Citrus Sinensis ID: 004908

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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----
Protein Sequence
MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGPSMPMRSIGAHGGHETLLSGPDFKDFHSMQDPNAKNLDPNWRRPSPSPGIRTSPTQGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAMVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATKSAEVAPGSSSARPLLAEPHVQSIEQLGNHYNPQAQSLTHHYASMSSTPSHSAQMLLGNNQLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNSPAGRGTGNQQ
Secondary Structure (PSIPRED)
ccHHHHHHHHHHcccEEEEEEEccccEEEEEEccHHHHHHHHHHccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccEEEEccccccccccccccccccccHHHHHHHHHHHcccEEEEEEccccccHHHHHHHHHHHcccccccEEEEccccEEEEEcccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHccccEEEEEEcccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccEEEEEEEEccccEccccccEEcccccccHHHHHHHHHHHcccEEEEEccccHHHHHHHHHHHHHHHccccEEEEEEccccEEEEEcccHHHHHEEEcccccEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccHHHHHHHHHHcccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccc
Coil and Loop (DISEMBL)
MDEQMLHNAMILFGEieriksypsrnysfvefRSVDEARRAKEglqgrlfndpritimfssselapgkdypgsysgtkgprsemffgdqirpsqldmlgpnqsmqpnnfaghlqpadirgpsmpmrsigahgghetllsgpdfkdfhsmqdpnaknldpnwrrpspspgirtsptqgirqplnhapgswdvydanqfqrdskrlrvdgsmpiddatfpsrkiddhglvldqsyglgsitggpasgafvnvqgrnrlspvaskvtaggfgrnpidsdfiwrgiiakggtpvcrarcvpfgkgieselpevvncsaRTGLDMLAKHYAEAIGFDivfflpdseddfASYTEFLRYLGsknragvakfddgttlflvppsdfLSKVLKVVGPERLYGVVLklpqqamvppqtvdkqnippphaeygltrpkeehvlpvdynrfshddskvqskmhfphasepliahsssmdygsnnaaaISQAGVKLTPELIATLTSlipatksaevapgsssarpllaephvQSIEQlgnhynpqaqslthhyasmsstpshsaqmllgnnqlqeSTASLsqqgmvysrplpnfsiapqaapvavsppvhqqyqfaapsnsqkgygmmqgteastlygssvfqqpnnptavsnqvnlsqpqnvmtvsvdkvnlehpnhvQQLQSVlsgagqgtsdgevdknqRYQSTLQFAANLLLQIQQQqqtnspagrgtgnqq
Flexible Loop (DISEMBL)
MDEQMLHNAMILFgeieriksypsrNYSFVEFRSVDEARRAKEglqgrlfndpriTIMFssselapgkdyPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGPSMPMRSIGAHGGHETLLSGPDFKDFHSMQDPnaknldpnwrrpsPSPGIRTSPTQGIRQPLNHAPGSWDVYDANQFQRdskrlrvdgsmpiddatfpsrkiddhGLVLDQSYGLGSITGGPASGAFVNVQGRNRLSPVaskvtaggfgrnpidsdfIWRGIIAKGGTPVCRARCVPFgkgieselpeVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAmvppqtvdkqnipPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATKSAEVAPGSSSARPLLAEPHVQSIEQLGNHYNPQAQSLTHHYASMSSTPSHSAQMLLGNNQLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQqqtnspagrgtgnqq
Low Complexity Region (SEG)
MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGPSMPMRSIGAHGGHETLLSGPDFKDFHSMQDPNAKNLDPNWRRPSPSPGIRTSPTQGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAMVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATKSAEVAPGSSSARPLLAEPHVQSIEQLGNHYNPQAQSLTHHYASMSSTPSHSAQMLLGNNQLQESTASLSQQGMVYSRPLPNFSIapqaapvavsppvhqqYQFAAPSNSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANlllqiqqqqqTNSPAGRGTGNQQ
Disordered region (IsUnstruct)
******HNAMILFGEIERIKSYPSRNYSFVEFRSVD*********QGRLFNDPRITIMF***********************************************************************************************************************************VY*****************************IDDHGLVLDQSYGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQ******************************************************************************AGVKLTPELIATLTSLI*******************************************************************************************************************************************************************************************************LQFAANLLL********************
Disordered Region (DISOPRED)
*DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT*****************************************************************************************************************************************************************************************************************************IWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLY************************************************************************************************************************************************************************************************************************************************************************************************************STLQFAAN***********************
Disordered Region (DISEMBL)
MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGPSMPMRSIGAHGGHETLLSGPDFKDFHSMQDPNAKNLDPNWRRPSPSPGIRTSPTQGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAMVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATK**********ARPLLAEPHVQSIEQLGNHYNPQAQSLTHH**********SAQMLLGNNQLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQ****************
Disordered Region (DISPRO)
MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA*********************GDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGPSMPMR**G***G****LSGPDFKDFHS**************************************GSWDVYDANQFQR*SKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLGSITGGPASGAFVNV***********************DSDFIWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAMVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQS**************************A**QAGVKLTPELIATLTSLIPA**********************************************************************************NF********VAVSPPVHQQYQFAAPSNSQKGYGMM*GTEAST*******QQP*****************************************************DKNQRYQSTLQFAANLLLQIQQQQQ*************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGPSMPMRSIGAHGGHETLLSGPDFKDFHSMQDPNAKNLDPNWRRPSPSPGIRTSPTQGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAMVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATKSAEVAPGSSSARPLLAEPHVQSIEQLGNHYNPQAQSLTHHYASMSSTPSHSAQMLLGNNQLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNSPAGRGTGNQQ
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	724	2.2.26 [Sep-21-2011]
Q8LPQ9	901	Flowering time control pr	yes	no	0.859	0.690	0.443	1e-137

>sp|Q8LPQ9|FPA_ARATH Flowering time control protein FPA OS=Arabidopsis thaliana GN=FPA PE=2 SV=2

 Score =  489 bits (1258), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 344/776 (44%), Positives = 427/776 (55%), Gaps = 154/776 (19%)

Query: 2   DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS 61
           DEQ+LHNAMILFGEIER+KSYPSRN++ VEFRS +EAR+ KEGLQGRLFN+PRI IM+S+
Sbjct: 221 DEQILHNAMILFGEIERVKSYPSRNFALVEFRSAEEARQCKEGLQGRLFNNPRIKIMYSN 280

Query: 62  SELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGP 121
            EL P +D    YSG K  R++MF  D   PS               F        I G 
Sbjct: 281 DELPPEQDDTSFYSGMKRSRTDMFNND---PS---------------FVSSPHSTGIPGS 322

Query: 122 SMPMRSIGAHGGHETLLSGPDFKDFHSMQDPNAKNLDPNWRRPS-------PSP---GIR 171
             P+R     G +E   +G ++ D            +PNWRRPS       PSP   GI 
Sbjct: 323 MRPLR-----GTNERSYNGAEYND--------VVGKEPNWRRPSANGTGILPSPTGPGIL 369

Query: 172 TSPTQGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQ 231
            SP QG R+P+   P SW+ YD  Q  R+SKR R DGS+      F    +D+      +
Sbjct: 370 PSPAQGTRRPMRSNPDSWEGYDPAQLVRESKRTRRDGSV----DGFTPMGVDE------R 419

Query: 232 SYGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVC 291
           S+G GS+   P                           R P DSD IWRG+IAKGGTPVC
Sbjct: 420 SFGRGSVAARPI--------------------------RGPPDSDHIWRGMIAKGGTPVC 453

Query: 292 RARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFL 351
            ARCVP GKGIE++LPEVVNCSART L+MLAKHYA AIG +IVFF+PD E+DFASYTEFL
Sbjct: 454 CARCVPMGKGIETKLPEVVNCSARTDLNMLAKHYAVAIGCEIVFFVPDREEDFASYTEFL 513

Query: 352 RYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAM------- 404
           RYL SK+RAGVAK DDGTTLFLVPPSDFL+ VL+V   ERLYGVVLKLP  A+       
Sbjct: 514 RYLSSKDRAGVAKLDDGTTLFLVPPSDFLTDVLQVTRQERLYGVVLKLPPPAVPVTASYR 573

Query: 405 -----VPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEP 459
                 P   +D+    P +A + L  P+E ++      R + +     SK   P  SEP
Sbjct: 574 QESQSNPLHYMDQARDSPANASHSLYPPRENYI------RGAPEHLTAASK---PSVSEP 624

Query: 460 LIAHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATKSAEVAPGS----SSARPLL 515
           L           NNAA   QAGV LTPEL+ATL S++PAT S   AP S    S    ++
Sbjct: 625 LRI--------PNNAAP--QAGVSLTPELLATLASILPAT-SQPAAPESHQPMSGPSTVV 673

Query: 516 AEPHV--------------------------QSIEQLGNHYNPQAQ--SLTHHYASMSST 547
           +  H                           QS +Q GN Y P  Q       Y   S+ 
Sbjct: 674 STAHQSNGLYNGEAPSQAWKRGPQTVHDASNQSFQQYGNQYTPAGQLPPPPSRYPPASNN 733

Query: 548 PSHSAQMLLGNNQLQESTASLSQQGMVYSRPLPNFSIAPQAAPV-AVSPPVHQQYQFAAP 606
           P++++ M+ GN Q Q  + ++ Q   + + P  N+S+  Q +    VS P+ QQYQ  A 
Sbjct: 734 PNYTSGMVHGNMQYQSQSVNMPQLSPLPNMPHNNYSMYTQGSSNHPVSQPMVQQYQPEA- 792

Query: 607 SNSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNH 666
           S   + YG +   + +  +G +  Q  N        +N SQ Q  M    DK NLE  N 
Sbjct: 793 SMPNQNYGPIPSYQQANFHGVTTNQAQN--------LNPSQFQAAMQPPADKANLEPQNQ 844

Query: 667 VQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNS---PAGRG 719
             +LQ ++SG GQGT+DGEVDKNQRYQSTLQFAANLLLQIQQ+QQ  S   PAG+G
Sbjct: 845 ALRLQPMISGDGQGTTDGEVDKNQRYQSTLQFAANLLLQIQQKQQQQSSGTPAGQG 900

Plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. Required for RNA-mediated chromatin silencing of a range of loci in the genome. Cotranscriptionally recognizes aberrant RNA and marks it for silencing. Controls alternative cleavage and polyadenylation on pre-mRNAs and antisense RNAs. Acts redundantly with FCA to prevent the expression of distally polyadenylated antisense RNAs at the FLC locus.
Arabidopsis thaliana (taxid: 3702)

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	724
356538883	970	PREDICTED: flowering time control protei	0.950	0.709	0.535	0.0
449471899	1000	PREDICTED: flowering time control protei	0.980	0.71	0.508	0.0
307136258	916	RNA-binding protein [Cucumis melo subsp.	0.995	0.787	0.509	0.0
449454582	999	PREDICTED: flowering time control protei	0.980	0.710	0.511	0.0
255577189	902	RNA recognition motif-containing protein	0.897	0.720	0.523	0.0
356544510	909	PREDICTED: flowering time control protei	0.895	0.712	0.513	0.0
357473075	973	Flowering time control protein FPA [Medi	0.895	0.665	0.469	1e-174
224133226	934	predicted protein [Populus trichocarpa]	0.899	0.697	0.488	1e-172
147801865	1976	hypothetical protein VITISV_007871 [Viti	0.917	0.336	0.492	1e-170
359478105	878	PREDICTED: flowering time control protei	0.860	0.709	0.474	1e-164

>gi|356538883|ref|XP_003537930.1| PREDICTED: flowering time control protein FPA-like [Glycine max]

 Score =  715 bits (1845), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/775 (53%), Positives = 501/775 (64%), Gaps = 87/775 (11%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +DEQMLHNAMILFGEIERIKS+PSRNYS VEFRSVDEARRAKEGLQGRLFNDPRITIM+S
Sbjct: 228 IDEQMLHNAMILFGEIERIKSFPSRNYSIVEFRSVDEARRAKEGLQGRLFNDPRITIMYS 287

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGDQ-IRPSQLDMLGPNQSMQPNNFAGHLQPADIR 119
            S+L PG DYPG + G+ GP+ ++   D   RP Q+D  G N+ M PNNF G L P+ I 
Sbjct: 288 ISDLVPGSDYPGFFPGSNGPKPDVLLNDHPFRPLQMDAFGHNRPMGPNNFPGQLPPSGIM 347

Query: 120 GPSMPMRSIGAHGGHETLLSGPDFKD---FHSMQDPNAK-NLDPNWRRPS-PSPGIRTSP 174
           GP++PMR  G H G E+++SGP+F +    H  QD ++K ++ PNW+RPS P+PG+ +SP
Sbjct: 348 GPNIPMRPFGPHSGVESVISGPEFNEINALHKFQDGSSKSSMGPNWKRPSPPAPGMLSSP 407

Query: 175 TQGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYG 234
             G R P     G+WDV D N   RDSKR R+DG +P+D+  FP R IDD G        
Sbjct: 408 APGARLPTRSTSGAWDVLDINHIPRDSKRSRIDGPLPVDEGPFPLRNIDDRG-------- 459

Query: 235 LGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRAR 294
                                L PV+S++TAG  G    D D IWRG+IAKGGTPVCRAR
Sbjct: 460 --------------------HLGPVSSRITAGVHGVAQPDIDHIWRGVIAKGGTPVCRAR 499

Query: 295 CVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYL 354
           CVP GKGI +ELP+VV+CSARTGLD+L KHYA+AIGFDIVFFLPDSEDDFASYTEFLRYL
Sbjct: 500 CVPIGKGIGTELPDVVDCSARTGLDILTKHYADAIGFDIVFFLPDSEDDFASYTEFLRYL 559

Query: 355 GSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLP--------QQA--M 404
            +KNRAGVAKF D TTLFLVPPSDFL++VLKV GPERLYGVVLK P        QQ   +
Sbjct: 560 SAKNRAGVAKFVDNTTLFLVPPSDFLTRVLKVTGPERLYGVVLKFPPVPSSAPMQQPSHL 619

