68.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ..++++|||+|||+++|+++|+++|++||.|.+|++     +++++|||||+|.+.++|++|++.|+|..|.|++|+|
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            456889999999999999999999999999999985     4788999999999999999999999999999999987

>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=99.60  E-value=1.1e-15  Score=132.79  Aligned_cols=74  Identities=27%  Similarity=0.466  Sum_probs=68.1

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----C---CCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCC
Q 002974          280 LFVRNINSNVEDSELKALFEQFGDIRTIYT-----A---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIP  351 (861)
Q Consensus       280 LfVgNLP~~vTEedL~elFsqfG~I~svki-----t---gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~  351 (861)
                      |||+|||+++|+++|+++|++||+|..|++     +   +.+||||||+|.+.++|++|++.|+|..+.|+.|+|+|+..
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            899999999999999999999999999885     1   24689999999999999999999999999999999999975


Q ss_pred             CC
Q 002974          352 KD  353 (861)
Q Consensus       352 k~  353 (861)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.60  E-value=1.1e-15  Score=131.11  Aligned_cols=72  Identities=25%  Similarity=0.450  Sum_probs=68.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      +|||+|||+++++++|+++|++||.|..|++    +++++|||||+|.+.++|++|++.|||+.+.|++|+|+++.
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            6999999999999999999999999999985    67889999999999999999999999999999999999885

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.59  E-value=7.5e-16  Score=137.12  Aligned_cols=82  Identities=23%  Similarity=0.328  Sum_probs=76.7

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ....++|||+|||.++++++|+++|++||.|..++..++.++||||+|.+.++|++|++.|||..|.|++|+|.|+.++.
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            34567999999999999999999999999999998888999999999999999999999999999999999999999986


Q ss_pred             hh
Q 002974          439 AR  440 (861)
Q Consensus       439 ~r  440 (861)
                      .+
T Consensus        93 ~~   94 (96)
T d1fjca_          93 GT   94 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.59  E-value=1.8e-15  Score=131.63  Aligned_cols=75  Identities=23%  Similarity=0.431  Sum_probs=69.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCc--ceeeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIH  347 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G--r~L~V~  347 (861)
                      ...++|||+|||+++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++.|||..+.|  ++|+|+
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            35678999999999999999999999999999984     57899999999999999999999999999976  889999


Q ss_pred             ec
Q 002974          348 YS  349 (861)
Q Consensus       348 ~a  349 (861)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=1.9e-15  Score=134.14  Aligned_cols=79  Identities=20%  Similarity=0.427  Sum_probs=72.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe------CCCCccEEEEEECCHHHHHHHHHHh-CCCeeCCcEEEEE
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD------TQHKHNHKFIEFYDIRAAETALRTL-NRSDVAGKQIKLE  432 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri------tgksKGfAFVeF~d~eaA~kAL~~L-NG~~I~Gr~IkVe  432 (861)
                      ...++|||+|||..+++++|+++|++||.|..|++      +++.+|||||+|.+.++|++|++.| |+..+.|++|+|+
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            34578999999999999999999999999999986      3457899999999999999999998 8999999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      ||+++.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998765

>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=99.59  E-value=1.8e-15  Score=135.87  Aligned_cols=79  Identities=14%  Similarity=0.260  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .+.+.++|||+|||+++++++|+++|++||+|..+.+    +++++|||||+|.+.++|++|++.|||+.|.||++.|.+
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            3455789999999999999999999999999988874    577899999999999999999999999999999999988


Q ss_pred             cCC
Q 002974          349 SIP  351 (861)
Q Consensus       349 a~~  351 (861)
                      +.|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=2.1e-15  Score=133.66  Aligned_cols=78  Identities=24%  Similarity=0.336  Sum_probs=72.1

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+|+++|+++|++||+|.+|++     ++..+|||||+|.+.++|++|++.|||..+.|++|+|+|+.
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            4579999999999999999999999999999986     45678899999999999999999999999999999999997


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ...
T Consensus        86 ~~~   88 (93)
T d1h2vz_          86 GFK   88 (93)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.58  E-value=1.9e-15  Score=131.63  Aligned_cols=73  Identities=23%  Similarity=0.400  Sum_probs=67.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCc--ceeeeeec
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYS  349 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~G--r~L~V~~a  349 (861)
                      .++|||+|||+++|+++|+++|++||+|.++++     +++++|||||+|.+.++|++|++.|||..+.|  ++|+|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            578999999999999999999999999999985     57899999999999999999999999999987  55888886

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=2.7e-15  Score=134.07  Aligned_cols=79  Identities=24%  Similarity=0.369  Sum_probs=73.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||+.+++++|+++|++||.|.+|++     +++++|||||+|.+.++|++||+.||+..|.|++|+|.+++
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            4568999999999999999999999999999986     35678999999999999999999999999999999999999


Q ss_pred             CCch
Q 002974          436 PGGA  439 (861)
Q Consensus       436 pk~~  439 (861)
                      ++..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            8753

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=2.1e-15  Score=129.32  Aligned_cols=73  Identities=21%  Similarity=0.378  Sum_probs=68.6

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ++|||+|||+++++++|+++|++||.|++|++    .++++|||||+|.+.++|++|++.|||..+.|++|+|+++.
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            36999999999999999999999999999987    45668899999999999999999999999999999999986

>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=99.58  E-value=1.9e-15  Score=134.85  Aligned_cols=76  Identities=16%  Similarity=0.347  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ..++|||+|||.++++++|+++|++||+|.+|++ .+.||||||+|.+.++|++|++.|+|+.|.|+.|+|.|++++
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 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEE-EecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4689999999999999999999999999999998 456999999999999999999999999999999999999764

>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=99.58  E-value=3e-15  Score=135.31  Aligned_cols=77  Identities=23%  Similarity=0.359  Sum_probs=71.4

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          277 SRTLFVRNINS-NVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       277 srtLfVgNLP~-~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      +++|||+|||+ .+++++|+++|++||+|..|++....+|||||+|.+.++|++|++.|+|..|.|+.|+|.|+..+.
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            68999999965 599999999999999999999877779999999999999999999999999999999999997543

>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=99.58  E-value=3.2e-15  Score=132.04  Aligned_cols=81  Identities=16%  Similarity=0.317  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ..+..++|||+|||+++|+++|+++|++||.|..|++     ++++||||||+|.+.++|++||+.  +..|.|+.|.|+
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~   81 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEE
Confidence            3456789999999999999999999999999999984     689999999999999999999984  447999999999


Q ss_pred             ecCCCCCC
Q 002974          348 YSIPKDNP  355 (861)
Q Consensus       348 ~a~~k~~~  355 (861)
                      ++.++..+
T Consensus        82 ~a~~k~~~   89 (90)
T d2cqga1          82 LPNSKQSQ   89 (90)
T ss_dssp             CCCTTCCC
T ss_pred             eCCCCCCC
Confidence            99887653

>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=99.58  E-value=8.7e-16  Score=134.71  Aligned_cols=79  Identities=22%  Similarity=0.449  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~~  354 (861)
                      ..+++|||+|||+++|+++|+++|++||+|..|++...++|||||+|.+.++|++|++  ++..|.|++|+|.++.++..
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            4589999999999999999999999999999999988999999999999999999995  78899999999999988765


Q ss_pred             C
Q 002974          355 P  355 (861)
Q Consensus       355 ~  355 (861)
                      .
T Consensus        81 ~   81 (88)
T d1wf0a_          81 S   81 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.58  E-value=2.8e-15  Score=129.91  Aligned_cols=76  Identities=18%  Similarity=0.320  Sum_probs=71.3

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeC-CcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVA-GKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~-Gr~IkVe~Ak  435 (861)
                      .+.++|||+|||..+++++|+++|++||.|++|++....+|||||+|.+.++|.+|++.|+|..|. |++|+|.||+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            456799999999999999999999999999999998888899999999999999999999999884 6999999997

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.8e-15  Score=130.33  Aligned_cols=73  Identities=29%  Similarity=0.352  Sum_probs=68.5

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      +|||+|||+.+|+++|+++|++||+|.+|++     +++++|||||+|.++++|.+|++.|||..+.|++|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            6999999999999999999999999999986     356689999999999999999999999999999999999963

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.2e-15  Score=133.89  Aligned_cols=79  Identities=29%  Similarity=0.511  Sum_probs=72.6

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||+.+++++|+++|++||.|..|.+     .+.++|||||+|.++++|++|++.|||..|.|++|+|+++.
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            3568999999999999999999999999999864     45678999999999999999999999999999999999998


Q ss_pred             CCch
Q 002974          436 PGGA  439 (861)
Q Consensus       436 pk~~  439 (861)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.58  E-value=3.6e-15  Score=134.49  Aligned_cols=81  Identities=25%  Similarity=0.380  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      .+...++|||+|||+.+++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.+++ .|.|++|+|+
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            3445678999999999999999999999999999985     478999999999999999999998876 6999999999


Q ss_pred             ecCCCCC
Q 002974          348 YSIPKDN  354 (861)
Q Consensus       348 ~a~~k~~  354 (861)
                      ++..+..
T Consensus        85 ~a~~~~~   91 (103)
T d2cqda1          85 LAYLGAK   91 (103)
T ss_dssp             ESTTTCC
T ss_pred             EcCCCCC
Confidence            9976544

>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=99.58  E-value=1.4e-15  Score=134.10  Aligned_cols=80  Identities=28%  Similarity=0.627  Sum_probs=72.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHH----HhhcCCCEEEEEe--CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          275 HPSRTLFVRNINSNVEDSELKA----LFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~e----lFsqfG~I~svki--tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      +|+++|||+|||++++++||++    +|++||+|..|++  +++++|||||+|.+.++|++|++.|+|..+.|+.|.|.|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4789999999999999999864    6899999999987  356799999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 002974          349 SIPKDN  354 (861)
Q Consensus       349 a~~k~~  354 (861)
                      ++++.+
T Consensus        81 ak~~~~   86 (91)
T d1nu4a_          81 AKTDSD   86 (91)
T ss_dssp             CSSCCT
T ss_pred             eCCCch
Confidence            987643

>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=99.57  E-value=5.4e-16  Score=133.82  Aligned_cols=77  Identities=22%  Similarity=0.361  Sum_probs=70.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCcc-ccCcceeeeeecCCCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK-PLRRRKLDIHYSIPKDNP  355 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~-~L~Gr~L~V~~a~~k~~~  355 (861)
                      ++|||+|||.++++++|+++|++||.|..+++ .+.||||||+|.+.++|++|++.|||. .+.|++|+|.|+.++..+
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            47999999999999999999999999877665 467899999999999999999999996 599999999999987654

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.4e-15  Score=137.27  Aligned_cols=78  Identities=27%  Similarity=0.388  Sum_probs=72.1

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+|||..+++++|+++|++||.|++|++  .+..+|||||+|.+.++|..|++.|||..|.|+.|+|.++.+..
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            3578999999999999999999999999999987  45678999999999999999999999999999999999987643

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3e-15  Score=130.86  Aligned_cols=77  Identities=29%  Similarity=0.422  Sum_probs=70.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-eCCCcccEEEEEeCCHHHHHHHHHHcCcccc-CcceeeeeecCC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-TACKHRGFVMISYYDIRAARNAMKALQNKPL-RRRKLDIHYSIP  351 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-itgksrGyAFVeF~d~e~A~kALkaLnG~~L-~Gr~L~V~~a~~  351 (861)
                      .|+++|||+|||.++++++|+++|++||.|..+. ..++.+|||||+|.+.++|.+|+..|+|..+ .|++|+|.|+++
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            4689999999999999999999999999988765 4678899999999999999999999999988 589999999975

>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=99.57  E-value=1.7e-15  Score=135.22  Aligned_cols=84  Identities=23%  Similarity=0.365  Sum_probs=74.0

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE--------e-----CCCcccEEEEEeCCHHHHHHHHHHcCcc
Q 002974          271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY--------T-----ACKHRGFVMISYYDIRAARNAMKALQNK  337 (861)
Q Consensus       271 ~~~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk--------i-----tgksrGyAFVeF~d~e~A~kALkaLnG~  337 (861)
                      |......++|||+|||.++++++|+++|++||.|..+.        +     +++++|||||+|.+.++|++|++.|+|+
T Consensus         2 p~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           2 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            34556789999999999999999999999999885432        1     4688999999999999999999999999


Q ss_pred             ccCcceeeeeecCCCCC
Q 002974          338 PLRRRKLDIHYSIPKDN  354 (861)
Q Consensus       338 ~L~Gr~L~V~~a~~k~~  354 (861)
                      .|.||+|+|.++.++..
T Consensus        82 ~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          82 DFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             EECCEEEEEEEcCCCCC
Confidence            99999999999987644

>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=99.57  E-value=2.7e-15  Score=141.74  Aligned_cols=79  Identities=25%  Similarity=0.423  Sum_probs=72.9

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||+|||.++++++|+++|++||+|++|++     +++++|||||+|.+.++|++||+.|||..|.|++|+|+++++
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            468999999999999999999999999999876     356789999999999999999999999999999999999987


Q ss_pred             Cchh
Q 002974          437 GGAR  440 (861)
Q Consensus       437 k~~r  440 (861)
                      +..+
T Consensus       122 ~~~~  125 (139)
T d1u6fa1         122 GHQR  125 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7644

>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=99.57  E-value=1.6e-15  Score=130.44  Aligned_cols=74  Identities=15%  Similarity=0.195  Sum_probs=66.6

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .+|||+|||+++|+++|+++|++||.|..+.+     .++++|||||+|.+.++|++|++.|||..+.|++|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            58999999999999999999999999977654     456789999999999999999999999999999999999987

>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=99.57  E-value=1.5e-15  Score=131.31  Aligned_cols=75  Identities=23%  Similarity=0.500  Sum_probs=68.8

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEE-Ee-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          280 LFVRNINSNVEDSELKALFEQFGDIRTI-YT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       280 LfVgNLP~~vTEedL~elFsqfG~I~sv-ki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      |||+|||+++++++|+++|++||.|..+ ++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+|+.++.
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            8999999999999999999999998654 32     57889999999999999999999999999999999999998765


Q ss_pred             C
Q 002974          354 N  354 (861)
Q Consensus       354 ~  354 (861)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.57  E-value=2.3e-15  Score=131.63  Aligned_cols=77  Identities=27%  Similarity=0.525  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      ..++|||+|||.++++++|+++|++||+|.+|++ .+.+|||||+|.+.++|++|++.|+|..|.|+.|+|+||.++.
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 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEE-ETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeee-ecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3578999999999999999999999999999998 4678999999999999999999999999999999999998754

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.2e-15  Score=131.42  Aligned_cols=76  Identities=17%  Similarity=0.357  Sum_probs=71.3

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      .+|||+|||..+|+++|+++|++||+|++|++     +++++|||||+|.++++|++|++.|||..|.|++|+|++|.++
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            47999999999999999999999999999986     4677899999999999999999999999999999999999876


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.57  E-value=8.4e-16  Score=137.57  Aligned_cols=82  Identities=21%  Similarity=0.392  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE-----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk-----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..++++|||+|||.++++++|+++|++||.|..+.     .+++++|||||+|.+.++|++|++.|+|..|.|+.|+|.|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35689999999999999999999999999877664     3688999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 002974          349 SIPKDNP  355 (861)
Q Consensus       349 a~~k~~~  355 (861)
                      +++++++
T Consensus        95 ak~k~~r  101 (102)
T d2cpxa1          95 GKNKKQR  101 (102)
T ss_dssp             CCCCSCC
T ss_pred             CCCcccC
Confidence            9987654

>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=99.56  E-value=1.9e-15  Score=131.99  Aligned_cols=76  Identities=20%  Similarity=0.392  Sum_probs=68.1

Q ss_pred             CCcEEEEcCCCCCCc-HHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          276 PSRTLFVRNINSNVE-DSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       276 ~srtLfVgNLP~~vT-EedL~elFsqfG~I~svki------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      ..++|||+|||++++ +++|+++|++||+|..|++      +++++|||||+|.+.++|++|++ |||+.+.|+.|+|++
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            478999999999986 5569999999999999985      46789999999999999999995 999999999999999


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>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=99.56  E-value=3.6e-15  Score=134.53  Aligned_cols=80  Identities=24%  Similarity=0.303  Sum_probs=72.1

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ++...++|||+|||+.+++++|+++|++||+|.+|++     +++++|||||+|.+.++|++||+.+|+ .|.|++|+|+
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            4455678999999999999999999999999999987     356799999999999999999998876 7999999999


Q ss_pred             eccCCc
Q 002974          433 ASRPGG  438 (861)
Q Consensus       433 ~Akpk~  438 (861)
                      ++..+.
T Consensus        85 ~a~~~~   90 (103)
T d2cqda1          85 LAYLGA   90 (103)
T ss_dssp             ESTTTC
T ss_pred             EcCCCC
Confidence            998764

>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=99.56  E-value=3.9e-15  Score=129.57  Aligned_cols=75  Identities=21%  Similarity=0.438  Sum_probs=69.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ...++|||+|||+++++++|+++|++||+|..+++     +++++|||||+|.+.++|++|++ ++++.|.|+.|+|..|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            34689999999999999999999999999999985     58899999999999999999997 6999999999999987


Q ss_pred             C
Q 002974          350 I  350 (861)
Q Consensus       350 ~  350 (861)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.56  E-value=4e-15  Score=132.80  Aligned_cols=77  Identities=21%  Similarity=0.325  Sum_probs=71.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+|||..+++++|+++|++||+|++|++.. .||||||+|.+.++|++|++.|||..|.|++|+|.|++++.
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 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe-cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            356899999999999999999999999999999864 58999999999999999999999999999999999998754

>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=99.56  E-value=2.7e-15  Score=128.92  Aligned_cols=76  Identities=18%  Similarity=0.350  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      .+..++|||+||+  +|+++|+++|++||+|..|++ .+.+|||||+|.+.++|++|++.|||..+.|++|+|.|++++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~-~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeee-ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            3567899999996  999999999999999999998 577899999999999999999999999999999999999764

>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=99.56  E-value=6.6e-15  Score=130.67  Aligned_cols=79  Identities=30%  Similarity=0.453  Sum_probs=72.1

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe--CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri--tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ...++|||+|||+.+++++|+++|++||.|+.+.+  ....++||||+|.+.++|++||+.||+..|.|++|+|+|+++.
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            34568999999999999999999999999999886  3456899999999999999999999999999999999999875


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        92 r   92 (95)
T d1x4aa1          92 R   92 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.56  E-value=3.8e-15  Score=134.93  Aligned_cols=77  Identities=19%  Similarity=0.258  Sum_probs=71.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ..++|||+|||+.+++++|+++|++||+|..|.+ .+.++||||+|.+.++|.+|++.|||..|.|++|+|+|+....
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l-~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC-CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEe-eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            4579999999999999999999999999999997 4678999999999999999999999999999999999997654

>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=99.56  E-value=4.7e-15  Score=128.90  Aligned_cols=75  Identities=24%  Similarity=0.407  Sum_probs=68.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCC--cEEEEE
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLE  432 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G--r~IkVe  432 (861)
                      ...++|||+|||..+++++|+++|++||+|.+|++     .++++|||||+|.+.++|++|++.|||..+.|  ++|+|+
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            34578999999999999999999999999999875     35678999999999999999999999999976  889999


Q ss_pred             ec
Q 002974          433 AS  434 (861)
Q Consensus       433 ~A  434 (861)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.56  E-value=3.6e-15  Score=134.79  Aligned_cols=77  Identities=26%  Similarity=0.503  Sum_probs=71.8

Q ss_pred             CcceEEecccC-CCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          362 QGTLVVFNLDS-SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       362 ~~tLfVgNLp~-svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      .++|||+||++ .+++++|+++|++||+|+.|++...++|||||+|.+.++|.+|++.|||..|.|++|+|++++.+.
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 599999999999999999999987889999999999999999999999999999999999997654

>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=99.56  E-value=5.9e-15  Score=132.25  Aligned_cols=77  Identities=18%  Similarity=0.321  Sum_probs=69.8

Q ss_pred             ccCCcceEEeccc-CCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          359 DANQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       359 ~~~~~tLfVgNLp-~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      .....+|||+||+ ..+++++|+++|++||.|++|++   .||||||+|.+.++|++||+.|||+.|.|++|+|++++++
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            3445689999997 56888999999999999999997   5899999999999999999999999999999999999865


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        89 ~   89 (98)
T d1wf2a_          89 K   89 (98)
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=99.55  E-value=1.4e-15  Score=136.92  Aligned_cols=80  Identities=23%  Similarity=0.381  Sum_probs=72.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||.++++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++.|||..|.|++|+|+++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4578999999999999999999999999999876     45678999999999999999999999999999999999998


Q ss_pred             CCchh
Q 002974          436 PGGAR  440 (861)
Q Consensus       436 pk~~r  440 (861)
                      ++..+
T Consensus        87 ~~~~~   91 (104)
T d1p1ta_          87 SEKNK   91 (104)
T ss_dssp             CTTHH
T ss_pred             CCCCc
Confidence            76533

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=5.1e-15  Score=128.89  Aligned_cols=74  Identities=30%  Similarity=0.413  Sum_probs=67.6

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCC--cEEEEEe
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLEA  433 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G--r~IkVe~  433 (861)
                      ..++|||+|||..+|+++|+++|++||+|++|++     .++++|||||+|.+.++|++|++.|||..+.|  ++|+|.|
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            3568999999999999999999999999999886     35678999999999999999999999999997  6699988