Query: 405 VPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHS 464
             P T   Q IPP   EYGL   KEEH+LP+DYNR  H+DSK+ +K  +P    P   HS
Sbjct: 620 RVPTTQYMQQIPPSQTEYGLIPVKEEHILPMDYNRPLHEDSKLPAKPVYPPTGGPPPVHS 679

Query: 465 SSMDYGSNNAAAISQAGVKLTPELIATLTSLI------PATKSAEVAPGSSSARPLL--A 516
              DY  NN  A SQAGV LTPELIATL S +      PAT  A+ A GSS+ +P     
Sbjct: 680 GPPDYAPNNTVAGSQAGVALTPELIATLASFLPTTTQSPATDGAKSAVGSSTMKPPFPPM 739

Query: 517 EPHVQSIEQLGNHYNPQAQSLTH--------------HYASM--SSTPS-HSAQMLLGNN 559
            P+  +   L    N  A   TH              HY     +S PS + +Q++ G++
Sbjct: 740 TPNDGNQSHLWKQDNQIADQSTHPPQQLRSMYNIHNAHYQPYPPASAPSGNPSQVVSGSS 799

Query: 560 QLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQGT 619
            +Q++ AS+ QQG V SR +PNF +  Q+  VAVSP   Q YQ     ++QKG+G++QGT
Sbjct: 800 HIQDTAASMQQQGAVSSRHMPNFMMPTQSGQVAVSPHASQNYQVEVSPSNQKGFGVVQGT 859

Query: 620 EASTLYGSSVFQQPNNPT----------AVSNQV---NLSQPQNVMTVSVDKVNLEHPNH 666
           +AS LY S  FQQPNN +          A+SNQV   N SQ Q  M  +VD+VN + PN 
Sbjct: 860 DASVLYNSQAFQQPNNNSLAFQQPNNSFALSNQVNSTNASQQQTAMPYTVDQVNPDTPN- 918

Query: 667 VQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNSPAGRGTG 721
            QQL   + G  QG ++ E DKNQRYQSTLQFAANLLLQ  QQQQ  +P G G G
Sbjct: 919 -QQLP--MFGVSQGQTEVEADKNQRYQSTLQFAANLLLQ-IQQQQQQAPGGHGPG 969

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449471899|ref|XP_004153439.1| PREDICTED: flowering time control protein FPA-like [Cucumis sativus]

 Score =  662 bits (1708), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 396/779 (50%), Positives = 495/779 (63%), Gaps = 69/779 (8%)

Query: 1    MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
            +DEQMLHNAMILFGEIERI S+ SR+++FVEFRSVDEARRAKEGLQGRLFNDPRITIMFS
Sbjct: 235  IDEQMLHNAMILFGEIERITSFHSRHFAFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 294

Query: 61   SSELAPGKDYPGSYSGTKGPRSEMFFGD-QIRPSQLDMLGPNQSMQPNNFAGHLQPADIR 119
            +S+  P K++PG Y G K  R +MFF + QIRP  +D+LG    M  N F G L  + I 
Sbjct: 295  NSDPGPVKEHPGFYPGGKEARPDMFFNEHQIRPPPMDLLGHPHPMVQNKFPGPLPSSGIL 354

Query: 120  GPSMPMRSIGAHGGHETLLSGPDFKDF---HSMQDPNAKNL-DPNWRRPSP-SPGIRTSP 174
            GP+  +R               +F D    HS QD N+KN+  PNWRR SP +PGI +SP
Sbjct: 355  GPNTGVRPPPFGPPPGISGPP-EFNDLATSHSFQDANSKNMMGPNWRRQSPPAPGILSSP 413

Query: 175  TQGIRQP--LNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQS 232
              GIR P  +   P SWDV D NQFQRDSKR R+DG   ++D +FP RK+D+  +  DQ 
Sbjct: 414  ATGIRPPPPVRSTPNSWDVLDVNQFQRDSKRSRIDGPPSLEDVSFPPRKMDNRSMGFDQQ 473

Query: 233  YGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCR 292
            YG+G I+ G +S  + N   +    P+ ++    G G++  ++DFIWRGIIAKGGTPVC 
Sbjct: 474  YGIGPISDGGSSVPYANAPAKTPPIPIGTRAPISGPGQSHAENDFIWRGIIAKGGTPVCH 533

Query: 293  ARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLR 352
            ARCVP G+GI SELPEVVNCSARTGLD L KHYAEA GFDIVFFLPDSEDDFASYTEFLR
Sbjct: 534  ARCVPIGEGIGSELPEVVNCSARTGLDQLTKHYAEATGFDIVFFLPDSEDDFASYTEFLR 593

Query: 353  YLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKL---------PQQA 403
            YLG+KNRAGVAKFDDGTT+FLVPPS+FL KVLKV GPERLYG+VLK          PQQ+
Sbjct: 594  YLGAKNRAGVAKFDDGTTMFLVPPSEFLRKVLKVSGPERLYGLVLKFPQVSVSEPAPQQS 653

Query: 404  MVPPQTVD---KQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPL 460
             +P  T D   +Q++ P   EYG    K+E + P+DY+R  HD+ K   K        PL
Sbjct: 654  YLPVSTSDYGERQHVLPSQTEYGSVPSKQEQLPPMDYSRVLHDEIKEPPK--------PL 705

Query: 461  IAHSSSMDY-GSNNAAAISQAGVKLTPELIATLTSLIPA---TKSAEVA----------- 505
            +  S   +Y G+NN A ISQAG+ LTPELIATL SL+P    + S E A           
Sbjct: 706  LPTSEPQEYSGNNNTATISQAGLALTPELIATLVSLLPGKTQSSSLESAKQPAVSPQPPV 765

Query: 506  --------PGSSSARPLL----AEPHVQSIEQLGNHYNPQAQSLTHH--YASMSSTPSHS 551
                     G++S   ++    ++ + Q  +Q+GNH+NPQ QSL+    Y  +  TP+  
Sbjct: 766  PIPPVVSNKGATSEGWMVGHQSSDLNGQPFQQMGNHFNPQGQSLSQFQPYPPLPQTPNQH 825

Query: 552  AQMLLGNNQLQESTASLSQQGMV--YSRPLPNFSIAP--QAAPVAVSPPVHQQYQFAAPS 607
            A   +G +Q+Q++  SL QQ  V    RPL  +S  P  QA+ +A++     QYQ     
Sbjct: 826  APQAIGTSQIQDAAVSLPQQQQVPIPYRPLSTYSAPPENQASGLALA---SSQYQHDVSQ 882

Query: 608  NSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSN--QVNLSQPQNVMTVSVDKVNLEHPN 665
             SQ+GYG + G + S  YG  V QQ  N   +SN  Q + +Q Q +  ++ D+VN E P 
Sbjct: 883  MSQRGYGPVNGVDTSG-YGPPVMQQSTNTVTLSNHGQSSTTQSQPITQLASDRVNPELPY 941

Query: 666  HVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLL-QIQQQQQTNSPAGRGTGNQ 723
             +Q LQS   G G G SD E  K+QRY+STLQFAANLLL   QQQQQ    AG G+GNQ
Sbjct: 942  QMQHLQSANLGTGTGPSDVESGKDQRYRSTLQFAANLLLQIQQQQQQQQQQAGWGSGNQ 1000

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136258|gb|ADN34086.1| RNA-binding protein [Cucumis melo subsp. melo]

 Score =  661 bits (1705), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/779 (50%), Positives = 497/779 (63%), Gaps = 58/779 (7%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +DEQMLHNAMILFGEIERI S+ +R+++FVEFRSVDEARRAKEGLQGRLFNDPRITIMFS
Sbjct: 140 IDEQMLHNAMILFGEIERITSFHTRHFAFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 199

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGD-QIRPSQLDMLGPNQSMQPNNFAGHLQPADIR 119
           +S+  P K++PG Y G K  R +MFF + QIRP  +D+LG    M  N F G L  + I 
Sbjct: 200 NSDPGPVKEHPGFYPGGKEARPDMFFNEHQIRPPPMDLLGHPHPMVQNKFPGPLPSSGIL 259

Query: 120 GPSMPMRSIGAHGGHETLLSGPDFKDF---HSMQDPNAKNL-DPNWRRPSP-SPGIRTSP 174
           GP+  +R               +F D    HS QD N+KN+  PNWRR SP +PGI +SP
Sbjct: 260 GPNTGVRPPPFGPPPGISGPP-EFNDLATSHSFQDANSKNMMGPNWRRQSPPAPGILSSP 318

Query: 175 TQGIRQP--LNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQS 232
             GIR P  +   P SWDV D NQFQRDSKR R+DG   +DD +FP RK+D+  +  DQ 
Sbjct: 319 ATGIRPPPPVRSTPNSWDVLDVNQFQRDSKRSRIDGPPSLDDVSFPPRKMDNRSMGFDQQ 378

Query: 233 YGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCR 292
           YG+G I+ G +S  + N   +    P+  +    G G++  ++DFIWRGIIAKGGTPVC 
Sbjct: 379 YGIGPISDGGSSVPYGNAPAKTPPIPIGVRAPVSGPGQSHAENDFIWRGIIAKGGTPVCH 438

Query: 293 ARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLR 352
           ARCVP G+GI SELPEVVNCSARTGLD L KHYAEA GFDIVFFLPDSEDDFASYTEFLR
Sbjct: 439 ARCVPIGEGIGSELPEVVNCSARTGLDQLTKHYAEATGFDIVFFLPDSEDDFASYTEFLR 498

Query: 353 YLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKL---------PQQA 403
           YLG+KNRAGVAKFDDGTT+FLVPPS+FL KVLKV GPERLYG+VLK          PQQ+
Sbjct: 499 YLGAKNRAGVAKFDDGTTMFLVPPSEFLRKVLKVSGPERLYGLVLKFPQVSVSEAAPQQS 558

Query: 404 MVPPQTVD---KQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPL 460
            +P  T D   +Q++ P   EYG   PK+E + P+DYNR  HD+ K   K+      +PL
Sbjct: 559 YLPVPTSDYGERQHVLPSQTEYGSVPPKQEQLPPMDYNRVLHDEIKEPPKLLPTSEPQPL 618

Query: 461 IAHSSSMDY-GSNNAAAISQAGVKLTPELIATLTSLIPA---TKSAEVA----------- 505
                  +Y G+NN AAISQAG+ LTPELIATL SL+P    + S E A           
Sbjct: 619 AVQPLPQEYSGNNNTAAISQAGLALTPELIATLVSLLPGKTQSSSLESAKQPAVSPQPPV 678

Query: 506 --------PGSSSARPLL----AEPHVQSIEQLGNHYNPQAQSLTHH--YASMSSTPSHS 551
                    G++S   ++    ++P+ Q  +Q+GNH+NPQ Q+L+    Y  +  TP+  
Sbjct: 679 PIPPVVSNKGATSEGWMVGHQSSDPNGQPFQQMGNHFNPQGQNLSQFQPYPPLPQTPNQH 738

Query: 552 AQMLLGNNQLQESTASLSQQGMV--YSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNS 609
           A   +G +Q+Q++  SL QQ  V    RPL  +S  P+ A  +     + QYQ      S
Sbjct: 739 APQAIGTSQIQDAAVSLPQQQQVPIPYRPLSTYSAPPENAQASGLALANSQYQHDVSQMS 798

Query: 610 QKGYGMMQGTEASTLYGSSVFQQPNNPTAVSN--QVNLSQPQNVMTVSVDKVNLEHPNHV 667
           Q+GYG + G + S  YG  V QQ  N   +SN  Q + +Q Q +  ++ D+VN E P  +
Sbjct: 799 QRGYGPVNGVDTSG-YGPPVMQQSTNTLTLSNQGQGSTAQSQPITQLASDRVNPELPYQM 857

Query: 668 QQLQS--VLSGAGQGTSDGEVDKNQRYQSTLQFAANLLL-QIQQQQQTNSPAGRGTGNQ 723
           Q LQS  + +G G GTSD E  K+QRY+STLQFAANLLL   QQQQQ    AG G+GNQ
Sbjct: 858 QHLQSANLGTGTGTGTSDVEAGKDQRYRSTLQFAANLLLQIQQQQQQQQQQAGWGSGNQ 916

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454582|ref|XP_004145033.1| PREDICTED: flowering time control protein FPA-like [Cucumis sativus]

 Score =  660 bits (1702), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/778 (51%), Positives = 497/778 (63%), Gaps = 68/778 (8%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +DEQMLHNAMILFGEIERI S+ SR+++FVEFRSVDEARRAKEGLQGRLFNDPRITIMFS
Sbjct: 235 IDEQMLHNAMILFGEIERITSFHSRHFAFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 294

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGD-QIRPSQLDMLGPNQSMQPNNFAGHLQPADIR 119
           +S+  P K++PG Y G K  R +MFF + QIRP  +D+LG    M  N F G L  + I 
Sbjct: 295 NSDPGPVKEHPGFYPGGKEARPDMFFNEHQIRPPPMDLLGHPHPMVQNKFPGPLPSSGIL 354

Query: 120 GPSMPMRSIGAHGGHETLLSGPDFKDF---HSMQDPNAKNL-DPNWRRPSP-SPGIRTSP 174
           GP+  +R               +F D    HS QD N+KN+  PNWRR SP +PGI +SP
Sbjct: 355 GPNTGVRPPPFGPPPGISGPP-EFNDLATSHSFQDANSKNMMGPNWRRQSPPAPGILSSP 413

Query: 175 TQGIRQP--LNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQS 232
             GIR P  +   P SWDV D NQFQRDSKR R+DG   ++D +FP RK+D+  +  DQ 
Sbjct: 414 ATGIRPPPPVRSTPNSWDVLDVNQFQRDSKRSRIDGPPSLEDVSFPPRKMDNRSMGFDQQ 473

Query: 233 YGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCR 292
           YG+G I+ G +S  + N   +    P+ ++    G G++  ++DFIWRGIIAKGGTPVC 
Sbjct: 474 YGIGPISDGGSSVPYANAPAKTPPIPIGTRAPISGPGQSHAENDFIWRGIIAKGGTPVCH 533

Query: 293 ARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLR 352
           ARCVP G+GI SELPEVVNCSARTGLD L KHYAEA GFDIVFFLPDSEDDFASYTEFLR
Sbjct: 534 ARCVPIGEGIGSELPEVVNCSARTGLDQLTKHYAEATGFDIVFFLPDSEDDFASYTEFLR 593