Q ss_pred             c
Q 002974          434 S  434 (861)
Q Consensus       434 A  434 (861)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=3.6e-15  Score=129.38  Aligned_cols=74  Identities=24%  Similarity=0.383  Sum_probs=67.6

Q ss_pred             eEEecccCCCcHHHHHHHhcccCcEEEEEeC-----C---CCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDT-----Q---HKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       365 LfVgNLp~svTeedLrelFskfGeI~sVrit-----g---ksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      |||+|||.++|+++|+++|++||+|++|++.     +   .+||||||+|.+.++|++|++.|||..+.|++|+|+++++
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            7999999999999999999999999998762     1   2478999999999999999999999999999999999976


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>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=99.55  E-value=4.8e-15  Score=129.36  Aligned_cols=76  Identities=22%  Similarity=0.354  Sum_probs=67.5

Q ss_pred             CCcceEEecccCCCcH-HHHHHHhcccCcEEEEEe------CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          361 NQGTLVVFNLDSSVST-EELHQIFGIYGEIREIRD------TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       361 ~~~tLfVgNLp~svTe-edLrelFskfGeI~sVri------tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ..++|||+|||.++++ ++|+++|++||+|++|++      .++++|||||+|.+.++|++|++ ||+..+.|++|+|.+
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            3579999999999865 569999999999999986      34568999999999999999996 999999999999999


Q ss_pred             ccCC
Q 002974          434 SRPG  437 (861)
Q Consensus       434 Akpk  437 (861)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9876

>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=99.55  E-value=2.5e-15  Score=129.79  Aligned_cols=76  Identities=20%  Similarity=0.354  Sum_probs=68.9

Q ss_pred             eEEecccCCCcHHHHHHHhcccCcEEEE-Ee-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          365 LVVFNLDSSVSTEELHQIFGIYGEIREI-RD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       365 LfVgNLp~svTeedLrelFskfGeI~sV-ri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      |||+|||+++++++|+++|++||.|.++ ++     +++++|||||+|.+.++|++|++.|+|..+.|++|+|+++.++.
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            7999999999999999999999998663 43     45678999999999999999999999999999999999999876


Q ss_pred             hh
Q 002974          439 AR  440 (861)
Q Consensus       439 ~r  440 (861)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.55  E-value=3.9e-15  Score=134.76  Aligned_cols=79  Identities=16%  Similarity=0.420  Sum_probs=72.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..++|||+|||+++++++|+++|++||.|..+.+     ++.++|||||+|.+.++|++|++ +++..|.|+.|.|.++.
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            3589999999999999999999999999999985     56899999999999999999996 89999999999999999


Q ss_pred             CCCCC
Q 002974          351 PKDNP  355 (861)
Q Consensus       351 ~k~~~  355 (861)
                      ++++.
T Consensus        98 ~ke~~  102 (103)
T d1x4ba1          98 AREES  102 (103)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            87653

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=5.1e-15  Score=132.66  Aligned_cols=77  Identities=26%  Similarity=0.496  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCC-CCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          274 EHPSRTLFVRNIN-SNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       274 ~~~srtLfVgNLP-~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ....++|||+||| ..+++++|+++|++||.|..|++   +||||||+|.+.++|++|++.|||+.|.|++|+|.|+.++
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            4456789999997 56889999999999999999998   6899999999999999999999999999999999999764


Q ss_pred             C
Q 002974          353 D  353 (861)
Q Consensus       353 ~  353 (861)
                      .
T Consensus        89 ~   89 (98)
T d1wf2a_          89 K   89 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.54  E-value=6.9e-15  Score=125.74  Aligned_cols=72  Identities=22%  Similarity=0.478  Sum_probs=67.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .++|||+|||+++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++ ++|+.|.||+|.|+.|
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            479999999999999999999999999999985     67889999999999999999996 8999999999999876

>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=99.54  E-value=6.8e-15  Score=130.70  Aligned_cols=81  Identities=21%  Similarity=0.344  Sum_probs=71.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCC-EEEEEe------CCCcccEEEEEeCCHHHHHHHHHHcCcc--ccCcceeeee
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGD-IRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNK--PLRRRKLDIH  347 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~-I~svki------tgksrGyAFVeF~d~e~A~kALkaLnG~--~L~Gr~L~V~  347 (861)
                      +|+|||+|||.++++++|+++|++||+ |..+++      +++++|||||+|.+.++|.+|++.|++.  .+.|+.|+|.
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            478999999999999999999999996 888885      3678999999999999999999999754  4579999999


Q ss_pred             ecCCCCCCCC
Q 002974          348 YSIPKDNPSE  357 (861)
Q Consensus       348 ~a~~k~~~~~  357 (861)
                      ||.++..+..
T Consensus        81 ~A~p~~~~~~   90 (96)
T d2disa1          81 WAEPEIDVDE   90 (96)
T ss_dssp             ESCSSCSTTT
T ss_pred             EcCCCCCCCh
Confidence            9998776643

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=1.1e-15  Score=131.81  Aligned_cols=77  Identities=25%  Similarity=0.298  Sum_probs=69.8

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCC-eeCCcEEEEEeccCCchh
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS-DVAGKQIKLEASRPGGAR  440 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~-~I~Gr~IkVe~Akpk~~r  440 (861)
                      .+|||+|||.++|+++|+++|++||.|..+++. .++|||||+|.+.++|++|++.|||. .+.|++|+|+++.++..|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~-~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe-cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            379999999999999999999999999876543 46899999999999999999999996 699999999999998654

>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=99.54  E-value=6.2e-15  Score=125.55  Aligned_cols=70  Identities=17%  Similarity=0.413  Sum_probs=65.4

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +|||+|||++++|++|+++|++||+|..|++     +++++|||||+|.+.++|++|++ +++..|.|+.|.|+.|
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            5999999999999999999999999999984     57899999999999999999997 7999999999999764

>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=99.54  E-value=1.2e-14  Score=130.77  Aligned_cols=81  Identities=17%  Similarity=0.384  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe------CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      ...+.++|||+|||+++++++|+++|++|| |..+++      +++++|||||+|.+.++|++|+ .|++..|.||.|+|
T Consensus        11 p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V   88 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEE
Confidence            345679999999999999999999999999 666653      4678999999999999998777 59999999999999


Q ss_pred             eecCCCCCC
Q 002974          347 HYSIPKDNP  355 (861)
Q Consensus       347 ~~a~~k~~~  355 (861)
                      .++.++...
T Consensus        89 ~~a~~~~~~   97 (104)
T d1wi8a_          89 DVADQAQDK   97 (104)
T ss_dssp             EECCCCCCC
T ss_pred             EECCCCCCC
Confidence            999877554

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=8.7e-15  Score=126.52  Aligned_cols=71  Identities=23%  Similarity=0.451  Sum_probs=66.2

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL  431 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkV  431 (861)
                      ..++|||+|||..+|+++|+++|++||.|.+|++     +++.+|||||+|.+.++|++|++.|||..|.|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4578999999999999999999999999999876     3567899999999999999999999999999999987

>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=99.54  E-value=3.6e-15  Score=130.92  Aligned_cols=76  Identities=14%  Similarity=0.334  Sum_probs=67.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      .+++|||+|||++++++||+++|++|| +..+.+ .+.+|||||+|.+.++|++|++.||++.|.|++|+|+|+..+.
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 333333 5689999999999999999999999999999999999996654

>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=99.54  E-value=2e-15  Score=136.19  Aligned_cols=76  Identities=17%  Similarity=0.389  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      .+.++|||+|||+++++++|+++|++||+|..|++     ++++||||||+|.+.++|++|++ |+|..|.|+.|+|+++
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            45689999999999999999999999999999985     57899999999999999999995 9999999999999998


Q ss_pred             CC
Q 002974          350 IP  351 (861)
Q Consensus       350 ~~  351 (861)
                      .+
T Consensus        95 ~~   96 (101)
T d2cq4a1          95 QA   96 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            64

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=1.2e-14  Score=128.60  Aligned_cols=79  Identities=22%  Similarity=0.392  Sum_probs=71.1

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhC------CCeeCCcEE
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLN------RSDVAGKQI  429 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LN------G~~I~Gr~I  429 (861)
                      ..++|||+|||+.+|+++|+++|++||.|.++.+     .+.++|||||+|.+.++|.+|++.||      |..+.|++|
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            3578999999999999999999999999999875     34578999999999999999999987      567899999


Q ss_pred             EEEeccCCch
Q 002974          430 KLEASRPGGA  439 (861)
Q Consensus       430 kVe~Akpk~~  439 (861)
                      +|+++.++.+
T Consensus        87 ~v~~a~~k~~   96 (98)
T d1x4ha1          87 KVDLAVTRDE   96 (98)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCc
Confidence            9999998753

>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=99.54  E-value=2.6e-15  Score=135.36  Aligned_cols=77  Identities=21%  Similarity=0.448  Sum_probs=70.5

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||..+++++|+++|+.||+|.+|++     ++++||||||+|.+.++|.+|++ |||..|.|+.|+|.+++
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            4578999999999999999999999999999986     46789999999999999999996 99999999999999987


Q ss_pred             CCc
Q 002974          436 PGG  438 (861)
Q Consensus       436 pk~  438 (861)
                      ++.
T Consensus        96 ~~~   98 (101)
T d2cq4a1          96 AEK   98 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>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=99.54  E-value=1.2e-14  Score=127.00  Aligned_cols=80  Identities=26%  Similarity=0.361  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHc--CccccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL--QNKPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaL--nG~~L~Gr~L~V~~a~  350 (861)
                      +..|+++|||+|||+++++++|+++|++||.|..+++ .+.++||||+|.+.++|++|++.+  ++..+.|++|+|.|++
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            4568999999999999999999999999999999997 567899999999999999999876  4678999999999997


Q ss_pred             CCC
Q 002974          351 PKD  353 (861)
Q Consensus       351 ~k~  353 (861)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>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=99.53  E-value=4e-15  Score=134.65  Aligned_cols=77  Identities=12%  Similarity=0.272  Sum_probs=71.3

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      .++|||+|||+++++++|+++|++||+|..+.+     ++.++|||||+|.+.++|++|++ +++..|.|+.|.|.+|.+
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            478999999999999999999999999999886     35678999999999999999997 799999999999999998


Q ss_pred             Cch
Q 002974          437 GGA  439 (861)
Q Consensus       437 k~~  439 (861)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.53  E-value=4.8e-15  Score=132.20  Aligned_cols=82  Identities=20%  Similarity=0.333  Sum_probs=72.3

Q ss_pred             cccCCcceEEecccCCCcHHHHHHHhcccCcEEEE--------Ee-----CCCCccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          358 KDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--------RD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       358 k~~~~~tLfVgNLp~svTeedLrelFskfGeI~sV--------ri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      ++...++|||+|||..+|+++|+++|++||.|..+        .+     +++.+|||||+|.++++|.+|++.|||..|
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            34567899999999999999999999999998643        21     356789999999999999999999999999


Q ss_pred             CCcEEEEEeccCCch
Q 002974          425 AGKQIKLEASRPGGA  439 (861)
Q Consensus       425 ~Gr~IkVe~Akpk~~  439 (861)
                      .|++|+|++++++..
T Consensus        84 ~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          84 QGSKLKVSLARKKPP   98 (101)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCEEEEEEEcCCCCC
Confidence            999999999998753

>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=5.7e-15  Score=129.09  Aligned_cols=77  Identities=25%  Similarity=0.361  Sum_probs=71.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ...+|||+|||.++++++|+++|++||+|.+|++. +.++||||+|.+.++|++|++.|||..|.|++|+|+||.++.
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 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE-TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeee-cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            34579999999999999999999999999999975 468999999999999999999999999999999999998765

>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=99.53  E-value=2.3e-15  Score=129.13  Aligned_cols=71  Identities=17%  Similarity=0.428  Sum_probs=66.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      |+|||+|||+++|+++|+++|++||+|..+++     ++++||||||+|.+.++|++|++ ++++.+.||.|.|++|
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            68999999999999999999999999998874     58899999999999999999997 7999999999999876

>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=6.9e-15  Score=127.99  Aligned_cols=76  Identities=24%  Similarity=0.245  Sum_probs=70.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      .++|||+|||..+++++|+++|++||.|..+++ .+.+|||||+|.+.++|.+|+..|||..|.|++|+|+|++|+.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~-~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE-EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE-ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            468999999999999999999999999877765 4679999999999999999999999999999999999999876

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=1e-14  Score=127.36  Aligned_cols=77  Identities=23%  Similarity=0.296  Sum_probs=70.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEE-eCCCCccEEEEEECCHHHHHHHHHHhCCCee-CCcEEEEEeccCC
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHNHKFIEFYDIRAAETALRTLNRSDV-AGKQIKLEASRPG  437 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVr-itgksKGfAFVeF~d~eaA~kAL~~LNG~~I-~Gr~IkVe~Akpk  437 (861)
                      +.++|||+|||.++++++|+++|++||.|.++. ..++.++||||+|.+.++|.+|+..|+|..| .|++|+|+|+++.
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            357899999999999999999999999998765 4667789999999999999999999999988 5899999999864

>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=99.53  E-value=7.6e-15  Score=133.23  Aligned_cols=82  Identities=23%  Similarity=0.321  Sum_probs=73.1

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHcCcccc--Ccceeeeeec
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPL--RRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-tgksrGyAFVeF~d~e~A~kALkaLnG~~L--~Gr~L~V~~a  349 (861)
                      ...+..+|||+|||..+|+++|+++|++||.|..|.+ ..+.+|||||+|.+.++|++|++.|+|..|  .+++|+|.|+
T Consensus         3 ~~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           3 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CCCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CCCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            3456889999999999999999999999999999885 456789999999999999999999999998  4788999998


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .++..
T Consensus        83 ~~~~~   87 (108)
T d2adba1          83 KLTSL   87 (108)
T ss_dssp             SSCSC
T ss_pred             CCccc
Confidence            77544

>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=99.53  E-value=1.4e-14  Score=129.03  Aligned_cols=78  Identities=29%  Similarity=0.511  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCc--ceeeeeecCC
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRR--RKLDIHYSIP  351 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~G--r~L~V~~a~~  351 (861)
                      ..|+++|||+|||+++++++|+++|++||+|..|++ .+.++||||+|.+.++|++|++.|++..|.|  ++|+|.|+++
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            356899999999999999999999999999999998 4678999999999999999999999999986  5899999976


Q ss_pred             C
Q 002974          352 K  352 (861)
Q Consensus       352 k  352 (861)
                      .
T Consensus        93 ~   93 (97)
T d1whya_          93 G   93 (97)
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=99.53  E-value=3e-15  Score=131.19  Aligned_cols=77  Identities=16%  Similarity=0.301  Sum_probs=71.9

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCch
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGGA  439 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~  439 (861)
                      ..++|||+|||+.+|+++|+++|++||+|.+|++...+++||||+|.+.++|++|+.  ++..|.|++|+|++++++..
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            357999999999999999999999999999999888889999999999999999996  88899999999999988763

>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=99.53  E-value=1.1e-14  Score=130.54  Aligned_cols=80  Identities=15%  Similarity=0.225  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      ..+..++|||+|||+++++++|+++|++||+|..|++  ..+|||||+|.+.++|++||+.|||..+.|+.|+|.+...+
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i--~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~   88 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADV--QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVY   88 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEE--ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccc--cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecC
Confidence            4456889999999999999999999999999999998  45799999999999999999999999999999999998765


Q ss_pred             CC
Q 002974          353 DN  354 (861)
Q Consensus       353 ~~  354 (861)
                      .+
T Consensus        89 ~~   90 (98)
T d1wg4a_          89 PE   90 (98)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.53  E-value=1.4e-14  Score=126.12  Aligned_cols=74  Identities=15%  Similarity=0.297  Sum_probs=68.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||+.+++++|+++|++||+|.+|++     +++++|||||+|.+.++|++|++ +++..|.|+.|+|+.|.
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            3478999999999999999999999999999876     46779999999999999999998 69999999999999875

>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=99.52  E-value=1.6e-15  Score=134.15  Aligned_cols=79  Identities=15%  Similarity=0.225  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .....++|||+|||+++++++|+++|++||.|..+++    +++++|||||+|.+.++|++||+ |+|..|.|++|+|.+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            3445789999999999999999999999998776653    68899999999999999999996 999999999999999


Q ss_pred             cCCC
Q 002974          349 SIPK  352 (861)
Q Consensus       349 a~~k  352 (861)
                      ++.|
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9754

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.3e-14  Score=128.10  Aligned_cols=77  Identities=17%  Similarity=0.364  Sum_probs=69.7

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||+++|+++|+++|++||.|.+|++     ++.+||||||+|.+.++|++||+.  ...|.|+.|+|+++.
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            4578999999999999999999999999999875     477799999999999999999984  458999999999999


Q ss_pred             CCch
Q 002974          436 PGGA  439 (861)
Q Consensus       436 pk~~  439 (861)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8753

>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=99.52  E-value=5.5e-15  Score=129.22  Aligned_cols=74  Identities=16%  Similarity=0.191  Sum_probs=68.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCCC
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKD  353 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k~  353 (861)
                      ++|||+|||+++++++|+++|++||+|..+++  ..+|||||+|.+.++|++||+.|+|..|.|+.|+|.++.++.
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 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV--YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEE--CTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccc--cccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            46999999999999999999999999999997  345999999999999999999999999999999999876543

>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=99.52  E-value=1.6e-14  Score=123.09  Aligned_cols=71  Identities=17%  Similarity=0.428  Sum_probs=65.9

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       280 LfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      |||+|||+++++++|+++|++|| +..+++ .+.+|||||+|.+.++|++|++.|||..+.|++|+|+|+..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 666665 678999999999999999999999999999999999999643

>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=99.51  E-value=7.5e-15  Score=123.99  Aligned_cols=70  Identities=19%  Similarity=0.427  Sum_probs=65.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +|||+|||+++|+++|+++|++||.|..+.+     ++.++|||||+|.+.++|++|++ ++|+.|.||+|+|++|
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            5999999999999999999999999999874     57889999999999999999996 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=99.51  E-value=4.7e-14  Score=127.17  Aligned_cols=81  Identities=17%  Similarity=0.261  Sum_probs=72.9

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcC--ccccCcceeeeeecC
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ--NKPLRRRKLDIHYSI  350 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLn--G~~L~Gr~L~V~~a~  350 (861)
                      ...++++|||+|||.+++|++|+++|++||.|..+++ .+.|+||||+|.+.++|++|++.|+  +..+.|++|+|.|+.
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            4467999999999999999999999999999999998 5789999999999999999999884  456889999999997


Q ss_pred             CCCC
Q 002974          351 PKDN  354 (861)
Q Consensus       351 ~k~~  354 (861)
                      .+..
T Consensus        90 ~~~~   93 (104)
T d1wexa_          90 SKRI   93 (104)
T ss_dssp             SSSC
T ss_pred             CCcc
Confidence            6543

>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=99.51  E-value=2e-14  Score=122.77  Aligned_cols=71  Identities=18%  Similarity=0.322  Sum_probs=65.9

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ++|||+|||+++|+++|+++|++||.|..+++     .++++|||||+|.+.++|.+|++ ++|..|.|++|+|+.|
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            68999999999999999999999999999875     45678999999999999999996 8999999999999876

>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=99.50  E-value=1.5e-14  Score=123.16  Aligned_cols=70  Identities=16%  Similarity=0.326  Sum_probs=64.8

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +|||+|||+++++++|+++|++||+|..|++     +++++|||||+|.+.++|++||+ +++..|.|++|+|+.|
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            5999999999999999999999999999986     46678999999999999999998 7999999999999654

>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=1.3e-14  Score=124.66  Aligned_cols=74  Identities=24%  Similarity=0.411  Sum_probs=68.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      .++|||+|++  +|+++|+++|++||+|.+|++. +.++||||+|.+.++|.+|++.|||..+.|++|+|+|++++.
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~-~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE-TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeec-cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            4689999996  8999999999999999999975 578999999999999999999999999999999999998763

>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=99.50  E-value=1.1e-14  Score=130.72  Aligned_cols=77  Identities=16%  Similarity=0.209  Sum_probs=70.4

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccC
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ..++|||+|||.++++++|+++|++||+|..+++    .++++|||||+|.+.++|++|++.|||..|.|+++.|.+++|
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            4578999999999999999999999999998765    455688999999999999999999999999999999988876


Q ss_pred             C
Q 002974          437 G  437 (861)
Q Consensus       437 k  437 (861)
                      -
T Consensus        97 l   97 (101)
T d1x5oa1          97 L   97 (101)
T ss_dssp             B
T ss_pred             c
Confidence            4

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=1e-14  Score=127.99  Aligned_cols=75  Identities=15%  Similarity=0.325  Sum_probs=66.8

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      .++|||+|||+++++++|+++|++|| ++.+. +...++||||+|.+.++|++|++.||+..|.|++|+|++++.+.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~-~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCY-VDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEE-EEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeee-eeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            56899999999999999999999999 22333 24679999999999999999999999999999999999997664

>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=99.50  E-value=6.5e-15  Score=131.68  Aligned_cols=81  Identities=23%  Similarity=0.281  Sum_probs=73.4