Query: 353 YLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKL---------PQQA 403
           YLG+KNRAGVAKFDDGTT+FLVPPS+FL KVLKV GPERLYG+VLK          PQQ+
Sbjct: 594 YLGAKNRAGVAKFDDGTTMFLVPPSEFLRKVLKVSGPERLYGLVLKFPQVSVSEPAPQQS 653

Query: 404 MVPPQTVD---KQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPL 460
            +P  T D   +Q++ P   EYG    K+E + P+DY+R  HD+ K   K        PL
Sbjct: 654 YLPVSTSDYGERQHVLPSQTEYGSVPSKQEQLPPMDYSRVLHDEIKEPPK--------PL 705

Query: 461 IAHSSSMDY-GSNNAAAISQAGVKLTPELIATLTSLIPA---TKSAEVA----------- 505
           +  S   +Y G+NN A ISQAG+ LTPELIATL SL+P    + S E A           
Sbjct: 706 LPTSEPQEYSGNNNTATISQAGLALTPELIATLVSLLPGKTQSSSLESAKQPAVSPQPPV 765

Query: 506 --------PGSSSARPLL----AEPHVQSIEQLGNHYNPQAQSLTHH--YASMSSTPSHS 551
                    G++S   ++    ++ + Q  +Q+GNH+NPQ QSL+    Y  +  TP+  
Sbjct: 766 PIPPVVSNKGATSEGWMVGHQSSDLNGQPFQQMGNHFNPQGQSLSQFQPYPPLPQTPNQH 825

Query: 552 AQMLLGNNQLQESTASLSQQGMV--YSRPLPNFSIAP--QAAPVAVSPPVHQQYQFAAPS 607
           A   +G +Q+Q++  SL QQ  V    RPL  +S  P  QA+ +A++     QYQ     
Sbjct: 826 APQAIGTSQIQDAAVSLPQQQQVPIPYRPLSTYSAPPENQASGLALA---SSQYQHDVSQ 882

Query: 608 NSQKGYGMMQGTEASTLYGSSVFQQPNNPTAVSN--QVNLSQPQNVMTVSVDKVNLEHPN 665
            SQ+GYG + G + S  YG  V QQ  N   +SN  Q + +Q Q +  ++ D+VN E P 
Sbjct: 883 MSQRGYGPVNGVDTSG-YGPPVMQQSTNTVTLSNHGQSSTTQSQPITQLASDRVNPELPY 941

Query: 666 HVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNSPAGRGTGNQ 723
            +Q LQS   G G G SD E  K+QRY+STLQFAANLLLQIQQQQQ    AG G+GNQ
Sbjct: 942 QMQHLQSANLGTGTGPSDVESGKDQRYRSTLQFAANLLLQIQQQQQQQQQAGWGSGNQ 999

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255577189|ref|XP_002529477.1| RNA recognition motif-containing protein, putative [Ricinus communis] gi|223531035|gb|EEF32887.1| RNA recognition motif-containing protein, putative [Ricinus communis]

 Score =  659 bits (1700), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/760 (52%), Positives = 476/760 (62%), Gaps = 110/760 (14%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +DEQMLHNAMILFGEIERIKS+P+R+YSFVEFRSVDEARRAKEGLQGRLFNDPRI+IM+S
Sbjct: 217 IDEQMLHNAMILFGEIERIKSFPARHYSFVEFRSVDEARRAKEGLQGRLFNDPRISIMYS 276

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRG 120
           SSELAPGK+Y    +G KGPR E+F               N+++                
Sbjct: 277 SSELAPGKEYSSFNAGGKGPRPEIF---------------NENL---------------- 305

Query: 121 PSMPMRSIGAHGGHETLLSGPDFKDF---HSMQDPNAK-NLDPNWRRPSP-SPGIRTSPT 175
           P++ +R  G  G  + +LSG +F D    HS +D N+     PNWRRPSP + GI  SP 
Sbjct: 306 PNLQLRPFGPQGSFDPVLSGAEFNDLAPLHSFRDGNSNIPTGPNWRRPSPPASGILPSPA 365

Query: 176 QGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGL 235
             +R P+      WDV D +Q+QR+ KR R+D S+PID+  FPSR               
Sbjct: 366 SRVRPPMRSVSTGWDVLDPSQYQREPKRSRLDASLPIDEDAFPSR--------------- 410

Query: 236 GSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARC 295
                             NR  P A    AGG  ++ ID DFIWRGIIAKGGTPVC ARC
Sbjct: 411 ------------------NRFGPPAD---AGGPHQHRIDHDFIWRGIIAKGGTPVCNARC 449

Query: 296 VPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLG 355
           VP  KG++ ELPEVVNCSARTGLDML KHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLG
Sbjct: 450 VPLDKGMDLELPEVVNCSARTGLDMLTKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLG 509

Query: 356 SKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQ-----AMVP---- 406
           SKNRAGVAKFDDGTTLFLVPPSDFL+ VLKV GPERLYGVVLKLPQQ     ++ P    
Sbjct: 510 SKNRAGVAKFDDGTTLFLVPPSDFLTNVLKVKGPERLYGVVLKLPQQTPSSASIQPQLCQ 569

Query: 407 ----PQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIA 462
               PQ +D+  IPPP  +Y     KEE   P+DYNR  H+DSK  SK+ +P A+E +  
Sbjct: 570 PNHIPQYMDRHQIPPPEIDYNQIARKEERFTPMDYNRILHEDSKPPSKIFYPPATESMTE 629

Query: 463 HSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATKSAEVAPGSS--------SARPL 514
            S    Y SN+  A+SQAGV  TPELIA+LTSL+PA        G            R L
Sbjct: 630 QSVHQAYASNSTVAVSQAGVSWTPELIASLTSLLPANAQLSTLEGGQPVSGSLVVDKRTL 689

Query: 515 LAEPHV--QSIEQLGNHYNPQAQS--LTHHYASMSSTPSHSAQMLLGNNQLQESTASLSQ 570
               H    S  Q G+ +N ++Q+  L+  Y S+SS P+ S  M+ G  Q+Q+ + +L  
Sbjct: 690 HGWKHSGNTSHMQYGSQFNSESQAPLLSQPYPSISSAPNSSEIMVPGTAQIQDFSVNLPH 749

Query: 571 QGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGY-GMMQGTEASTLYGSSV 629
           QG + SRPL + ++  Q   VA+ P V QQYQ   P   QK Y GMM GTE S  Y  SV
Sbjct: 750 QGGIASRPLNSVNLPSQGGQVALPPHVSQQYQLEVP--HQKAYSGMMHGTEGS--YSPSV 805

Query: 630 FQQPNNPTAVSNQV---NLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGAGQGTSDGEV 686
            QQ NNP   S+Q    N SQ Q+ + +S DKVN E  +   QLQ+    A QGTS+ EV
Sbjct: 806 IQQSNNPVVFSSQAQGGNHSQTQSGLPLSSDKVNWEVSS---QLQTAPFVADQGTSEVEV 862

Query: 687 DKNQRYQSTLQFAAN--LLLQIQQQQQTNSPAGRGTGNQQ 724
           DKNQRYQSTLQFAA+  L +Q QQQQQT +PA RG+GNQQ
Sbjct: 863 DKNQRYQSTLQFAASLLLQIQQQQQQQTGNPAVRGSGNQQ 902

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356544510|ref|XP_003540693.1| PREDICTED: flowering time control protein FPA-like [Glycine max]

 Score =  645 bits (1665), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/769 (51%), Positives = 477/769 (62%), Gaps = 121/769 (15%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +DEQMLHNAMILFGEIERIKS+P RNYS VEFRSVDEARRAKEGLQGRLFNDPRITIM+S
Sbjct: 213 IDEQMLHNAMILFGEIERIKSFPLRNYSIVEFRSVDEARRAKEGLQGRLFNDPRITIMYS 272

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRG 120
           SS+L PG DYP  + G+ GPR ++F                                I G
Sbjct: 273 SSDLVPGSDYPSFFPGSNGPRPDVF-------------------------------GIMG 301

Query: 121 PSMPMRSIGAHGGHETLLSGPDFKD---FHSMQDPNAK-NLDPNWRRPSPSPGIRTSPTQ 176
            ++PMR  G HGG E+++SGP+F +    H  QD ++K N+ PNW+RPSP       P Q
Sbjct: 302 LNVPMRPFGNHGGVESVISGPEFNEIDALHKFQDGSSKSNMGPNWKRPSP-------PAQ 354

Query: 177 GIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLG 236
             R P     G+WDV D N   RDSKR R+DG +P+ +A FP R IDD G          
Sbjct: 355 STRLPTRSTSGAWDVLDKNHIPRDSKRSRIDGPLPVAEALFPFRNIDDRG---------- 404

Query: 237 SITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCV 296
                              L PV+S++TAG       D D IWRG+IAKGGTPVCRARCV
Sbjct: 405 ------------------HLGPVSSRITAGVHDIVQPDIDHIWRGVIAKGGTPVCRARCV 446

Query: 297 PFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGS 356
           P GKGI +ELP VV+CSARTGLD+L KHYA+AIGFDIVFFLPDSEDDFASYTEFLRYL +
Sbjct: 447 PIGKGIGTELPGVVDCSARTGLDILTKHYADAIGFDIVFFLPDSEDDFASYTEFLRYLSA 506

Query: 357 KNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLP---------QQAMVP- 406
           KNRAGVAKF D TTLFLVPPSDFL++VLKV GPERLYGVVLK P         Q + +P 
Sbjct: 507 KNRAGVAKFVDNTTLFLVPPSDFLTRVLKVTGPERLYGVVLKFPPVPSSAPMQQPSHLPV 566

Query: 407 PQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHSSS 466
           P T   Q+IPP   EYGL   KEE VLP+DYNR  H+DSK+ +K  +P A  P   HS  
Sbjct: 567 PTTQYMQHIPPSQTEYGLIPVKEEQVLPMDYNRPLHEDSKLPAKPVYPPAGGPPPVHSGP 626

Query: 467 MDYGSNNAAAISQAGVKLTPELIATLTSLIPATKS------AEVAPGSSSAR----PL-- 514
            DY +NN  A SQAGV LTPELIATL SL+P T        A+ A GSS+ +    P+  
Sbjct: 627 PDYSTNNTVAGSQAGVALTPELIATLASLLPTTTQLPTTDGAKSAVGSSTMKLPFPPMTP 686

Query: 515 --------LAEPHVQSIEQLGNHYNPQAQSLTHHYASMSSTPSHSAQMLLGNNQLQESTA 566
                   +A+      +QL N YN    +    Y  +S+   + AQ + G++ +Q++ A
Sbjct: 687 NDGNQSHQIADQSTHPPQQLRNMYNVH-NAPYQPYPPLSAPAGNPAQ-VSGSSHIQDTAA 744

Query: 567 SL-SQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQGTEASTLY 625
           ++  QQG V SR +PNF +  Q+  VAVSP   Q YQ     ++QKG+G++QGT+AS LY
Sbjct: 745 NMQQQQGAVSSRHMPNFMMPTQSGQVAVSPHASQHYQVEVSPSNQKGFGVVQGTDASALY 804

Query: 626 GSSVFQQPNNPT----------AVSNQV---NLSQPQNVMTVSVDKVNLEHPNHVQQLQS 672
            S  FQQPNN +          A+SNQ    N SQ Q  M  +VD+VN + PN  QQL  
Sbjct: 805 NSQAFQQPNNNSQAFQQPNNSFALSNQTNSANASQQQTAMLYTVDQVNSDTPN--QQLP- 861

Query: 673 VLSGAGQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNSPAGRGTG 721
            + G  QG ++ E DKNQRYQSTLQFAANLLLQ  QQQQ  +P G G G
Sbjct: 862 -MFGVSQGQTEVEADKNQRYQSTLQFAANLLLQ-LQQQQQQAPGGHGPG 908

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473075|ref|XP_003606822.1| Flowering time control protein FPA [Medicago truncatula] gi|355507877|gb|AES89019.1| Flowering time control protein FPA [Medicago truncatula]

 Score =  617 bits (1592), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 362/771 (46%), Positives = 457/771 (59%), Gaps = 123/771 (15%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +DEQMLHNAMILFGEIERIKS PSRN+SFVEFRSVDEARRAKEGLQGRLFNDP ITI +S
Sbjct: 236 IDEQMLHNAMILFGEIERIKSVPSRNFSFVEFRSVDEARRAKEGLQGRLFNDPHITINYS 295

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGDQ-IRPSQLDMLGPNQSMQPNNFAGHLQPADIR 119
           +++   GKDYPG Y G+ GPR ++F  +   RP+Q+D+ G N+ M PN+F G L      
Sbjct: 296 NADQVQGKDYPGFYPGSNGPRPDLFLNEHPYRPAQMDLFGHNRPMIPNSFPGQLPSGGNV 355

Query: 120 GPSMPMRSIGAHGGHETLLSGPDFKDFHSMQDPNAKNLDPNWRRPSP-SPGIRTSPTQGI 178
           GP++PMR  G +GG E+++SGP+F +  ++         PNW+RPSP + G+ +SP  G 
Sbjct: 356 GPNIPMRPFGPNGGPESVVSGPEFNENSTLHK------GPNWKRPSPPAQGLLSSPVPGA 409

Query: 179 RQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLGSI 238
           R P   + G+WDV D N   RDSKR R+DG++P DD                        
Sbjct: 410 RLPARSSSGAWDVLDINHIPRDSKRSRIDGALPNDDP----------------------- 446

Query: 239 TGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCVPF 298
                        GR  L   ++++T G     P   D IWRG+IAKGGTPVCRARC+P 
Sbjct: 447 -----------YAGRGILGSASTRITGGVHAVQP---DHIWRGLIAKGGTPVCRARCIPV 492

Query: 299 GKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSKN 358
           GKGI +ELPEVV+CSARTGLD LA HYA+AI F+IVFFLPDSE+DF SYTEFLRYLG+KN
Sbjct: 493 GKGIGTELPEVVDCSARTGLDTLAAHYADAIDFEIVFFLPDSENDFGSYTEFLRYLGAKN 552