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...++|||+|||.++++++|+++|++||.|..+.+     .++.+|||||+|.+.++|.+|++.|||..|.|++|+|+|+
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            34678999999999999999999999999877543     5778999999999999999999999999999999999999


Q ss_pred             cCCchh
Q 002974          435 RPGGAR  440 (861)
Q Consensus       435 kpk~~r  440 (861)
                      +++..|
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            987654

>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=99.50  E-value=2.3e-14  Score=124.87  Aligned_cols=74  Identities=14%  Similarity=0.327  Sum_probs=68.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      ..++|||+|||.++|+++|+++|++||.|..|++    +++++|||||+|.+.++|++|++ +++..+.|+.|.|.|..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4689999999999999999999999999999985    57889999999999999999996 89999999999999863

>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=1.5e-14  Score=127.40  Aligned_cols=79  Identities=22%  Similarity=0.422  Sum_probs=71.0

Q ss_pred             CcceEEecccCCCcHHHHHH----HhcccCcEEEEEeC--CCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          362 QGTLVVFNLDSSVSTEELHQ----IFGIYGEIREIRDT--QHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLre----lFskfGeI~sVrit--gksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      .++|||+|||..+++++|++    +|++||+|.+|++.  ++.+|||||+|.+.++|.+|++.|||..+.|++|+|.||+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak   82 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK   82 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            57899999999999998864    68999999999873  3468999999999999999999999999999999999999


Q ss_pred             CCchh
Q 002974          436 PGGAR  440 (861)
Q Consensus       436 pk~~r  440 (861)
                      ++...
T Consensus        83 ~~~~~   87 (91)
T d1nu4a_          83 TDSDI   87 (91)
T ss_dssp             SCCTH
T ss_pred             CCchh
Confidence            87643

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=3.5e-14  Score=120.97  Aligned_cols=72  Identities=15%  Similarity=0.341  Sum_probs=66.0

Q ss_pred             eEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       365 LfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      |||+|||+++++++|+++|++|| +..+++ ++.+|||||+|.+.++|++|++.|||..+.|++|+|+++..+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 555553 5689999999999999999999999999999999999997653

>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=99.49  E-value=1.5e-14  Score=123.56  Aligned_cols=70  Identities=20%  Similarity=0.476  Sum_probs=65.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       279 tLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      +|||+|||+++|+++|+++|++||+|..|++     ++++||||||+|.+.++|++|++ .++..|.|+.|.|+.|
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            5999999999999999999999999999985     57899999999999999999996 6778899999999865

>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=99.49  E-value=4.9e-15  Score=130.95  Aligned_cols=77  Identities=23%  Similarity=0.275  Sum_probs=69.9

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ....+|||+|||+++++++|+++|++||.|..+++    +++++|||||+|.+.++|++||+ |||..|.|++|+|++++
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            34568999999999999999999999999877654    57789999999999999999996 99999999999999998


Q ss_pred             CC
Q 002974          436 PG  437 (861)
Q Consensus       436 pk  437 (861)
                      .|
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>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=99.48  E-value=1.8e-14  Score=121.68  Aligned_cols=70  Identities=14%  Similarity=0.308  Sum_probs=65.1

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +|||+|||+++|+++|+++|++||.|..+.+     ++..++||||+|.+.++|++|++ +||..|.|++|+|++|
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     45678999999999999999997 9999999999999876

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=4.9e-14  Score=125.53  Aligned_cols=78  Identities=21%  Similarity=0.376  Sum_probs=71.6

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCC--cEEEEEeccCC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG--KQIKLEASRPG  437 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G--r~IkVe~Akpk  437 (861)
                      ...++|||+|||+++++++|+++|++||+|+.|++. +.++||||+|.+.++|++|++.||+..|.|  ++|+|+|++++
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~-~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEEC-SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeee-ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            456899999999999999999999999999999975 468999999999999999999999999986  68999999875


Q ss_pred             c
Q 002974          438 G  438 (861)
Q Consensus       438 ~  438 (861)
                      .
T Consensus        94 ~   94 (97)
T d1whya_          94 P   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=1.2e-14  Score=127.06  Aligned_cols=73  Identities=18%  Similarity=0.147  Sum_probs=67.8

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      +|||+|||+.+++++|+++|++||+|.+|++.  .+|||||+|.+.++|++||+.|||..|.|+.|+|.+++++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVY--RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEEC--TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccc--ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            69999999999999999999999999999975  46999999999999999999999999999999998876543

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=1.3e-14  Score=124.40  Aligned_cols=71  Identities=23%  Similarity=0.411  Sum_probs=66.0

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      .+|||+|||+++|+++|+++|++||+|++|++     ++++||||||+|.+.++|++|++ +++..+.|++|+|+.|
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            37999999999999999999999999998875     46789999999999999999998 7999999999999876

>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=99.47  E-value=2.2e-14  Score=120.51  Aligned_cols=66  Identities=21%  Similarity=0.434  Sum_probs=62.6

Q ss_pred             EEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          280 LFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       280 LfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      |||+|||+++|+++|+++|++||.|..+++     +++++|||||+|.+.++|++|++.|||+.+.|+.|+
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            899999999999999999999999999874     578999999999999999999999999999999875

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.1e-14  Score=125.55  Aligned_cols=78  Identities=21%  Similarity=0.224  Sum_probs=68.9

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCc-EEEEEeC------CCCccEEEEEECCHHHHHHHHHHhCCC--eeCCcEEEEEe
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGE-IREIRDT------QHKHNHKFIEFYDIRAAETALRTLNRS--DVAGKQIKLEA  433 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGe-I~sVrit------gksKGfAFVeF~d~eaA~kAL~~LNG~--~I~Gr~IkVe~  433 (861)
                      ++|||+|||..+++++|+++|++||+ |..|++.      ++++|||||+|.+.++|.+|++.|++.  .+.|+.|+|.|
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 8888862      457899999999999999999999755  55799999999


Q ss_pred             ccCCchh
Q 002974          434 SRPGGAR  440 (861)
Q Consensus       434 Akpk~~r  440 (861)
                      |+|+...
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9987643

>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=99.46  E-value=3.2e-14  Score=127.39  Aligned_cols=76  Identities=18%  Similarity=0.147  Sum_probs=70.8

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~  438 (861)
                      ...+|||+|||+.+++++|+++|++||+|+.|++.  .+|||||+|.+.++|++||+.|||..+.|+.|+|.+++.+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~--~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ--KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE--TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc--ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            45689999999999999999999999999999974  57999999999999999999999999999999999987654

>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=99.46  E-value=5.1e-14  Score=126.18  Aligned_cols=80  Identities=15%  Similarity=0.183  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHH--HcCccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK--ALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~-vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALk--aLnG~~L~Gr~L~V~~a  349 (861)
                      ...++++|||+|||.+ +|+++|+++|++||.|..+++ .+.+|||||+|.+.++|.+|++  .+++..+.|+.|+|.|+
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            3456899999999985 899999999999999999998 5678999999999999999998  46788899999999999


Q ss_pred             CCCC
Q 002974          350 IPKD  353 (861)
Q Consensus       350 ~~k~  353 (861)
                      ..+.
T Consensus        93 ~~~~   96 (99)
T d1x4fa1          93 EKYK   96 (99)
T ss_dssp             CSCS
T ss_pred             CCcc
Confidence            7553

>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=99.46  E-value=8.2e-14  Score=118.67  Aligned_cols=71  Identities=21%  Similarity=0.215  Sum_probs=64.7

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe---CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD---TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri---tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ++|||+|||+++++++|+++|+.||+|+.|++   ....++||||+|.+.++|++|+. +|++.|+|++|.|+.+
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            47999999999999999999999999999886   33456799999999999999996 8999999999999864

>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=99.45  E-value=2.7e-14  Score=121.95  Aligned_cols=70  Identities=19%  Similarity=0.359  Sum_probs=64.4

Q ss_pred             ceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       364 tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +|||+|||+++|+++|+++|++||+|.+|++     +++++|||||+|.+.++|++||+ +++..|.|+.|+|+.|
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     46678999999999999999997 5778999999999865

>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=1.1e-13  Score=124.14  Aligned_cols=77  Identities=22%  Similarity=0.324  Sum_probs=67.4

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe------CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD------TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri------tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...+|||+|||+++++++|+++|++|| |+++++      .++.+|||||+|.+.++|++|++ ||+..|.|++|+|.++
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 666654      34568899999999999987775 9999999999999999


Q ss_pred             cCCch
Q 002974          435 RPGGA  439 (861)
Q Consensus       435 kpk~~  439 (861)
                      .++..
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=99.45  E-value=8.6e-14  Score=121.22  Aligned_cols=74  Identities=8%  Similarity=0.161  Sum_probs=68.0

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ..++|||+|||.++|+++|+++|+.||.|..|++    .++.+|||||+|.+.++|++||+ +++..+.|+.|+|.+++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4679999999999999999999999999999986    35568999999999999999997 79999999999999864

>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=3.7e-14  Score=128.65  Aligned_cols=77  Identities=22%  Similarity=0.330  Sum_probs=69.6

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeC-CCCccEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEEeccCCc
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDT-QHKHNHKFIEFYDIRAAETALRTLNRSDV--AGKQIKLEASRPGG  438 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVrit-gksKGfAFVeF~d~eaA~kAL~~LNG~~I--~Gr~IkVe~Akpk~  438 (861)
                      ..+|||+|||+.+|+++|+++|++||.|++|.+. .+.+|||||+|.+.++|++|++.|||..|  .|++|+|.+++++.
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcc
Confidence            4579999999999999999999999999998763 34689999999999999999999999988  47899999998764

>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=99.44  E-value=1.1e-13  Score=121.67  Aligned_cols=79  Identities=15%  Similarity=0.139  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEcCCCCC-CcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHc--CccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSN-VEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKAL--QNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~-vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaL--nG~~L~Gr~L~V~~a  349 (861)
                      ...++++|||+|||.. +|++||+++|++||.|..|++ ...+++|||+|.+.++|.+|++.|  ++..+.|++|+|.|+
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            4567999999999986 889999999999999999998 466789999999999999999976  566799999999999


Q ss_pred             CCC
Q 002974          350 IPK  352 (861)
Q Consensus       350 ~~k  352 (861)
                      ...
T Consensus        83 ~~~   85 (89)
T d1x4da1          83 QKY   85 (89)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            753

>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=99.44  E-value=1.7e-13  Score=119.68  Aligned_cols=79  Identities=19%  Similarity=0.190  Sum_probs=71.4

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHh--CCCeeCCcEEEEEeccC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRP  436 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~L--NG~~I~Gr~IkVe~Akp  436 (861)
                      ..+.++|||+|||.++++++|+++|++||.|.++++. +.++||||+|.+.++|++|++.+  ++..+.|++|+|.|++.
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 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML-KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc-ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            3467899999999999999999999999999999875 56899999999999999999865  56789999999999987


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      +.
T Consensus        84 ~~   85 (88)
T d2cq1a1          84 KE   85 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.44  E-value=1e-13  Score=118.11  Aligned_cols=71  Identities=17%  Similarity=0.245  Sum_probs=64.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe---CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT---ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki---tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ++|||+|||+++++++|+++|++||+|..+++   ....++||||+|.+.++|++|++ ++++.|.|++|.|..+
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            48999999999999999999999999999985   45566899999999999999995 8999999999999764

>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=99.44  E-value=2.3e-13  Score=122.42  Aligned_cols=80  Identities=14%  Similarity=0.189  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeee
Q 002974          274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHY  348 (861)
Q Consensus       274 ~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svki-----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~  348 (861)
                      .....+|||+|||+++|++||+++|.+||.|..+.+     +++++|||||+|.++++|++|++ +++..|.||.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            445678999999999999999999999999877542     67889999999999999999996 999999999999999


Q ss_pred             cCCCCC
Q 002974          349 SIPKDN  354 (861)
Q Consensus       349 a~~k~~  354 (861)
                      +.+++.
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            987644

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=1.1e-13  Score=121.47  Aligned_cols=72  Identities=18%  Similarity=0.369  Sum_probs=64.0

Q ss_pred             CCcceEEecccCCCcHHHH---HHHhcccCcEEEEEeC-----CC---CccEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Q 002974          361 NQGTLVVFNLDSSVSTEEL---HQIFGIYGEIREIRDT-----QH---KHNHKFIEFYDIRAAETALRTLNRSDVAGKQI  429 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedL---relFskfGeI~sVrit-----gk---sKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~I  429 (861)
                      ..++|||+|||+++++++|   +++|++||+|+.|.+.     +.   .+|||||+|.+.++|++|++.|||..+.|+.|
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            3467999999999999999   6789999999999862     12   24899999999999999999999999999999


Q ss_pred             EEE
Q 002974          430 KLE  432 (861)
Q Consensus       430 kVe  432 (861)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.43  E-value=2.2e-13  Score=132.38  Aligned_cols=121  Identities=12%  Similarity=0.171  Sum_probs=99.3

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeccCC
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASRPG  437 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Akpk  437 (861)
                      ++|||+|||+.+|+++|+++|++||.|.++.+     ++.++|||||+|.+.++|++|+. +++..+.++.+.+.+..++
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhc
Confidence            68999999999999999999999999999875     55678999999999999999998 6778889999999888766


Q ss_pred             chhhhchhhhhhhccccCC-CCCCCCCCcccc----CCcccEEEEe----CCCCCccee
Q 002974          438 GARRFMVQSEQEQDDLNLC-QIPFDDLSSGQM----VSSGVITSTC----MDNGSIQVL  487 (861)
Q Consensus       438 ~~rrl~qq~eq~q~E~~vg-kNLp~s~tee~L----s~fG~I~Sv~----~enG~srGF  487 (861)
                      .....   .........+. .+||.+++++.|    ..||.|..+.    .++|.++||
T Consensus        86 ~~~~~---~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~  141 (183)
T d1u1qa_          86 EDSQR---PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF  141 (183)
T ss_dssp             TGGGS---TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEE
T ss_pred             ccccc---cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCcccee
Confidence            53321   11122222334 999999999999    8999999887    567888886

>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=99.43  E-value=1.4e-13  Score=123.70  Aligned_cols=81  Identities=10%  Similarity=0.211  Sum_probs=70.0

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEE---eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY---TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~svk---itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ......+|||+|||+++|++||+++|+.||.+....   .++..+|||||+|.+.++|++|++ ++++.|.||.|+|.++
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            445678999999999999999999999999543222   267889999999999999999996 8999999999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .++..
T Consensus        90 ~~~~~   94 (102)
T d1weza_          90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.43  E-value=6e-14  Score=121.80  Aligned_cols=75  Identities=19%  Similarity=0.246  Sum_probs=66.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE-E----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTI-Y----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~sv-k----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ....+|||+|||.+++++||+++|+.||.|... .    .+++++|||||+|.+.++|++|++.||++.|.||+|+|.++
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            345679999999999999999999999987442 2    26889999999999999999999999999999999999864

>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=6.8e-14  Score=122.88  Aligned_cols=72  Identities=19%  Similarity=0.337  Sum_probs=64.4

Q ss_pred             CCcEEEEcCCCCCCcHHHH---HHHhhcCCCEEEEEe-----C---CCcccEEEEEeCCHHHHHHHHHHcCccccCccee
Q 002974          276 PSRTLFVRNINSNVEDSEL---KALFEQFGDIRTIYT-----A---CKHRGFVMISYYDIRAARNAMKALQNKPLRRRKL  344 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL---~elFsqfG~I~svki-----t---gksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L  344 (861)
                      ..++|||+|||+++++++|   +++|++||+|..|.+     +   +..+|||||+|.+.++|++|++.|||..+.||.|
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            4678999999999999999   678999999999985     2   2345899999999999999999999999999999


Q ss_pred             eee
Q 002974          345 DIH  347 (861)
Q Consensus       345 ~V~  347 (861)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            974

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=4e-13  Score=121.01  Aligned_cols=79  Identities=19%  Similarity=0.169  Sum_probs=71.2

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHh--CCCeeCCcEEEEEeccC
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRP  436 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~L--NG~~I~Gr~IkVe~Akp  436 (861)
                      .....+|||+|||..+++++|+++|++||.|+.|++. +.|++|||+|.+.++|++|++.|  ++..+.|++|+|.|++.
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 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM-PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE-TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE-ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            3457799999999999999999999999999999975 57899999999999999999988  45678899999999987


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      +.
T Consensus        91 ~~   92 (104)
T d1wexa_          91 KR   92 (104)
T ss_dssp             SS
T ss_pred             Cc
Confidence            65

>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=5.7e-14  Score=117.96  Aligned_cols=66  Identities=24%  Similarity=0.375  Sum_probs=61.5

Q ss_pred             eEEecccCCCcHHHHHHHhcccCcEEEEEe-----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          365 LVVFNLDSSVSTEELHQIFGIYGEIREIRD-----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       365 LfVgNLp~svTeedLrelFskfGeI~sVri-----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      |||+|||.++|+++|+++|++||.|..+++     .+..+|||||+|.+.++|++|++.|||+.|.|+.|+
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     456789999999999999999999999999998875

>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=99.39  E-value=8.9e-14  Score=125.95  Aligned_cols=79  Identities=16%  Similarity=0.177  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCc-----HHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVE-----DSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vT-----EedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ..+++|||+||+.++.     +++|+++|++||.|.++++ .++++||||+|.+.++|++|++.|||+.|.|+.|+|.|+
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            4578999999999873     3579999999999999997 578999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 002974          350 IPKDN  354 (861)
Q Consensus       350 ~~k~~  354 (861)
                      .++..
T Consensus        82 ~~~~~   86 (104)
T d1weya_          82 QTLHI   86 (104)
T ss_dssp             CCSSC
T ss_pred             ccCCC
Confidence            77644

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=1.3e-13  Score=119.54  Aligned_cols=74  Identities=20%  Similarity=0.270  Sum_probs=66.2

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEE-EE----eCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IR----DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~s-Vr----itgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      ...+|||+|||+++++++|+++|+.||.|.. +.    ..++++|+|||+|.+.++|++|++.||++.|.||+|+|+++
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            4567999999999999999999999998754 22    25677899999999999999999999999999999999875

>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=99.38  E-value=6.7e-13  Score=119.38  Aligned_cols=79  Identities=22%  Similarity=0.247  Sum_probs=69.8

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEE-Ee----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-RD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEA  433 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sV-ri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~  433 (861)
                      ..+..+|||+|||+++|+++|+++|+.||.|..+ .+    .++.+|||||+|.++++|++|++ +|+..|.||.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3455689999999999999999999999998774 32    45678999999999999999996 999999999999999


Q ss_pred             ccCCc
Q 002974          434 SRPGG  438 (861)
Q Consensus       434 Akpk~  438 (861)
                      +.++.
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            98765

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=3.3e-13  Score=120.79  Aligned_cols=78  Identities=18%  Similarity=0.158  Sum_probs=69.7

Q ss_pred             cCCcceEEecccCC-CcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHH--HhCCCeeCCcEEEEEeccC
Q 002974          360 ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALR--TLNRSDVAGKQIKLEASRP  436 (861)
Q Consensus       360 ~~~~tLfVgNLp~s-vTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~--~LNG~~I~Gr~IkVe~Akp  436 (861)
                      ...++|||+|||.+ +|+++|+++|++||.|.+|++. +.+|+|||+|.+.++|.+|++  .+++..+.|++|+|.+++.
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 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEe-ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            34578999999985 8999999999999999999975 468999999999999999997  5788899999999999976


Q ss_pred             Cc
Q 002974          437 GG  438 (861)
Q Consensus       437 k~  438 (861)
                      +.
T Consensus        95 ~~   96 (99)
T d1x4fa1          95 YK   96 (99)
T ss_dssp             CS
T ss_pred             cc
Confidence            53

>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=99.36  E-value=1.1e-12  Score=115.29  Aligned_cols=77  Identities=19%  Similarity=0.236  Sum_probs=69.2

Q ss_pred             cCCcceEEecccCC-CcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHh--CCCeeCCcEEEEEeccC
Q 002974          360 ANQGTLVVFNLDSS-VSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTL--NRSDVAGKQIKLEASRP  436 (861)
Q Consensus       360 ~~~~tLfVgNLp~s-vTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~L--NG~~I~Gr~IkVe~Akp  436 (861)
                      ...++|||+|||.. +|++||+++|++||+|.+|++. ..+++|||+|.+.++|.+|++.|  ++..+.|++|+|.|++.
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 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEEC-SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEee-ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            45678999999986 8999999999999999999975 46789999999999999999966  67789999999999985


Q ss_pred             C
Q 002974          437 G  437 (861)
Q Consensus       437 k  437 (861)
                      .
T Consensus        85 ~   85 (89)
T d1x4da1          85 Y   85 (89)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=6.3e-13  Score=119.26  Aligned_cols=78  Identities=10%  Similarity=0.174  Sum_probs=68.0

Q ss_pred             ccCCcceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       359 ~~~~~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      .....+|||+|||+++|+++|+++|+.||.+ .|.+    .+..+|||||+|.+.++|++|++ ||+..|.||.|+|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3445689999999999999999999999854 3332    45668999999999999999987 8999999999999999


Q ss_pred             cCCc
Q 002974          435 RPGG  438 (861)
Q Consensus       435 kpk~  438 (861)
                      .++.
T Consensus        90 ~~~~   93 (102)
T d1weza_          90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8775