Query: 359 RAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKL-PQQAMVP---------PQ 408
           RAGVAKF++ TTLFLVPPSDFL+ VLKV GPERLYGVVLK  P Q+ VP         P 
Sbjct: 553 RAGVAKFEN-TTLFLVPPSDFLTDVLKVTGPERLYGVVLKFAPVQSGVPVHQSSHLPVPS 611

Query: 409 TVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIAHSSSMD 468
               Q +PP  AEY +   KEE VL ++YNR  H+DSK+ +K  +P    P     ++ D
Sbjct: 612 NQYMQQMPPSQAEYDMNPAKEEQVLAMNYNRMLHEDSKLPAKQVYPPTGGPSSVQPAASD 671

Query: 469 YGSNNAAAISQAGVKLTPELIATLTSLI------PATKSAEVAPGSSSARP--------- 513
           Y  N AA+ SQAGV LTPELIATL S +      PA   A+   GSS+ +P         
Sbjct: 672 YALNTAASGSQAGVALTPELIATLASFLPTNVQSPAIDGAKSGAGSSTVKPPFPPVAPND 731

Query: 514 -----------LLAEPHVQSIEQLGNHYNPQAQSLTHHYASMSSTPSHSAQMLLGNNQLQ 562
                       +A+  +   +Q  N YN  + +  H     +S P H+AQ   G++ +Q
Sbjct: 732 GNQSQIWKQDHQIADQSIHPSQQFRNMYN--SHNAHHQPYPPASAPGHTAQAFSGSSHIQ 789

Query: 563 ESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQGTEAS 622
           ++  +  QQG+V SR + NF    Q+  VA SP    QYQ   P N+QKG+    G++ S
Sbjct: 790 DNAVNQQQQGVVSSRLVSNFVTPTQSGQVAASPHFSHQYQAEVPPNTQKGF---PGSDVS 846

Query: 623 TLYGSSV------------------------------FQQPNNPTAVSNQVNLSQPQN-- 650
            LY S                                FQQPNN  A+S+QVN + PQ+  
Sbjct: 847 VLYNSQAFQQPNNNHHPFQQPNNNPQHFQQSNNNPQPFQQPNNSIALSSQVNSANPQHQP 906

Query: 651 VMTVSVDKVNLEHPNHVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAAN 701
           VM  + D+VN   P  +QQ  +   G GQG  + E DKNQRYQSTLQFAAN
Sbjct: 907 VMQYTADQVNSNPP--IQQHPAF--GVGQGPPELEADKNQRYQSTLQFAAN 953

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133226|ref|XP_002327991.1| predicted protein [Populus trichocarpa] gi|222837400|gb|EEE75779.1| predicted protein [Populus trichocarpa]

 Score =  611 bits (1575), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 377/772 (48%), Positives = 456/772 (59%), Gaps = 121/772 (15%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +DEQMLHNAMILFGEIERIKS+PSR+YSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS
Sbjct: 236 IDEQMLHNAMILFGEIERIKSFPSRHYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 295

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRG 120
           SS LAPGK+Y   Y G KGPR EMF      P  +D++  +Q   P NF     P+ I  
Sbjct: 296 SSGLAPGKEYSSFYPGVKGPRPEMFNEHPFTP--MDVMF-DQPGGPGNFGSPFPPSGIHR 352

Query: 121 PSMPMRSIGAHGGHETLLSGPDFKDF---HSMQDPNAKNLDPNWRRPSPSPGIRTSPTQG 177
           P++P+R  G  G  +TLL G +F D    HS +DP +              GI  SP  G
Sbjct: 353 PNLPVRPFGPQGVFDTLLQGGEFNDLAPSHSTRDPAS--------------GILPSPASG 398

Query: 178 IRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGLGS 237
           IR  +      WDV D +QF R++KR R+D +  IDD +FP+RK+DD  L          
Sbjct: 399 IRPSMRSVSSGWDVLDPSQFPREAKRSRIDAAPSIDDDSFPARKMDDRDL---------- 448

Query: 238 ITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARCVP 297
                             LSPV      GG  +   D+DFIWRGI+AKGGTP+     + 
Sbjct: 449 -----------------GLSPV------GGRFKGHFDNDFIWRGIVAKGGTPLRHMAGLA 485

Query: 298 FGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLGSK 357
               ++   P V+NCSARTGLDMLAKHYAEAIGFDIVFFLPDSE+DFASYTEFLRYLG K
Sbjct: 486 CQISLKFTKPHVINCSARTGLDMLAKHYAEAIGFDIVFFLPDSEEDFASYTEFLRYLGLK 545

Query: 358 NRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQAMVPPQT-------- 409
           NRAGVAKFDDGTTLFLVPPSDFL  VLKV GPERLYGVVLKLPQQ  VP  T        
Sbjct: 546 NRAGVAKFDDGTTLFLVPPSDFLKNVLKVAGPERLYGVVLKLPQQ--VPSNTSIQEQLPQ 603

Query: 410 -------VDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIA 462
                   D Q IPPP A+Y   R  EE  +P+ +NRF H+DSK+  K  +P  +E +  
Sbjct: 604 PIHFSQYTDNQ-IPPPEADYNQLRQGEERGMPIHHNRFLHEDSKLPPKSFYPSTTESIAV 662

Query: 463 HSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATK------SAEVAPGSSSARPLLA 516
                +Y  N +A  S AGV LTPELIATL + +P  K      S + A GSS  RP  +
Sbjct: 663 PPVPQEYAPNLSAGPSTAGV-LTPELIATLATFLPTNKQSSSSESNQPALGSSIVRPQFS 721

Query: 517 E------------PHVQSIE------QLGNHYNPQAQSLTHH--YASMSSTPSHSAQMLL 556
                         H   +       Q+GN +N Q Q  +    Y S+ +T SHSA ++ 
Sbjct: 722 SVAPDRGISSQGWKHDNQVSGNASHLQMGNQFNSQVQVQSQFQPYPSVPNTYSHSATVVP 781

Query: 557 GNNQLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMM 616
            N+Q+Q+STASLS Q +  SRPL NFS+  Q+   A+SP V Q+     P  +QKG+G++
Sbjct: 782 SNSQIQDSTASLSHQSVTSSRPLTNFSMPSQSGQFALSPQVSQKNLLKVPHATQKGHGVV 841

Query: 617 QGTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSG 676
            GT+                       N SQ Q+ +  S D+ N E PN VQQ Q  LSG
Sbjct: 842 HGTDVQG-------------------ANYSQTQSGIPPSADRGNWELPNQVQQFQPALSG 882

Query: 677 AGQGTSDGEVDKNQRYQSTLQFAAN----LLLQIQQQQQTNSPAGRGTGNQQ 724
           +GQGTS+ E DKNQRYQSTLQFAAN    +  Q QQQ+   +PA  G+GNQQ
Sbjct: 883 SGQGTSEVEADKNQRYQSTLQFAANLLLQIQQQQQQQKTATNPAAHGSGNQQ 934

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147801865|emb|CAN74982.1| hypothetical protein VITISV_007871 [Vitis vinifera]

 Score =  603 bits (1556), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 377/766 (49%), Positives = 474/766 (61%), Gaps = 102/766 (13%)

Query: 1    MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
            ++EQML+NAMILFGEIERIKS+PSR+YSFVEFRS+DEARRAKEGLQGRLFNDPRI+IM+S
Sbjct: 1271 LEEQMLYNAMILFGEIERIKSFPSRHYSFVEFRSIDEARRAKEGLQGRLFNDPRISIMYS 1330

Query: 61   SSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRG 120
            SS + PGK+Y     G    R + F  +++    +D+  PN  M  NNF G   P+ I  
Sbjct: 1331 SSGVVPGKEYN---PGIPESRPDTFV-NELPFRHVDVFSPNGPMVSNNFPGPSPPSGILA 1386

Query: 121  PSMPMRSIGAHGGHETLLSGPDFKDFHSM---QDPNAKNL-DPNWRRPSPSP-GIRTSPT 175
             ++ MR++G+H   E   SGP   +  ++   QD +  NL  PNWRRPSPS  G+  SP 
Sbjct: 1387 SNV-MRTVGSH---EPPRSGPGLNELAALRNFQDTSPNNLMGPNWRRPSPSTLGMLPSPV 1442

Query: 176  QGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGL 235
              IR  +     +WDV DANQFQRDSKR RVDG++ I + +FP RK DD GL LD  YG 
Sbjct: 1443 PSIRPSVRPVSAAWDVSDANQFQRDSKRSRVDGAVSISNPSFPLRKSDDLGLGLDDLYGQ 1502

Query: 236  GSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARC 295
                 G AS +F N+QG+NR   V  ++T     ++   +D+IWRGIIAKGG  VC ARC
Sbjct: 1503 HD---GSASSSFSNIQGKNRSGLVDPRLTNAVAAQSHSGTDYIWRGIIAKGGATVCHARC 1559

Query: 296  VPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLG 355
            V   KG+ S+LPE+VNCSARTGLD+L KHYAEA+GF++VFFLPDSEDDFASYTEFL YLG
Sbjct: 1560 VAIEKGLSSKLPEIVNCSARTGLDLLTKHYAEAVGFEVVFFLPDSEDDFASYTEFLCYLG 1619

Query: 356  SKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQA------------ 403
            SK+RAGVAK DDGTTLFLVPPSDFLSKVLKV GPERLYGVVLKL QQ             
Sbjct: 1620 SKDRAGVAKLDDGTTLFLVPPSDFLSKVLKVSGPERLYGVVLKLAQQVPSAASMQQQSHR 1679

Query: 404  -MVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFPHASEPLIA 462
             +   Q  D+Q I PPH EY L   KE                        P  SE L  
Sbjct: 1680 PVPSSQYSDRQQI-PPHVEYSLIPQKER-----------------------PSTSESLAT 1715

Query: 463  HSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIP------ATKSAEVAPGSSSARPLL- 515
             S S D  S+N A +SQAG+ LTPELIA L SL+P      A+ SA  + GSS ARP L 
Sbjct: 1716 QSISQDRASSNTAVVSQAGLTLTPELIAHLASLLPGGMQSSASVSAPQSLGSSIARPSLP 1775

Query: 516  --AEPHVQSI-------------EQLGNHYNPQAQSL--THHYASMSSTPSHSAQMLLGN 558
                P   ++             +Q GN ++PQAQ L    +Y +++ TP H+A + + +
Sbjct: 1776 PSVAPDRGTLSQGRNQDHQTPPSQQSGNQFHPQAQPLPQFQNYPTVTQTPGHTA-LAVPD 1834

Query: 559  NQLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQG 618
             Q+Q++T +L Q G + SRPL N  +  Q+   AVSP V+QQYQ     NSQ  YGM   
Sbjct: 1835 GQIQDNTFNLPQLGTISSRPLTNLPVPSQSGQFAVSPQVNQQYQLEIHQNSQNAYGM--- 1891

Query: 619  TEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGAG 678
                         + + PT  S+QV+ +          ++VN   PN VQQLQS+++GAG
Sbjct: 1892 ------------GRADGPTTFSSQVDGAS---------NRVNPALPNQVQQLQSMINGAG 1930

Query: 679  QGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNSPAGRGTGNQQ 724
            Q  SD + DK+QRYQST+QFAA+LL QI++QQQ  + A +  G QQ
Sbjct: 1931 QWLSDDDADKSQRYQSTIQFAADLLEQIRKQQQQTNQAEQWPGKQQ 1976

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478105|ref|XP_002269583.2| PREDICTED: flowering time control protein FPA-like [Vitis vinifera]

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 364/767 (47%), Positives = 454/767 (59%), Gaps = 144/767 (18%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           ++EQML+NAMILFGEIERIKS+PSR+YSFVEFRS+DEARRAKEGLQGRLFNDPRI+IM+S
Sbjct: 213 LEEQMLYNAMILFGEIERIKSFPSRHYSFVEFRSIDEARRAKEGLQGRLFNDPRISIMYS 272

Query: 61  SSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRG 120
           SS + PGK+Y     G    R + F  +++    +D+  PN                   
Sbjct: 273 SSGVVPGKEY---NPGIPESRPDTFV-NELPFRHVDVFSPN------------------- 309

Query: 121 PSMPMRSIGAHGGHETLLSGPDFKDFHSM---QDPNAKNL-DPNWRRPSPSP-GIRTSPT 175
                      G HE   SGP   +  ++   QD +  NL  PNWRRPSPS  G+  SP 
Sbjct: 310 -----------GSHEPPRSGPGLNELAALRNFQDTSPNNLMGPNWRRPSPSTLGMLPSPV 358

Query: 176 QGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGLVLDQSYGL 235
             IR  +     +WDV DANQFQRDSKR RVDG++ I + +FP RK DD GL      G 
Sbjct: 359 PSIRPSVRPVSAAWDVSDANQFQRDSKRSRVDGAVSISNPSFPLRKSDDLGLAAQSHSG- 417

Query: 236 GSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGGTPVCRARC 295
                                                  +D+IWRGIIAKGG  VC ARC
Sbjct: 418 ---------------------------------------TDYIWRGIIAKGGATVCHARC 438

Query: 296 VPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASYTEFLRYLG 355
           V   KG+ S+LPE+VNCSARTGLD+L KHYAEA+GF++VFFLPDSEDDFASYTEFL YLG
Sbjct: 439 VAIEKGLSSKLPEIVNCSARTGLDLLTKHYAEAVGFEVVFFLPDSEDDFASYTEFLCYLG 498

Query: 356 SKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKLPQQA------------ 403
           SK+RAGVAK DDGTTLFLVPPSDFLSKVLKV GPERLYGVVLKL QQ             
Sbjct: 499 SKDRAGVAKLDDGTTLFLVPPSDFLSKVLKVSGPERLYGVVLKLAQQVPSAASMQQQSHR 558

Query: 404 MVP-PQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYN-RFSHDDSKVQSKMHFPHASEPLI 461
            VP  Q  D+Q I PPH EY L  P++E VL +D+N    H+DS +  K+  P  SE L 
Sbjct: 559 PVPSSQYSDRQQI-PPHVEYSLI-PQKERVLHMDHNSSILHEDSSLSPKLRLPSTSESLA 616

Query: 462 AHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIP------ATKSAEVAPGSSSARPLL 515
             S S D  S+N A +SQAG+ LTPELIA L SL+P      A+ SA  + GSS ARP L
Sbjct: 617 TQSISQDRASSNTAVVSQAGLTLTPELIAHLASLLPGGMQSSASVSAPQSLGSSIARPSL 676

Query: 516 ---AEPHVQSI-------------EQLGNHYNPQAQSL--THHYASMSSTPSHSAQMLLG 557
                P   ++             +Q GN ++PQAQ L    +Y +++ TP H+A + + 
Sbjct: 677 PPSVAPDRGTLSQGRNQDHQTPPSQQSGNQFHPQAQPLPQFQNYPTVTQTPGHTA-LAVP 735

Query: 558 NNQLQESTASLSQQGMVYSRPLPNFSIAPQAAPVAVSPPVHQQYQFAAPSNSQKGYGMMQ 617
           + Q+Q++T +L Q G + SRPL N  +  Q+   AVSP V+QQYQ     NSQ  YGM +
Sbjct: 736 DGQIQDNTFNLPQLGTISSRPLTNLPVPSQSGQFAVSPQVNQQYQLEIHQNSQNAYGMGR 795

Query: 618 GTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLSGA 677
                           + PT  S+QV+ +          ++VN   PN VQQLQS+++GA
Sbjct: 796 A---------------DGPTTFSSQVDGAS---------NRVNPALPNQVQQLQSMINGA 831

Query: 678 GQGTSDGEVDKNQRYQSTLQFAANLLLQIQQQQQTNSPAGRGTGNQQ 724
           GQ  SD + DK+QRYQST+QFAA+LL QI++QQQ  + A +  G QQ
Sbjct: 832 GQWLSDDDADKSQRYQSTIQFAADLLEQIRKQQQQTNQAEQWPGKQQ 878

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	724
TAIR|locus:2058203	901	FPA [Arabidopsis thaliana (tax	0.580	0.466	0.463	5e-108
TAIR|locus:2135605	823	AT4G12640 [Arabidopsis thalian	0.298	0.262	0.396	8.5e-47

TAIR|locus:2058203 FPA [Arabidopsis thaliana (taxid:3702)]

 Score = 773 (277.2 bits), Expect = 5.0e-108, Sum P(2) = 5.0e-108
 Identities = 213/460 (46%), Positives = 261/460 (56%)

Query:   270 RNPIDSDFIWRGIIAKGGTPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAI 329
             R P DSD IWRG+IAKGGTPVC ARCVP GKGIE++LPEVVNCSART L+MLAKHYA AI
Sbjct:   432 RGPPDSDHIWRGMIAKGGTPVCCARCVPMGKGIETKLPEVVNCSARTDLNMLAKHYAVAI 491

Query:   330 GFDIVFFLPDSEDDFASYTEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGP 389
             G +IVFF+PD E+DFASYTEFLRYL SK+RAGVAK DDGTTLFLVPPSDFL+ VL+V   
Sbjct:   492 GCEIVFFVPDREEDFASYTEFLRYLSSKDRAGVAKLDDGTTLFLVPPSDFLTDVLQVTRQ 551

Query:   390 ERLYGVVLKLPQQAMVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQ- 448
             ERLYGVVLKLP  A VP     +Q        Y + + ++       ++ +   ++ ++ 
Sbjct:   552 ERLYGVVLKLPPPA-VPVTASYRQESQSNPLHY-MDQARDSPA-NASHSLYPPRENYIRG 608

Query:   449 SKMHFPHASEPLIAHSSSMDYGSNNAAAISQAGVKLTPELIATLTSLIPATKSAEVAPGS 508
             +  H   AS+P ++    +    NNAA   QAGV LTPEL+ATL S++PAT S   AP  
Sbjct:   609 APEHLTAASKPSVSEPLRIP---NNAAP--QAGVSLTPELLATLASILPAT-SQPAAP-- 660

Query:   509 SSARPLLAEPHVQSIEQLGNH-YNPQAQSL-------THHYASMSSTPSHSAQMLLGNNQ 560
              S +P+     V S     N  YN +A S        T H AS  S   +  Q      Q
Sbjct:   661 ESHQPMSGPSTVVSTAHQSNGLYNGEAPSQAWKRGPQTVHDASNQSFQQYGNQYTPAG-Q 719

Query:   561 L-----QESTASLSQQ---GMVYSR-PLPNFSIXXXXXXXXXXXXXXXXYQFA-APSNSQ 610
             L     +   AS +     GMV+      + S+                  +    SN  
Sbjct:   720 LPPPPSRYPPASNNPNYTSGMVHGNMQYQSQSVNMPQLSPLPNMPHNNYSMYTQGSSNHP 779

Query:   611 KGYGMMQG--TEASTL---YGS-SVFQQPNNPTAVSNQ---VNLSQPQNVMTVSVDKVNL 661
                 M+Q    EAS     YG    +QQ N     +NQ   +N SQ Q  M    DK NL
Sbjct:   780 VSQPMVQQYQPEASMPNQNYGPIPSYQQANFHGVTTNQAQNLNPSQFQAAMQPPADKANL 839

Query:   662 EHPNHVQQLQSVLSGAGQGTSDGEVDKNQRYQSTLQFAAN 701
             E  N   +LQ ++SG GQGT+DGEVDKNQRYQSTLQFAAN
Sbjct:   840 EPQNQALRLQPMISGDGQGTTDGEVDKNQRYQSTLQFAAN 879

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:0005737 "cytoplasm" evidence=ISM

GO:0009911 "positive regulation of flower development" evidence=IMP

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=IMP

GO:0000785 "chromatin" evidence=IDA

GO:0009553 "embryo sac development" evidence=IGI

GO:0009790 "embryo development" evidence=IGI

GO:0031048 "chromatin silencing by small RNA" evidence=IMP

GO:0006378 "mRNA polyadenylation" evidence=IDA

TAIR|locus:2135605 AT4G12640 [Arabidopsis thaliana (taxid:3702)]

 Score = 376 (137.4 bits), Expect = 8.5e-47, Sum P(3) = 8.5e-47
 Identities = 92/232 (39%), Positives = 126/232 (54%)

Query:   168 PGIRTSPTQGIRQPLNHAPGSWDVYDANQFQRDSKRLRVDGSMPIDDATFPSRKIDDHGL 227
             PG + S  +  R+P + A   +   DA +   ++ +LR + ++         R  D   L
Sbjct:   376 PGHQLSGIEQERRPFSRASADFSPKDAFERNYEAGQLRYNQTVE-QPLNLAIRNGDKSSL 434

Query:   228 VLDQSYGLGSITGGPASGAFVNVQGRNRLSPVASKVTAGGFGRNPIDSDFIWRGIIAKGG 287
                    +G   G P       V  R R +P  ++         P   D+ W G IAKGG
Sbjct:   435 REPHEELMG---GYPLPSV---VPERKRYTPELNR---------PSLKDWNWEGTIAKGG 479

Query:   288 TPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKHYAEAIGFDIVFFLPDSEDDFASY 347
              P+CRA+C P GK ++  LPE ++C+ARTGLDMLAKHY ++    +VFF+P S+ D   Y
Sbjct:   480 NPICRAKCFPVGKVMDMMLPEFLDCTARTGLDMLAKHYYQSSKAWVVFFVPGSDADIVFY 539

Query:   348 TEFLRYLGSKNRAGVAKFDDGTTLFLVPPSDFLSKVLKVVGPERLYGVVLKL 399
              EF+ YL  K RA V+K DD TTLFLVPPSDF  KVLKV G   + GV+L+L
Sbjct:   540 DEFMHYLEEKQRAAVSKLDDTTTLFLVPPSDFSEKVLKVPGKLSISGVILRL 591

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:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	724
pfam07744	109	pfam07744, SPOC, SPOC domain	1e-19
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-09
smart00360	73	smart00360, RRM, RNA recognition motif	8e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-08
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	3e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	3e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	4e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	4e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	7e-05
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	1e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-04
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	3e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-04
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	4e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	4e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	6e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.001
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.001
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.003
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	0.003
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.003
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.004
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.004

>gnl|CDD|219549 pfam07744, SPOC, SPOC domain

 Score = 84.3 bits (209), Expect = 1e-19
 Identities = 34/109 (31%), Positives = 47/109 (43%), Gaps = 12/109 (11%)

Query: 279 WRGIIAKGGTPVCRARCVP---FGKGIESELPEVVNCSARTGLDMLAKHYAEAIGF---D 332
           W+G +A  G      R        K + S LP  +    R  L  + K+  +        
Sbjct: 1   WQGTLAMKGVAEFSVRAHLVSGDEKLVNSLLPLRLEIRGRLDLSQVEKYLRKLRKSSTKA 60

Query: 333 IVFFL--PDSEDDFASYTEFLRYLGSKNRAGVAKFDD----GTTLFLVP 375
           +V     PDSE D A++ E + YL SK RAGVAK  D       L+L+P
Sbjct: 61  VVVLALSPDSESDRAAFDELIDYLQSKQRAGVAKVGDPGSQVKDLYLIP 109

The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling. Length = 109

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

 Score = 74.5 bits (184), Expect = 1e-16
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 2  DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDP--RITIMF 59
              L      FG I RI   P RNY+++E+ S++ A+ AKE L+G     P  R+ + F
Sbjct: 11 SLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLGGPGRRLRVDF 70

Query: 60 S 60
          +
Sbjct: 71 A 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 5/62 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            E+ L      FGEIE ++        S+ ++FVEF S ++A +A E L G+  +  ++
Sbjct: 10 TTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKL 69

Query: 56 TI 57
           +
Sbjct: 70 KV 71

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|214636 smart00360, RRM, RNA recognition motif

 Score = 52.2 bits (126), Expect = 8e-09
 Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 6/63 (9%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
            E+ L      FG++E ++      +  S+ ++FVEF S ++A +A E L G+  +   
Sbjct: 11 TTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRP 70

Query: 55 ITI 57
          + +
Sbjct: 71 LKV 73

Length = 73

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

 Score = 49.8 bits (120), Expect = 4e-08
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 6  LHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          L+     FG +E+IK       ++FVEF + + A +A + L G LF    + + +S
Sbjct: 1  LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 1  MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            E+ L +    FG IE I+        S+ ++FVEF   ++A +A E L G+      +
Sbjct: 10 TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69

Query: 56 T 56
           
Sbjct: 70 R 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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 6/65 (9%)

Query: 2  DEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
           E+ L      +G IE++      K+  SR + FV F SV++A+ AKE L G   +  RI
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71

Query: 56 TIMFS 60
           + +S
Sbjct: 72 RVDYS 76

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

>gnl|CDD|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 = 45.9 bits (109), Expect = 2e-06
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 13 FGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
          FG + R      + ++FVEF   ++A +A E L G   +   +T+ F
Sbjct: 24 FGPLVRCDI--RKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEF 68

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF-NDPRITIM 58
          + E+ L +    FGEI  I   P +  +FV F + + A +A E L  +L  N  R+ + 
Sbjct: 13 VTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNKLIINGRRLKLK 71

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

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 6/46 (13%)

Query: 2  DEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRA 41
          DE++LH A I FG+I+ I      ++   R ++FVEF   ++A  A
Sbjct: 11 DEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAA 56

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|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 8/67 (11%)

Query: 2  DEQMLHNAMILFGE-------IERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRL-FNDP 53
           E+ + NA++  G        + R  +  SR ++FVEF S++EA R  E  QG+L   D 
Sbjct: 15 TEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMELNQGKLQLQDY 74

Query: 54 RITIMFS 60
          +IT+ +S
Sbjct: 75 KITLHYS 81

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>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 = 42.5 bits (101), Expect = 3e-05
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 6/52 (11%)

Query: 1  MDEQMLHNAMILFGEIERI----KSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
          +   +LH     +G +E+I    K+   +  + V+F SV+ A  AK+ L GR
Sbjct: 13 VTVDVLHQVFSPYGAVEKILIFEKNTGVQ--ALVQFDSVESAENAKKALNGR 62

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

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYS-FVEFRSVDEARRAKEGLQGRLFNDPRITIM 58
          + +Q L +    FGE++ I+  P R    FVEF  +  A  A + L GR F   R+ + 
Sbjct: 13 ISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRPFLGGRLKVK 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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
          E  +      +G ++ +K     N++FVEF S++ A RAK+ + G++ N+  + + +
Sbjct: 13 ESAIREIFSPYGAVKEVKMI--SNFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 6/54 (11%)

Query: 13 FGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          FG +ER        +  S+ Y FVE+ S   A +AK  L G+     ++ + ++
Sbjct: 23 FGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKLQVDWA 76

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

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

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI 57
          E+ L      +GE+ER+K    ++Y+FV F   D+A +A E + G+      I +
Sbjct: 15 EEQLRELFSEYGEVERVKKI--KDYAFVHFEERDDAVKAMEEMNGKELEGSPIEV 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|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 11/24 (45%), Positives = 17/24 (70%)

Query: 29 FVEFRSVDEARRAKEGLQGRLFND 52
          FVEF  V++A++A+  L GR F+ 
Sbjct: 60 FVEFADVEDAQKAQLALAGRKFDG 83

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|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 = 39.5 bits (93), Expect = 2e-04
 Identities = 14/51 (27%), Positives = 24/51 (47%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
          + E+ L      FG IE ++ +  + Y+FV F + + A  A   + G   N
Sbjct: 12 LTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTSIN 62

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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 6/55 (10%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRL 49
          MDE  +++A    GE+  +K      +  S  Y FVEF + + A +A + L G+ 
Sbjct: 11 MDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKP 65

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|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR-LFNDPRITI 57
          E++L      +G+IE I+  PS+  +FV ++    A  AKE +  + L     + +
Sbjct: 19 EEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEAMADQSLDGGEVLNV 74

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          E++L  A   FG++ER+K    ++Y+F+ F   D A +A E + G+      I I+F+
Sbjct: 15 EEILEKAFGQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKELEGENIEIVFA 70

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

 Score = 39.6 bits (93), Expect = 4e-04
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 9/47 (19%)

Query: 13 FGEIERI-----KSYP----SRNYSFVEFRSVDEARRAKEGLQGRLF 50
          +G+I++      KS P     R Y FV F + +EA +A + L G+  
Sbjct: 23 YGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTA 69