>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=99.35  E-value=3.7e-13  Score=120.67  Aligned_cols=76  Identities=14%  Similarity=0.192  Sum_probs=67.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEE-EE----eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRT-IY----TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~s-vk----itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ....+|||+|||+++|+++|+++|..||.|.. +.    .+++++|||||+|.+.++|++|++ |+++.|.||.|.|.++
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            34678999999999999999999999998754 33    267899999999999999999996 9999999999999887


Q ss_pred             CC
Q 002974          350 IP  351 (861)
Q Consensus       350 ~~  351 (861)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>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=99.33  E-value=3.6e-14  Score=124.41  Aligned_cols=73  Identities=15%  Similarity=0.320  Sum_probs=64.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----------CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeee
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYT----------ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDI  346 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svki----------tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V  346 (861)
                      .|+|||+|||.++||++|+++|++||.|..+.+          +++++|||||+|.+.++|++|++ |+|+.+.|+.|+|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI   79 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEE
Confidence            379999999999999999999999998765432          35789999999999999999995 9999999999999


Q ss_pred             eecC
Q 002974          347 HYSI  350 (861)
Q Consensus       347 ~~a~  350 (861)
                      +.++
T Consensus        80 ~r~k   83 (90)
T d1u2fa_          80 RRPH   83 (90)
T ss_dssp             BCTT
T ss_pred             CCCC
Confidence            8654

>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=99.33  E-value=5.4e-13  Score=121.76  Aligned_cols=78  Identities=9%  Similarity=0.175  Sum_probs=68.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEE---E--eCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeee
Q 002974          273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI---Y--TACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIH  347 (861)
Q Consensus       273 ~~~~srtLfVgNLP~~vTEedL~elFsqfG~I~sv---k--itgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~  347 (861)
                      ...+.++|||+|||+++|+++|+++|+.||.|..+   .  .++.++|||||+|.+.++|++|++ |+|..|+||.|.|.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~   92 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEE
Confidence            44567899999999999999999999999986432   2  368999999999999999999996 99999999999998


Q ss_pred             ecCC
Q 002974          348 YSIP  351 (861)
Q Consensus       348 ~a~~  351 (861)
                      .+.+
T Consensus        93 ~~~~   96 (112)
T d1wela1          93 PITK   96 (112)
T ss_dssp             EECH
T ss_pred             EcCh
Confidence            7753

>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=99.33  E-value=3.6e-13  Score=120.78  Aligned_cols=76  Identities=12%  Similarity=0.145  Sum_probs=67.4

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEE-EEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE-IRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~s-Vri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...+|||+|||+++|+++|+++|+.||.|.. +.+    .++++|||||+|.+.++|++||+ ||+..|.|+.|+|.++.
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            4578999999999999999999999998865 333    46679999999999999999996 99999999999999986


Q ss_pred             CC
Q 002974          436 PG  437 (861)
Q Consensus       436 pk  437 (861)
                      .+
T Consensus        86 ~~   87 (103)
T d2cpya1          86 LE   87 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=99.31  E-value=5.4e-13  Score=120.70  Aligned_cols=78  Identities=17%  Similarity=0.216  Sum_probs=69.7

Q ss_pred             CCcceEEecccCCCc-----HHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVS-----TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svT-----eedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...+|||+||+.++.     +++|+++|++||+|+++++. ++++||||+|.+.++|.+|++.|||..|.|++|+|.|++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            356899999998763     35699999999999999875 578999999999999999999999999999999999998


Q ss_pred             CCch
Q 002974          436 PGGA  439 (861)
Q Consensus       436 pk~~  439 (861)
                      +...
T Consensus        83 ~~~~   86 (104)
T d1weya_          83 TLHI   86 (104)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            7653

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=1.5e-12  Score=118.70  Aligned_cols=78  Identities=12%  Similarity=0.146  Sum_probs=68.3

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEE---E--eCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI---R--DTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sV---r--itgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      ...+|||+|||+++|+++|+++|+.||.|..+   .  ..+..+|||||+|.+.++|++|++ ||+..|+|+.|.|.++.
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            35689999999999999999999999987542   1  256788999999999999999997 99999999999999987


Q ss_pred             CCch
Q 002974          436 PGGA  439 (861)
Q Consensus       436 pk~~  439 (861)
                      ++..
T Consensus        96 ~~~~   99 (112)
T d1wela1          96 KKGM   99 (112)
T ss_dssp             HHHH
T ss_pred             hHHH
Confidence            6653

>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=99.23  E-value=7.2e-12  Score=112.54  Aligned_cols=67  Identities=16%  Similarity=0.305  Sum_probs=60.7

Q ss_pred             CCCCCcEEEEcC--CCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccC
Q 002974          273 GEHPSRTLFVRN--INSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLR  340 (861)
Q Consensus       273 ~~~~srtLfVgN--LP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~  340 (861)
                      ...|+++|||.|  ||.++|+++|+++|++||.|..|++ .+.++||||+|.+.++|.+|++.|||+.+.
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            346788999955  9999999999999999999999997 467899999999999999999999998873

>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=99.21  E-value=1.5e-13  Score=120.38  Aligned_cols=72  Identities=17%  Similarity=0.322  Sum_probs=63.2

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe----------CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----------TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE  432 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri----------tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe  432 (861)
                      ++|||+|||..+|+++|+++|++||.|..+.+          +++++|||||+|.+.++|++|++ |||..+.|++|+|.
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            68999999999999999999999998765432          34578999999999999999996 99999999999997


Q ss_pred             ecc
Q 002974          433 ASR  435 (861)
Q Consensus       433 ~Ak  435 (861)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            443

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=2.1e-12  Score=116.73  Aligned_cols=72  Identities=22%  Similarity=0.274  Sum_probs=67.3

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe----CCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEec
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD----TQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLEAS  434 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri----tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~A  434 (861)
                      +.++|.++..++++++|+++|++||+|++|++    +++++|+|||+|.+.++|.+|++.|||+.+.||+|+|+++
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            56899999999999999999999999999987    4567899999999999999999999999999999999985

>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=99.20  E-value=1.4e-11  Score=110.15  Aligned_cols=82  Identities=17%  Similarity=0.290  Sum_probs=71.6

Q ss_pred             CCCCCCcEEEEcCC--CCCCc---------HHHHHHHhhcCCCEEEEEe-CCCcccEEEEEeCCHHHHHHHHHHcCcccc
Q 002974          272 YGEHPSRTLFVRNI--NSNVE---------DSELKALFEQFGDIRTIYT-ACKHRGFVMISYYDIRAARNAMKALQNKPL  339 (861)
Q Consensus       272 ~~~~~srtLfVgNL--P~~vT---------EedL~elFsqfG~I~svki-tgksrGyAFVeF~d~e~A~kALkaLnG~~L  339 (861)
                      ...+.+++|+|+||  |.++.         ++||++.|++||.|..|++ ....+|||||+|.+.++|.+|++.|||..+
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            45677999999999  55432         3689999999999999986 667889999999999999999999999999


Q ss_pred             CcceeeeeecCCCC
Q 002974          340 RRRKLDIHYSIPKD  353 (861)
Q Consensus       340 ~Gr~L~V~~a~~k~  353 (861)
                      .||+|.|.++.++.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987654

>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=99.19  E-value=1.5e-11  Score=112.43  Aligned_cols=78  Identities=19%  Similarity=0.166  Sum_probs=68.0

Q ss_pred             CcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCH-HHHHHHHHHhCCCeeCCcEEEEEeccCCchh
Q 002974          362 QGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDI-RAAETALRTLNRSDVAGKQIKLEASRPGGAR  440 (861)
Q Consensus       362 ~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~-eaA~kAL~~LNG~~I~Gr~IkVe~Akpk~~r  440 (861)
                      ...+||+|||..+|+++|+++|++||+|.+|++. +.++||||+|.+. ++|.+|+..|++..+.++.+.|.++..+...
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~-~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~~~   89 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEV   89 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC-TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHHH
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEe-cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccchh
Confidence            4467999999999999999999999999999976 5799999999985 7899999999999998877777777665533

>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=99.17  E-value=2.1e-11  Score=111.44  Aligned_cols=75  Identities=17%  Similarity=0.268  Sum_probs=66.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCH-HHHHHHHHHcCccccCcceeeeeecCCC
Q 002974          277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDI-RAARNAMKALQNKPLRRRKLDIHYSIPK  352 (861)
Q Consensus       277 srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~-e~A~kALkaLnG~~L~Gr~L~V~~a~~k  352 (861)
                      -..+||||||+.+|+++|+++|++||+|..|++ .+.+|||||.|.+. ++|.+|+..+++..+.++.+.|.++..+
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i-~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEEC-CTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEE-ecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            445699999999999999999999999999998 46799999999995 7899999999999999888888887643

>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=99.15  E-value=4.1e-11  Score=107.56  Aligned_cols=63  Identities=24%  Similarity=0.313  Sum_probs=57.8

Q ss_pred             CCcceEEec--ccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCee
Q 002974          361 NQGTLVVFN--LDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV  424 (861)
Q Consensus       361 ~~~tLfVgN--Lp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I  424 (861)
                      +..+|+|.|  ||..+|+++|+++|++||.|+.|++. ..++||||+|.+.++|++|++.|||+.|
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~-~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP-PNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECC-TTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeec-cCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456889965  99999999999999999999999965 5689999999999999999999999987

>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=99.15  E-value=3.5e-12  Score=115.26  Aligned_cols=72  Identities=13%  Similarity=0.208  Sum_probs=67.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe----CCCcccEEEEEeCCHHHHHHHHHHcCccccCcceeeeeec
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT----ACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYS  349 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki----tgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a  349 (861)
                      ..++|++++.+++|++|+++|++||+|..|++    +++++|||||+|.+.++|.+|++.|||+.+.||+|.|.|+
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            45889999999999999999999999999996    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=99.13  E-value=3.2e-11  Score=104.31  Aligned_cols=75  Identities=17%  Similarity=0.171  Sum_probs=65.4

Q ss_pred             CCcceEEecccCCCcHHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCc-EEEEEeccCCc
Q 002974          361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGK-QIKLEASRPGG  438 (861)
Q Consensus       361 ~~~tLfVgNLp~svTeedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr-~IkVe~Akpk~  438 (861)
                      +.+.|+|+++|++.+++.| +.|++||+|.++++ ++.++||||+|.++++|++||+ +||..|+|+ .|.|.++..+.
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-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   78 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCChh
Confidence            4567999999999987655 57999999999996 4678999999999999999996 999999997 46799988764

>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=4.6e-11  Score=106.77  Aligned_cols=80  Identities=20%  Similarity=0.286  Sum_probs=69.3