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|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 39.5 bits (93), Expect = 4e-04
 Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 7/51 (13%)

Query: 13 FGEIERIKSYPSRNYS-------FVEFRSVDEARRAKEGLQGRLFNDPRIT 56
          +G++  +  +   +         FVEF   DEA +A   L GR F   ++T
Sbjct: 30 YGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFGGRKVT 80

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain. . Length = 85

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 13/59 (22%), Positives = 26/59 (44%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
          +  + L      +G +E +   P + Y FV + S+++A  A + L G+    P+     
Sbjct: 15 VSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELELPQQNKPL 73

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          E++L  +   FG++ER+K    ++Y+FV F   D A RA + + G+      I I+ +
Sbjct: 15 EEILEKSFSEFGKLERVKKL--KDYAFVHFEERDAAVRAMDEMNGKEIEGEEIEIVLA 70

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R 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 R binds RNA through its RRM domains. . Length = 72

>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 = 7e-04
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 2  DEQMLHNAMILFGEIER------IKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
           E+ L      +G+I R      I +  S+ Y+FVE+    +A RA       + +   I
Sbjct: 16 TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEI 75

Query: 56 TIMFSSSELAPG 67
           + F      PG
Sbjct: 76 FVDFERERTLPG 87

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

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 6/53 (11%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQG 47
          + E  L      FGEIE ++      +  S+ Y F++F   ++A++A E L G
Sbjct: 10 ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNG 62

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

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 24 SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
          S+ Y FV F + + A RA E + G L ND ++
Sbjct: 42 SKGYGFVHFETEEAAVRAIEKVNGMLLNDKKV 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|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 = 37.6 bits (88), Expect = 0.001
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 6/63 (9%)

Query: 1  MDEQMLHNAMILFGEIE--RIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
            E+ L      FG +E   +   P    SR + FV F SV++A  A   L G+      
Sbjct: 13 TTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRV 72

Query: 55 ITI 57
          I +
Sbjct: 73 IKV 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 25 RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI 57
          +NY FV     ++A  A + L G  F   RI +
Sbjct: 33 KNYGFVHMEEEEDAEDAIKALNGYEFMGKRINV 65

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 4/55 (7%)

Query: 1  MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
          + E+ L      +G++E ++        R ++FVEF S ++A  A + L G + +
Sbjct: 10 VTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLD 64

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

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 36.5 bits (84), Expect = 0.003
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQG 47
          + EQ++      FG+I  I+ +P + YSF+ F + + A  A   + G
Sbjct: 12 LTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNG 58

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 15/47 (31%), Positives = 25/47 (53%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQG 47
          + EQ++      FG+I  ++ +P + YSFV F S + A  A   + G
Sbjct: 12 LTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNG 58

This subgroup corresponds to the RRM3 of p40-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 function 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 6/65 (9%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          M ++ L +     G IE  K      +  S  Y FV++   ++A++A   L G    + R
Sbjct: 12 MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKR 71

Query: 55 ITIMF 59
          + + +
Sbjct: 72 LKVSY 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	724
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.46
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.42
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.38
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.36
PF07744	119	SPOC: SPOC domain; InterPro: IPR012921 Spen (split	99.32
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.29
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.26
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.25
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.21
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.21
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.2
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.19
smart00361	70	RRM_1 RNA recognition motif.	99.18
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.16
smart00360	71	RRM RNA recognition motif.	99.14
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.13
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.12
KOG0122	270	consensus Translation initiation factor 3, subunit	99.12
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.1
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.09
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.09
smart00362	72	RRM_2 RNA recognition motif.	99.07
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.06
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.02
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.02
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.01
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.01
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.99
PLN03120	260	nucleic acid binding protein; Provisional	98.98
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.98
PLN03213	759	repressor of silencing 3; Provisional	98.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.83
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.83
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.82
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.78
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.77
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.77
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.76
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.75
PLN03121	243	nucleic acid binding protein; Provisional	98.75
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.75
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.72
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.69
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.68
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.6
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.58
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.57
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.56
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.56
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.49
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.48
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.46
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.45
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.45
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.44
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.37
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.36
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.32
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.3
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.28
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.25
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.18
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.03
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.02
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	97.99
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.99
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.98
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.98
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	97.97
KOG0226	290	consensus RNA-binding proteins [General function p	97.64
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.62
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	97.59
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.55
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	97.52
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.44
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.42
KOG0151	877	consensus Predicted splicing regulator, contains R	97.36
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.27
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.19
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.16
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.14
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.14
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	97.13
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.1
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.09
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.01
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	96.93
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.89
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	96.83
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.58
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	96.48
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.43
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.29
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.28
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.26
KOG2314	698	consensus Translation initiation factor 3, subunit	96.07
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.01
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	95.68
KOG4210	285	consensus Nuclear localization sequence binding pr	95.57
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	95.48
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.35
KOG1855	484	consensus Predicted RNA-binding protein [General f	94.83
KOG1995	351	consensus Conserved Zn-finger protein [General fun	94.82
KOG1457	284	consensus RNA binding protein (contains RRM repeat	94.65
KOG1548	382	consensus Transcription elongation factor TAT-SF1	93.98
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	93.9
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	93.7
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.45
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	92.87
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.12
KOG2068	327	consensus MOT2 transcription factor [Transcription	91.38
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.31
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	90.13
KOG2135	526	consensus Proteins containing the RNA recognition	87.69
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	86.93
KOG3152	278	consensus TBP-binding protein, activator of basal	86.52
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	84.85
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	83.71

>PF13893 RRM_5: RNA recognition motif

Probab=99.46  E-value=1.7e-13  Score=107.36  Aligned_cols=55  Identities=36%  Similarity=0.714  Sum_probs=51.9

Q ss_pred             HHHHhhhcCceeEeeecCCC-CeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            6 LHNAMILFGEIERIKSYPSR-NYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         6 LrelFS~FGeI~sVkt~~SR-GFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      |+++|++||+|++|++.+.+ |+|||+|.+.++|.+|++.|||..|+|++|+|+||
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            78999999999999988776 99999999999999999999999999999999997

(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 ....

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.42  E-value=7.2e-13  Score=124.25  Aligned_cols=65  Identities=25%  Similarity=0.412  Sum_probs=60.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|++.++|++|++.|||..|+|++|+|++++.+..
T Consensus        46 ~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         46 TDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             CCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            6899999999999999999864      4799999999999999999999999999999999999986544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.38  E-value=8.6e-13  Score=134.10  Aligned_cols=64  Identities=25%  Similarity=0.431  Sum_probs=59.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||.|++|++.      .+||||||+|.+.++|.+|+++|||..|+||+|+|+|+..+.
T Consensus       281 ~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       281 TDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             CCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            5899999999999999999854      479999999999999999999999999999999999997553

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.36  E-value=9.2e-13  Score=133.87  Aligned_cols=77  Identities=23%  Similarity=0.331  Sum_probs=69.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSY   74 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~   74 (724)
                      ++|++|+++|+.||+|.+|++.      ++||||||+|.+.++|++|++.|||..|.|++|+|+|+++.....+....|+
T Consensus        15 ~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~~~~~~~l~v   94 (352)
T TIGR01661        15 MTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYV   94 (352)
T ss_pred             CCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecccccccccceEEE
Confidence            6899999999999999999864      4789999999999999999999999999999999999987766555556788


Q ss_pred             CCC
Q 004908           75 SGT   77 (724)
Q Consensus        75 sG~   77 (724)
                      .++
T Consensus        95 ~~l   97 (352)
T TIGR01661        95 SGL   97 (352)
T ss_pred             CCc
Confidence            776

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

>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways

Probab=99.32  E-value=1.5e-12  Score=115.13  Aligned_cols=97  Identities=25%  Similarity=0.417  Sum_probs=75.7

Q ss_pred             eeeeeccCCcceeeeEeeec-cc-ccc-ccC------CceeecccccchhHHHHHhhh---ccCceEEEEeC-----CCc
Q 004908          279 WRGIIAKGGTPVCRARCVPF-GK-GIE-SEL------PEVVNCSARTGLDMLAKHYAE---AIGFDIVFFLP-----DSE  341 (724)
Q Consensus       279 W~G~iAKgG~pvC~arC~~~-gk-~~~-~~~------P~~ldctaRT~ld~l~khy~~---a~~~~vvff~P-----~s~  341 (724)
                      |+|.|...++.-|.++|..+ |. .+. ..|      |..|+++-|.+++.+.+...+   +...+||+|..     +++
T Consensus         1 W~G~i~m~~~~~f~~~a~~v~G~~~~~~~~l~~~~~~p~~i~i~gRl~~~~~~~yl~~i~~s~~~~v~v~~~~~~~~~~~   80 (119)
T PF07744_consen    1 WQGTISMKSVASFSARAHFVSGNCDLLDNVLPWQQLPPKKIDIRGRLDPEKVWDYLRQIRKSRSKDVCVVALSSPESDSN   80 (119)
T ss_dssp             EEEEEEETT-EEEEEEEEEEEE-HHHHHHHS-------EEE-EEEE-SHHHHHHHHHHTSSTTT-EEEEEEE-SSHHHHH
T ss_pred             CceEEEcCCCCeEEEEEEEEEcchhHhhhhcccccCCCcEEEEEeecCHHHHHHHHHhcccCCCceEEEEEEcCCcccCH
Confidence            99999999999999999999 52 222 235      999999999999999888874   33448888877     788


Q ss_pred             hhhhhHHHHHHhhccccccceEeecC-----CcEEEEeC
Q 004908          342 DDFASYTEFLRYLGSKNRAGVAKFDD-----GTTLFLVP  375 (724)
Q Consensus       342 ~D~~~y~eFl~YL~~K~rAgV~K~~~-----~ttLFLVP  375 (724)
                      +|...|++|+.||.+|+|||||++.+     ...|||||
T Consensus        81 ~~~~~~~~l~~Yl~~k~r~GVv~~~~~~~~~~~dlYl~P  119 (119)
T PF07744_consen   81 SDRRPFQKLVDYLKSKQRAGVVSVGNSPSGQVKDLYLFP  119 (119)
T ss_dssp             HHHHHHHHTHHHHHHHTEEEEEEE--TT--S-EEEEEE-
T ss_pred             HHHHHHHHHHHHHhhCCEEEEEecCCCCCCceeEEEEcC
Confidence            99999999999999999999999997     68999998

They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.29  E-value=4.9e-12  Score=133.70  Aligned_cols=78  Identities=22%  Similarity=0.284  Sum_probs=68.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSY   74 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~   74 (724)
                      +||++|+++|+.||+|++|++.      ++||||||+|++.++|++|+++|||..|.|++|+|.||++.....+....|+
T Consensus       119 ~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~~~~~~~lfV  198 (346)
T TIGR01659       119 MTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYV  198 (346)
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccccccccccceeEE
Confidence            6899999999999999999864      4789999999999999999999999999999999999987655444556777


Q ss_pred             CCCC
Q 004908           75 SGTK   78 (724)
Q Consensus        75 sG~~   78 (724)
                      .++.
T Consensus       199 ~nLp  202 (346)
T TIGR01659       199 TNLP  202 (346)
T ss_pred             eCCC
Confidence            7763

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.26  E-value=6.9e-12  Score=98.42  Aligned_cols=56  Identities=39%  Similarity=0.638  Sum_probs=52.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEE
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT   56 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIr   56 (724)
                      +++++|+++|+.||.|..|++..     .+|||||+|++.++|++|++.|||..|+|+.||
T Consensus        10 ~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   10 VTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             SSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            58999999999999999998654     589999999999999999999999999999986

(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 ....

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.25  E-value=3.8e-12  Score=129.05  Aligned_cols=67  Identities=27%  Similarity=0.467  Sum_probs=62.6

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPG   67 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pg   67 (724)
                      |||..|+.+|.+||.|++|++      .+.||||||+|...|||..||++||+.++.||.|+|+||++.+..+
T Consensus        22 VtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~kike   94 (298)
T KOG0111|consen   22 VTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKIKE   94 (298)
T ss_pred             HHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccccC
Confidence            689999999999999999984      4789999999999999999999999999999999999999887763

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

Probab=99.21  E-value=2e-11  Score=126.36  Aligned_cols=66  Identities=15%  Similarity=0.358  Sum_probs=63.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++||++|++||.|.+|++++-+|||||.|++.|.|.+||..|||++++|..+||.|.|.....
T Consensus       176 lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  176 LTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             ccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            589999999999999999999999999999999999999999999999999999999999977654

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

Probab=99.21  E-value=1.2e-11  Score=128.08  Aligned_cols=64  Identities=25%  Similarity=0.462  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      |+.|+||++|.+||+|.+.|+      .++||||||.|-+.+||++||+.|||+.|++|.||-+||.++.
T Consensus        74 I~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   74 IDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             cchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            678999999999999998884      4799999999999999999999999999999999999997665

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.20  E-value=2.2e-11  Score=119.83  Aligned_cols=66  Identities=21%  Similarity=0.326  Sum_probs=60.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +++.||+.+|+.||.|.+|++. ...|||||||++..||++|+..|||+.|+|.+|+||+++.....
T Consensus        22 a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r~   88 (195)
T KOG0107|consen   22 ATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPRG   88 (195)
T ss_pred             cchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCccc
Confidence            5789999999999999999976 57799999999999999999999999999999999999876553

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.19  E-value=2.3e-11  Score=128.28  Aligned_cols=77  Identities=19%  Similarity=0.315  Sum_probs=66.4

Q ss_pred             CHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCC-CCCCCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGK-DYPGSYSG   76 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk-~~p~y~sG   76 (724)
                      .|.||+..|.+||+|.+|.++    -+||||||+|++.+||++|.++|||..|+||+|.|+-|..+...+| .+..|.-|
T Consensus       109 RdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV~n~K~~v~p~~~g  188 (376)
T KOG0125|consen  109 RDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARVHNKKKKVLPYPNG  188 (376)
T ss_pred             cCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhhccCCcccCCCccc
Confidence            578999999999999999964    4789999999999999999999999999999999999987755444 55666555


Q ss_pred             CC
Q 004908           77 TK   78 (724)
Q Consensus        77 ~~   78 (724)
                      -+
T Consensus       189 ~~  190 (376)
T KOG0125|consen  189 WK  190 (376)
T ss_pred             cc
Confidence            43

>smart00361 RRM_1 RNA recognition motif

Probab=99.18  E-value=3.7e-11  Score=99.01  Aligned_cols=57  Identities=23%  Similarity=0.464  Sum_probs=51.3

Q ss_pred             CHHHHHHHhh----hcCceeEee-e--------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEE
Q 004908            2 DEQMLHNAMI----LFGEIERIK-S--------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIM   58 (724)
Q Consensus         2 dEedLrelFS----~FGeI~sVk-t--------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVe   58 (724)
                      .|++|++.|+    +||+|.+|. +        ..+||||||+|.+.++|.+|++.|||+.++|+.|++.
T Consensus         1 ~~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        1 KDEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             CchhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            4789999999    999999984 2        2469999999999999999999999999999999873

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.16  E-value=3.9e-11  Score=124.00  Aligned_cols=80  Identities=26%  Similarity=0.355  Sum_probs=74.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSY   74 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~   74 (724)
                      +|+|+||.+|...|||++||++      .+-|||||.|.+.+||++||..|||-.+..+.|||.||++..+..|+.+.|+
T Consensus        53 MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYv  132 (360)
T KOG0145|consen   53 MTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDSIKDANLYV  132 (360)
T ss_pred             cCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhhhcccceEE
Confidence            4899999999999999999965      3669999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCC
Q 004908           75 SGTKGPRS   82 (724)
Q Consensus        75 sG~~~~rs   82 (724)
                      +|+  ++.
T Consensus       133 SGl--Pkt  138 (360)
T KOG0145|consen  133 SGL--PKT  138 (360)
T ss_pred             ecC--Ccc
Confidence            998  555

>smart00360 RRM RNA recognition motif

Probab=99.14  E-value=1.3e-10  Score=88.12  Aligned_cols=58  Identities=29%  Similarity=0.562  Sum_probs=53.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEE
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIM   58 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVe   58 (724)
                      +++++|+++|..||.|.+|++..      ++|||||+|.+.++|.+|++.|+|..++|++|+|+
T Consensus         8 ~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        8 VTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             cCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            47899999999999999998643      47899999999999999999999999999999884

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

Probab=99.13  E-value=1e-10  Score=127.89  Aligned_cols=63  Identities=25%  Similarity=0.449  Sum_probs=59.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|++|++.     ++||||||+|.+.++|.+|+++|||+.|+|++|+|.+|..+
T Consensus       297 ~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       297 VTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             cCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            6899999999999999999864     57899999999999999999999999999999999999764

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

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.12  E-value=8.3e-11  Score=118.53  Aligned_cols=64  Identities=16%  Similarity=0.355  Sum_probs=59.1

Q ss_pred             CHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +.++|+.+|++||.|-+|.|      ..+||||||.|.+..||++|+++|+|.+|+|+.|+|.+|+-.+.
T Consensus        26 spd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~arygr~   95 (256)
T KOG4207|consen   26 SPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARYGRP   95 (256)
T ss_pred             CHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhcCCC
Confidence            57899999999999999975      45899999999999999999999999999999999999986655

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.12  E-value=8.5e-11  Score=120.33  Aligned_cols=63  Identities=30%  Similarity=0.449  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      .+|++|++||.+||.|.+|.+      ..+||||||+|.+.++|.+||+.|||.-++.-.|+|+||++.
T Consensus       201 ~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  201 MREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             cChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCC
Confidence            479999999999999999974      468999999999999999999999999999999999999975

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

Probab=99.10  E-value=1.4e-10  Score=126.81  Aligned_cols=77  Identities=21%  Similarity=0.256  Sum_probs=64.8

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCC--CCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGK--DYPG   72 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk--~~p~   72 (724)
                      |||++|+++|++||+|++|++      .+++|||||+|.+.++|++|++.||+..|+|+.|+|.|+..+....+  ....
T Consensus        12 vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~~~~~~~v   91 (562)
T TIGR01628        12 VTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNI   91 (562)
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccccccccCCCce
Confidence            689999999999999999986      35789999999999999999999999999999999999975543322  2245


Q ss_pred             CCCCC
Q 004908           73 SYSGT   77 (724)
Q Consensus        73 y~sG~   77 (724)
                      |+.++
T Consensus        92 fV~nL   96 (562)
T TIGR01628        92 FVKNL   96 (562)
T ss_pred             EEcCC
Confidence            55554

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.09  E-value=2.1e-10  Score=121.51  Aligned_cols=66  Identities=18%  Similarity=0.303  Sum_probs=58.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~~~~p   66 (724)
                      |||++|+++|++||+|++|++.      ++||||||+|++.++|++||++|||.+|+|  ++|+|.+|+.....
T Consensus       205 vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       205 ITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             ccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccccc
Confidence            6899999999999999999864      457999999999999999999999999977  68999999865443

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

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

Probab=99.09  E-value=1.9e-10  Score=125.01  Aligned_cols=65  Identities=18%  Similarity=0.274  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      |||++|+++|+.||+|++|++++ .||||||+|.+.++|.+|++.|||..|.|++|+|.+++.+..
T Consensus       288 vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~  353 (481)
T TIGR01649       288 VNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNV  353 (481)
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccc
Confidence            68999999999999999999775 579999999999999999999999999999999999976643

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).

>smart00362 RRM_2 RNA recognition motif

Probab=99.07  E-value=3.9e-10  Score=85.92  Aligned_cols=58  Identities=29%  Similarity=0.503  Sum_probs=53.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCC----CCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEE
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPS----RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIM   58 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~S----RGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVe   58 (724)
                      +++++|+++|.+||+|.+|++...    +|+|||+|.+.++|.+|++.|+|..|.|++|+|.
T Consensus        11 ~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       11 VTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            478999999999999999987654    5999999999999999999999999999999874

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

Probab=99.06  E-value=3.1e-10  Score=123.36  Aligned_cols=64  Identities=20%  Similarity=0.264  Sum_probs=59.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHh--cCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGL--QGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaL--NGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.++||||||+|++.|+|++|++.|  |+..|+|++|+|.||+.+.
T Consensus        14 ~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~   79 (481)
T TIGR01649        14 VVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQE   79 (481)
T ss_pred             CCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcc
Confidence            689999999999999999999999999999999999999999974  7899999999999997543

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=99.02  E-value=4.2e-10  Score=119.16  Aligned_cols=62  Identities=26%  Similarity=0.478  Sum_probs=58.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++.|||..|.|++|+|.||+.
T Consensus       198 ~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       198 ITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            6899999999999999999865      5789999999999999999999999999999999999983

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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.02  E-value=4.8e-10  Score=126.01  Aligned_cols=63  Identities=25%  Similarity=0.550  Sum_probs=58.8

Q ss_pred             CCHHHHHHHhhhc--CceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILF--GEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~F--GeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++|  |+|++|++.  |+||||+|++.++|++|+++|||++|+|++|+|+||++...
T Consensus       245 ~tee~L~~~F~~f~~G~I~rV~~~--rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       245 TTEEIIEKSFSEFKPGKVERVKKI--RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             CCHHHHHHHHHhcCCCceEEEEee--cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            6899999999999  999999875  78999999999999999999999999999999999986543

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

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

Probab=99.01  E-value=5.7e-10  Score=126.07  Aligned_cols=64  Identities=14%  Similarity=0.243  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||+|++|++.      ++||||||+|++.++|.+|+++|||..|+|+.|+|.+|....
T Consensus       216 vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       216 LSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             CCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            5899999999999999999854      479999999999999999999999999999999999998543

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.01  E-value=4.4e-10  Score=90.15  Aligned_cols=56  Identities=32%  Similarity=0.579  Sum_probs=50.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCC-----CCeEEEEeCCHHHHHHHHHHhcCCccCCCcEE
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPS-----RNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT   56 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~S-----RGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIr   56 (724)
                      +++++|+++|+.||.|.+|++...     ||+|||+|.+.++|.+|++.++|..|+|+.|+
T Consensus        10 ~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   10 TTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             --HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            589999999999999999987644     79999999999999999999999999999985

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 ....

>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=98.99  E-value=1.6e-09  Score=83.01  Aligned_cols=59  Identities=27%  Similarity=0.558  Sum_probs=54.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEe
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF   59 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVef   59 (724)
                      +++++|++.|..||+|.++++..     .+|+|||+|.+.++|..|++.++|..++|++|+|.|
T Consensus        11 ~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          11 VTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             cCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            47899999999999999998664     379999999999999999999999999999999975

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.98  E-value=1.2e-09  Score=112.73  Aligned_cols=62  Identities=21%  Similarity=0.287  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC---CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP---SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~---SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||+|++|++..   .+|||||+|++.++|+.|+. |||..|+|++|+|+.+..-
T Consensus        16 tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120         16 ATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            58999999999999999999763   57999999999999999995 9999999999999998643

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.98  E-value=1.1e-09  Score=100.25  Aligned_cols=62  Identities=27%  Similarity=0.479  Sum_probs=57.6

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|..||.|.+|++      ..+||||||+|.+.++|..|++.|+|..|.|++|+|.++..
T Consensus       127 ~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         127 VTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            689999999999999988874      36789999999999999999999999999999999999864

>PLN03213 repressor of silencing 3; Provisional

Probab=98.97  E-value=7.6e-10  Score=121.65  Aligned_cols=62  Identities=10%  Similarity=0.304  Sum_probs=57.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCH--HHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSV--DEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~--EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      |++++|+++|+.||.|.+|++.  .+||||||+|.+.  +++.+||+.|||..++|+.|+|+-|++
T Consensus        22 VTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         22 VGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            6899999999999999999976  3699999999987  789999999999999999999999976

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

Probab=98.96  E-value=8.9e-10  Score=124.52  Aligned_cols=61  Identities=25%  Similarity=0.435  Sum_probs=56.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++.|||+.|+||+|+|.++.
T Consensus       119 ~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       119 LREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            5899999999999999999853      589999999999999999999999999999999998654

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.94  E-value=1.6e-09  Score=116.16  Aligned_cols=64  Identities=17%  Similarity=0.351  Sum_probs=58.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||.|+.|++.      .++|||||+|.+.++|..|+++|||..|+|+.|+|.+|....
T Consensus       307 ~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~  376 (509)
T TIGR01642       307 LGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGA  376 (509)
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCC
Confidence            6899999999999999998754      478999999999999999999999999999999999997543

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.90  E-value=2.3e-09  Score=114.83  Aligned_cols=59  Identities=25%  Similarity=0.414  Sum_probs=54.1

Q ss_pred             HHHHHHhhhcCceeEeeecC---------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            4 QMLHNAMILFGEIERIKSYP---------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~---------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|+++|++||.|++|++.+         ++|||||+|.++++|++|+++|||+.|+|+.|.|.|...
T Consensus       434 edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       434 EDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            67999999999999998753         469999999999999999999999999999999999754

Members of this subfamily are found in plants, metazoa and fungi.

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

Probab=98.83  E-value=6e-09  Score=110.48  Aligned_cols=61  Identities=26%  Similarity=0.343  Sum_probs=56.3

Q ss_pred             HHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++||+++|++||+|++|.+.  ..+|++||+|.+.++|.+|+++|||+.|+|+.|.|.|...+
T Consensus       386 ~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       386 LDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             HHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            47899999999999999875  56899999999999999999999999999999999998654

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=98.83  E-value=7.6e-09  Score=112.83  Aligned_cols=74  Identities=24%  Similarity=0.425  Sum_probs=63.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSYSG   76 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~sG   76 (724)
                      +|||.|+++|+.||+|++|++.  |-||||.|.+.++|.+|+++|||++|+|..|-|.+||+.....+.-+.+..|
T Consensus       271 tTeE~lk~~F~~~G~veRVkk~--rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~~r~~~~~g  344 (506)
T KOG0117|consen  271 TTEETLKKLFNEFGKVERVKKP--RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKKERKAMRQG  344 (506)
T ss_pred             hhHHHHHHHHHhccceEEeecc--cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhccchhhhhcc
Confidence            6899999999999999999986  6699999999999999999999999999999999999865544333333333

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.82  E-value=5.6e-09  Score=104.33  Aligned_cols=65  Identities=22%  Similarity=0.394  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCC---CCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPS---RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~S---RGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      |.|.+|+++|.+||.|.+|.+...   -.||||+|++..||++||..-||..++|-+|+|+|+...+.
T Consensus        18 iRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr~   85 (241)
T KOG0105|consen   18 IREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRS   85 (241)
T ss_pred             hhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCCc
Confidence            578999999999999999987533   36999999999999999999999999999999999987653

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.78  E-value=6.7e-09  Score=113.68  Aligned_cols=67  Identities=21%  Similarity=0.346  Sum_probs=61.5

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPG   67 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pg   67 (724)
                      ++|++|.++|+..|.|.++++      .+.||||||+|.+.++|.+|++.|||.+++||+|+|+|+..+....
T Consensus        30 ~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~~~  102 (435)
T KOG0108|consen   30 GSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKNAE  102 (435)
T ss_pred             ccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccchhH
Confidence            589999999999999999984      4789999999999999999999999999999999999998766543

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.77  E-value=7.7e-09  Score=112.52  Aligned_cols=66  Identities=23%  Similarity=0.356  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCc-cC--CCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRL-FN--DPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~-f~--GRrIrVefAk~~~~p   66 (724)
                      ++|+++|++|++||.|++|.+.+     +||||||+|.+.|.|..||++|||.. +.  ..+|.|.||..++.+
T Consensus       136 ~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  136 CTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             ccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCc
Confidence            48999999999999999999764     89999999999999999999999986 34  468999999776654

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.77  E-value=1.4e-08  Score=106.53  Aligned_cols=66  Identities=21%  Similarity=0.383  Sum_probs=59.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      .+|.+|++.|+.||+|++|+++      ++||||||+|++..+...|.+..+|..|+|++|-|++-+...-+
T Consensus       113 T~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgRTvk  184 (335)
T KOG0113|consen  113 TSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGRTVK  184 (335)
T ss_pred             ccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEeccccccc
Confidence            4799999999999999999854      68999999999999999999999999999999999998755443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=98.76  E-value=1.2e-08  Score=115.09  Aligned_cols=62  Identities=23%  Similarity=0.276  Sum_probs=56.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccC-CCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFN-DPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~-GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|.+|+++     ++||||||+|.+.|+|++|++.|||.+|. |+.|.|+.+..
T Consensus        70 ~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~  137 (578)
T TIGR01648        70 LYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVD  137 (578)
T ss_pred             CCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccccc
Confidence            6899999999999999999864     58999999999999999999999999995 88899887753

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.