Q ss_pred             ccCCcceEEecc--cCCCc---------HHHHHHHhcccCcEEEEEe-CCCCccEEEEEECCHHHHHHHHHHhCCCeeCC
Q 002974          359 DANQGTLVVFNL--DSSVS---------TEELHQIFGIYGEIREIRD-TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG  426 (861)
Q Consensus       359 ~~~~~tLfVgNL--p~svT---------eedLrelFskfGeI~sVri-tgksKGfAFVeF~d~eaA~kAL~~LNG~~I~G  426 (861)
                      ....++|+|.||  |.++.         +++|++.|++||.|..|++ .++.+|+|||+|.+.++|.+|+..|||+.++|
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  54332         3789999999999999886 55678999999999999999999999999999


Q ss_pred             cEEEEEeccCCc
Q 002974          427 KQIKLEASRPGG  438 (861)
Q Consensus       427 r~IkVe~Akpk~  438 (861)
                      |+|+|+++.++.
T Consensus        85 r~i~v~~~~g~~   96 (99)
T d2dita1          85 RQITAQAWDGTT   96 (99)
T ss_dssp             EECEEEECCSCC
T ss_pred             EEEEEEEeCCcC
Confidence            999999998765

>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=99.09  E-value=5.7e-11  Score=102.70  Aligned_cols=73  Identities=16%  Similarity=0.195  Sum_probs=63.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcce-eeeeecCC
Q 002974          276 PSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRK-LDIHYSIP  351 (861)
Q Consensus       276 ~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~-L~V~~a~~  351 (861)
                      +.+.|+|.++|++++++.| ++|++||+|.++++ .+.+|||||+|.+.++|++||+ +||+.|.|+. |.|..+..
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~-~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE-CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEe-cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            3578999999999987655 57999999999998 6778999999999999999996 9999999985 56887754

>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=98.92  E-value=6.3e-10  Score=99.91  Aligned_cols=76  Identities=16%  Similarity=0.347  Sum_probs=65.8

Q ss_pred             CCCcEEEEcCC--CCCCc--------HHHHHHHhhcCCCEEEEEeC-------CCcccEEEEEeCCHHHHHHHHHHcCcc
Q 002974          275 HPSRTLFVRNI--NSNVE--------DSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAMKALQNK  337 (861)
Q Consensus       275 ~~srtLfVgNL--P~~vT--------EedL~elFsqfG~I~svkit-------gksrGyAFVeF~d~e~A~kALkaLnG~  337 (861)
                      .|++.|.|+||  +..+.        .+||++.|++||.|..|++.       ...+|+|||+|.+.++|.+|++.|+|.
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  55442        35789999999999999962       234589999999999999999999999


Q ss_pred             ccCcceeeeeecC
Q 002974          338 PLRRRKLDIHYSI  350 (861)
Q Consensus       338 ~L~Gr~L~V~~a~  350 (861)
                      .+.||.|.|.|..
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            9999999999975

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=1.2e-09  Score=98.05  Aligned_cols=76  Identities=17%  Similarity=0.321  Sum_probs=64.6

Q ss_pred             CCcceEEecc--cCCC--------cHHHHHHHhcccCcEEEEEeCC-------CCccEEEEEECCHHHHHHHHHHhCCCe
Q 002974          361 NQGTLVVFNL--DSSV--------STEELHQIFGIYGEIREIRDTQ-------HKHNHKFIEFYDIRAAETALRTLNRSD  423 (861)
Q Consensus       361 ~~~tLfVgNL--p~sv--------TeedLrelFskfGeI~sVritg-------ksKGfAFVeF~d~eaA~kAL~~LNG~~  423 (861)
                      +.+.|.|.|+  +..+        ..+||++.|++||.|++|.+..       ..+|++||+|.+.++|.+|+..|||+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4568999999  4443        2367999999999999998732       235899999999999999999999999


Q ss_pred             eCCcEEEEEeccC
Q 002974          424 VAGKQIKLEASRP  436 (861)
Q Consensus       424 I~Gr~IkVe~Akp  436 (861)
                      ++||+|+|.++.+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999874

>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=96.57  E-value=0.0033  Score=51.84  Aligned_cols=59  Identities=17%  Similarity=0.358  Sum_probs=52.5

Q ss_pred             HHHHHHhcccCcEEEEEeCCCCcc--EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEecc
Q 002974          377 EELHQIFGIYGEIREIRDTQHKHN--HKFIEFYDIRAAETALRTLNRSDVAGKQIKLEASR  435 (861)
Q Consensus       377 edLrelFskfGeI~sVritgksKG--fAFVeF~d~eaA~kAL~~LNG~~I~Gr~IkVe~Ak  435 (861)
                      +.|..+|+++|.|..+.+.+...+  .|-|...+..+|..|+..|+...|++++|.|.++.
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            456678999999999998766654  69999999999999999999999999999999875

>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=96.04  E-value=0.008  Score=49.54  Aligned_cols=59  Identities=12%  Similarity=0.236  Sum_probs=52.1

Q ss_pred             HHHHHHhhcCCCEEEEEeCCCccc--EEEEEeCCHHHHHHHHHHcCccccCcceeeeeecC
Q 002974          292 SELKALFEQFGDIRTIYTACKHRG--FVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSI  350 (861)
Q Consensus       292 edL~elFsqfG~I~svkitgksrG--yAFVeF~d~e~A~kALkaLnG~~L~Gr~L~V~~a~  350 (861)
                      +.|.+.|.++|.|..+.+...+.|  .|-|...+..+|..|+..|+...|++++|.|.++.
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            345678999999999998555554  89999999999999999999999999999999875

>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=96.02  E-value=0.005  Score=53.14  Aligned_cols=73  Identities=26%  Similarity=0.395  Sum_probs=57.5

Q ss_pred             cCCcceEEecccCCCc---------HHHHHHHhcccCcEEEEEeCCCCccEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Q 002974          360 ANQGTLVVFNLDSSVS---------TEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIK  430 (861)
Q Consensus       360 ~~~~tLfVgNLp~svT---------eedLrelFskfGeI~sVritgksKGfAFVeF~d~eaA~kAL~~LNG~~I~Gr~Ik  430 (861)
                      ....||.|.=..++..         -.+|.+.|..||+|.-||...   +-..|+|.+-++|.+|++ ++|.++.|+.|+
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~---d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~   88 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ---GQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET---TEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC---CeEEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            3456777754443322         256889999999999999753   468999999999999999 999999999999


Q ss_pred             EEeccC
Q 002974          431 LEASRP  436 (861)
Q Consensus       431 Ve~Akp  436 (861)
                      |....+
T Consensus        89 It~~~~   94 (95)
T d1ufwa_          89 ISGPSS   94 (95)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            976443

>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=95.73  E-value=0.0066  Score=52.35  Aligned_cols=71  Identities=17%  Similarity=0.327  Sum_probs=56.9

Q ss_pred             CCCcEEEEcCCCCCCcH---------HHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcCccccCcceee
Q 002974          275 HPSRTLFVRNINSNVED---------SELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPLRRRKLD  345 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTE---------edL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLnG~~L~Gr~L~  345 (861)
                      .+.-||.|.=..++.++         .+|.+.|.+||+|.-++.   -.+-.+|.|.+-+.|.+|++ ++|+.+.|+.|+
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            35677888655544333         477888999999999986   34578999999999999996 999999999999


Q ss_pred             eeec
Q 002974          346 IHYS  349 (861)
Q Consensus       346 V~~a  349 (861)
                      |...
T Consensus        89 It~~   92 (95)
T d1ufwa_          89 ISGP   92 (95)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9754

>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=94.99  E-value=0.023  Score=49.06  Aligned_cols=64  Identities=5%  Similarity=0.050  Sum_probs=53.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEe-CC------CcccEEEEEeCCHHHHHHHHHHcCccccCc
Q 002974          278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYT-AC------KHRGFVMISYYDIRAARNAMKALQNKPLRR  341 (861)
Q Consensus       278 rtLfVgNLP~~vTEedL~elFsqfG~I~svki-tg------ksrGyAFVeF~d~e~A~kALkaLnG~~L~G  341 (861)
                      ++|.|++||+..||+++.+.+...|++...+. .+      ..-.-|||.|.+.++.....+..+|+.+.+
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            57999999999999999999999999887762 11      122379999999999999999999988753

>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=94.61  E-value=0.074  Score=45.73  Aligned_cols=72  Identities=11%  Similarity=0.082  Sum_probs=57.1

Q ss_pred             cceEEecccCCCcHHHHHHHhcccCcEEEEEe-CCC------CccEEEEEECCHHHHHHHHHHhCCCeeCC-----cEEE
Q 002974          363 GTLVVFNLDSSVSTEELHQIFGIYGEIREIRD-TQH------KHNHKFIEFYDIRAAETALRTLNRSDVAG-----KQIK  430 (861)
Q Consensus       363 ~tLfVgNLp~svTeedLrelFskfGeI~sVri-tgk------sKGfAFVeF~d~eaA~kAL~~LNG~~I~G-----r~Ik  430 (861)
                      ++|.|+.||+.+|++++.+.++..|++..... .++      .-.-|+|.|.+.++...-.+..+|+.+-+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            57999999999999999999999999887653 111      11359999999999999999999997742     2445


Q ss_pred             EEec
Q 002974          431 LEAS  434 (861)
Q Consensus       431 Ve~A  434 (861)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5555

>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=83.39  E-value=1.1  Score=38.70  Aligned_cols=56  Identities=21%  Similarity=0.376  Sum_probs=46.3

Q ss_pred             cCCcceEEecccCCCcHHHHHHHhcccCcEE--EEEeCCCCccEEEEEECCHHHHHHHHHHhC
Q 002974          360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIR--EIRDTQHKHNHKFIEFYDIRAAETALRTLN  420 (861)
Q Consensus       360 ~~~~tLfVgNLp~svTeedLrelFskfGeI~--sVritgksKGfAFVeF~d~eaA~kAL~~LN  420 (861)
                      .....+|.-..|..+...||.++|+.||.|.  -|..+     -|||...+.++|+.++..+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIddT-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDT-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEETT-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEecCc-----eEEEEecCHHHHHHHHHHhc
Confidence            4456899999999999999999999999764  34322     69999999999999988543

>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=83.10  E-value=1.6  Score=37.57  Aligned_cols=58  Identities=16%  Similarity=0.216  Sum_probs=48.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhhcCCCEEEEEeCCCcccEEEEEeCCHHHHHHHHHHcC
Q 002974          275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQ  335 (861)
Q Consensus       275 ~~srtLfVgNLP~~vTEedL~elFsqfG~I~svkitgksrGyAFVeF~d~e~A~kALkaLn  335 (861)
                      .....||.-..|..+...||.++|+.||.|.--.+..   --|||...+.++|+.+++.+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIdd---TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDD---TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEET---TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEecC---ceEEEEecCHHHHHHHHHHhc
Confidence            3456799999999999999999999999876666622   279999999999999987543