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.75  E-value=1.4e-08  Score=103.70  Aligned_cols=80  Identities=24%  Similarity=0.335  Sum_probs=62.6

Q ss_pred             CHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCC--C-CCCC
Q 004908            2 DEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPG--K-DYPG   72 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pg--k-~~p~   72 (724)
                      ..|+||+.|++||+|++..+      .++||||||+|+|.|+|.+|++..| -.|+||+-.|+.|.-...+.  . ..|.
T Consensus        25 ~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~lg~~pR~~~~~~~~  103 (247)
T KOG0149|consen   25 HKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLASLGGKPRPVPPSQPQ  103 (247)
T ss_pred             chHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-CcccccccccchhhhcCccCCCCCCCcc
Confidence            57899999999999998864      4799999999999999999999988 47899999999986533322  2 4455


Q ss_pred             CCCCCCCCCC
Q 004908           73 SYSGTKGPRS   82 (724)
Q Consensus        73 y~sG~~~~rs   82 (724)
                      ..+|....|+
T Consensus       104 ~~~g~~~~~~  113 (247)
T KOG0149|consen  104 QAPGGQQNRP  113 (247)
T ss_pred             cccccccCCc
Confidence            5555444444

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.75  E-value=1.8e-08  Score=103.33  Aligned_cols=60  Identities=20%  Similarity=0.205  Sum_probs=55.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC---CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP---SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~---SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      +||++|+++|+.||+|++|++.+   .+|||||+|++.++|+.|+ .|||..|.|++|.|.-+.
T Consensus        17 tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121         17 ATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            58999999999999999999764   4589999999999999999 899999999999998765

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.75  E-value=9.1e-09  Score=98.83  Aligned_cols=64  Identities=22%  Similarity=0.384  Sum_probs=58.1

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      .+|+++++.|..||+|++|.+      .-.||||.|+|++.++|..||++|||..|.|..|.|+|+.-+.
T Consensus        84 atEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~g  153 (170)
T KOG0130|consen   84 ATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKG  153 (170)
T ss_pred             hhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecC
Confidence            479999999999999999973      2368999999999999999999999999999999999996543

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.72  E-value=1.6e-08  Score=100.59  Aligned_cols=67  Identities=18%  Similarity=0.403  Sum_probs=60.8

Q ss_pred             CCHHHHHHHhhhcCceeEe-------eecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERI-------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPG   67 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sV-------kt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pg   67 (724)
                      |||..|+++|+.||.|.+.       .+..++|||||.|++.|.+++|++.|||+.+++++|+|+||+++...|
T Consensus       108 vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  108 VDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             hhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            6899999999999999763       245789999999999999999999999999999999999998887664

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.69  E-value=1.2e-08  Score=109.48  Aligned_cols=60  Identities=23%  Similarity=0.435  Sum_probs=55.6

Q ss_pred             CCHHHHHHHhhhcCceeEee------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +.|+.||.+|.+||.|++|.      +.+.||||||+|+-.|.|..|.|.|||..++||.|+|..-
T Consensus       125 l~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  125 LREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             echHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            46899999999999999997      4578999999999999999999999999999999999843

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=98.68  E-value=3.4e-08  Score=102.69  Aligned_cols=62  Identities=26%  Similarity=0.450  Sum_probs=57.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      .||..|+.+|.+||.|++||+.      +-||||||++.+.+||.-||..|||..+++|.|.|.|-..
T Consensus       290 ~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  290 ADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             chHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            3789999999999999999965      4799999999999999999999999999999999999754

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=98.60  E-value=6.4e-08  Score=92.37  Aligned_cols=60  Identities=27%  Similarity=0.373  Sum_probs=55.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++||.|++||++.|+|.+|.+.      ..=||+||+|.+.++|.+|+.-+||..++.++|+|+|-
T Consensus        48 ttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   48 TTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             ecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            4899999999999999999754      34599999999999999999999999999999999884

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.58  E-value=7.5e-08  Score=102.74  Aligned_cols=62  Identities=27%  Similarity=0.472  Sum_probs=57.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCc-cCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRL-FNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~-f~GRrIrVefAk~   62 (724)
                      |+|.+|++.|.+||+|++|.+...++||||+|.+.++|+.|.+++-.++ |+|.||+|.|+++
T Consensus       240 v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  240 VLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             hhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            5799999999999999999999999999999999999999998876666 4999999999988

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.57  E-value=1.2e-07  Score=96.18  Aligned_cols=64  Identities=27%  Similarity=0.364  Sum_probs=57.2

Q ss_pred             HHHHHH----HhhhcCceeEeee---cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            3 EQMLHN----AMILFGEIERIKS---YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         3 EedLre----lFS~FGeI~sVkt---~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      .++|++    +|+.||+|.+|..   .+.||-|||.|.+.+.|..|+++|+|..|-|+.++|.||+.+..-
T Consensus        23 ~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdi   93 (221)
T KOG4206|consen   23 KDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDI   93 (221)
T ss_pred             HHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccch
Confidence            345555    9999999999974   468999999999999999999999999999999999999987654

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=98.56  E-value=9.5e-08  Score=104.52  Aligned_cols=71  Identities=20%  Similarity=0.216  Sum_probs=62.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCcc-CCCcEEEEeccCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLF-NDPRITIMFSSSELAPGKDYPGS   73 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f-~GRrIrVefAk~~~~pgk~~p~y   73 (724)
                      +.|++|.-+|++-|+|.+++++      .+||||||+|.+.++|++||+.||+.+| .|+.|+|+-+-.+.+      .|
T Consensus        95 ~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~R------LF  168 (506)
T KOG0117|consen   95 VFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCR------LF  168 (506)
T ss_pred             ccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecce------eE
Confidence            4699999999999999999965      4799999999999999999999999999 899999999875544      36


Q ss_pred             CCCC
Q 004908           74 YSGT   77 (724)
Q Consensus        74 ~sG~   77 (724)
                      +.++
T Consensus       169 iG~I  172 (506)
T KOG0117|consen  169 IGNI  172 (506)
T ss_pred             eccC
Confidence            6666

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.56  E-value=9.6e-08  Score=102.55  Aligned_cols=64  Identities=31%  Similarity=0.469  Sum_probs=57.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +|..+|.++|+.||+|.+|++.    -+||| ||+|++.++|.+||+.|||.+++|+.|.|.....+..
T Consensus        88 ~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   88 IDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             cCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            5788999999999999999965    37999 9999999999999999999999999999988865543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.49  E-value=1.9e-07  Score=100.28  Aligned_cols=66  Identities=24%  Similarity=0.392  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      |||.+|.++|+++|.|.+|++-   .+-|||||+|.+.++|++|+++||...+.|++|+|.|+.++..-
T Consensus        10 v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~~   78 (369)
T KOG0123|consen   10 VTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPSL   78 (369)
T ss_pred             CChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCce
Confidence            6899999999999999999832   47899999999999999999999999999999999999866553

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.48  E-value=3.3e-07  Score=85.09  Aligned_cols=65  Identities=18%  Similarity=0.358  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ||.|+..++|.+||.|..|++.   ..||-|||.|+++.+|++|++.|+|.-++++-|.|.|-.....
T Consensus        30 ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~~   97 (124)
T KOG0114|consen   30 ITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPEDA   97 (124)
T ss_pred             ccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHHH
Confidence            6889999999999999999976   4689999999999999999999999999999999999876543

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.46  E-value=1.6e-07  Score=98.80  Aligned_cols=63  Identities=24%  Similarity=0.327  Sum_probs=59.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|.+|+.+|.+||+|+++.++  |+||||..++...|++||.+|||..|+|..|.|+=||.+..
T Consensus        14 ~~~~elr~lFe~ygkVlECDIv--KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk   76 (346)
T KOG0109|consen   14 ATEQELRSLFEQYGKVLECDIV--KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSK   76 (346)
T ss_pred             cchHHHHHHHHhhCceEeeeee--cccceEEeecccccHHHHhhcccceecceEEEEEeccccCC
Confidence            4789999999999999999998  78999999999999999999999999999999999987743

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.45  E-value=2.6e-07  Score=100.97  Aligned_cols=66  Identities=18%  Similarity=0.297  Sum_probs=57.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCcc-C--CCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLF-N--DPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f-~--GRrIrVefAk~~~~p   66 (724)
                      ++|+|||++|++||.|.+|.+.      .+|||+||+|.+.+||.+|+.+|+.... -  ..+|.|.||..++..
T Consensus        46 ~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er  120 (510)
T KOG0144|consen   46 ASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERER  120 (510)
T ss_pred             ccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhc
Confidence            5899999999999999999754      4789999999999999999999998764 3  468999999877664

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.45  E-value=1.8e-07  Score=104.08  Aligned_cols=65  Identities=26%  Similarity=0.471  Sum_probs=58.8

Q ss_pred             CCHHHHHHHhhhcCceeEee------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+.+|++||.|+.|.      +..+||||||+|.+.++|.+|.+.|||-+|.|+.|+|.--.....
T Consensus       290 ite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  290 ITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             chHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            68999999999999999997      446899999999999999999999999999999999987765544

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.44  E-value=2.8e-07  Score=105.78  Aligned_cols=63  Identities=29%  Similarity=0.413  Sum_probs=60.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      |+|.||.++|+.||+|.+|.+...||||||++....||.+|+.+|+...|.++.|+|.||...
T Consensus       433 v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  433 VTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             hhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            689999999999999999999999999999999999999999999999999999999999543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.37  E-value=4.8e-07  Score=91.33  Aligned_cols=62  Identities=27%  Similarity=0.385  Sum_probs=55.8

Q ss_pred             CHHHHHHHhhhc-CceeEee------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            2 DEQMLHNAMILF-GEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         2 dEedLrelFS~F-GeI~sVk------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      .|..+...|.+| |.|++++      ++.+||||||+|++.|.|.=|.|.||+.+|.|+.|.|.|=.++
T Consensus        62 ~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   62 FETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             hHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            467888999999 8888776      4579999999999999999999999999999999999998766

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.36  E-value=3.6e-07  Score=96.18  Aligned_cols=63  Identities=25%  Similarity=0.455  Sum_probs=58.6

Q ss_pred             CHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +.++||..|.+||.|.+++++  |+|+||.|.-.|+|..||++|||++|.|++++|..+..+...
T Consensus        91 tn~ElRa~fe~ygpviecdiv--kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrt  153 (346)
T KOG0109|consen   91 TNQELRAKFEKYGPVIECDIV--KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT  153 (346)
T ss_pred             cCHHHhhhhcccCCceeeeee--cceeEEEEeeccchHHHHhcccccccccceeeeeeecccccc
Confidence            568999999999999999997  889999999999999999999999999999999999776543

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.32  E-value=7.9e-07  Score=99.39  Aligned_cols=63  Identities=19%  Similarity=0.325  Sum_probs=56.5

Q ss_pred             CHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      .+.+|..+|+.||.|.+|.+-     +-.|||||+|.+..+|.+|++.|||..|+||+|-|+||-...
T Consensus       130 k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  130 KKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             CcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            456999999999999999863     235999999999999999999999999999999999996543

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.30  E-value=9.5e-07  Score=92.43  Aligned_cols=64  Identities=25%  Similarity=0.395  Sum_probs=55.8

Q ss_pred             CHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCcc-CC--CcEEEEeccCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLF-ND--PRITIMFSSSELA   65 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f-~G--RrIrVefAk~~~~   65 (724)
                      .|||+|++|.+||+|++|.+.     .+||||||.|.+..||..||.+|+|..- -|  ..|.|.||..++.
T Consensus        32 ~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdkE  103 (371)
T KOG0146|consen   32 SEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADTDKE  103 (371)
T ss_pred             cHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccchHH
Confidence            599999999999999999865     4799999999999999999999999764 33  5799999976544

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.28  E-value=6.4e-08  Score=96.58  Aligned_cols=65  Identities=18%  Similarity=0.230  Sum_probs=57.1

Q ss_pred             CCHHHHHHHhhhcCceeEee------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      .||.||--.|++||+|.+|.      +.+++||||..|++...-..|+++|||..|.||.|+|+.-..-+.
T Consensus        47 LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Yk~  117 (219)
T KOG0126|consen   47 LTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNYKK  117 (219)
T ss_pred             ccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccccC
Confidence            36778888999999999996      457999999999999999999999999999999999987644333

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.25  E-value=1.1e-06  Score=87.87  Aligned_cols=61  Identities=23%  Similarity=0.298  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      |+|+.|+++|-.-|.|.+|++-      ..+|||||+|.+.|||+=|++-||+-.+-||+|+|.-|.
T Consensus        21 vs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   21 VSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             HHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            5789999999999999999853      478999999999999999999999999999999999987

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.18  E-value=1.2e-06  Score=94.38  Aligned_cols=62  Identities=27%  Similarity=0.416  Sum_probs=56.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      .++++|+-+|+.||.|.++.+++      +-.||||+|++.++.++|.-.|+..+|++++|+|+|+..
T Consensus       251 TtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  251 TTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             ccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            36899999999999999998653      457999999999999999999999999999999999854

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.03  E-value=3.9e-06  Score=87.99  Aligned_cols=64  Identities=22%  Similarity=0.377  Sum_probs=57.9

Q ss_pred             CHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      .+.||-..|-+||.|.+.|++      .+|-||||.|.+..+|..||.+|||..|+=+||||..-+++..
T Consensus       298 gDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  298 GDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             ccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            467999999999999999865      5899999999999999999999999999999999998776543

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.02  E-value=5e-06  Score=93.18  Aligned_cols=67  Identities=15%  Similarity=0.223  Sum_probs=60.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPG   67 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pg   67 (724)
                      ++.++|.++|+.+|.|..+.++      ..||||||+|+-.||+.+|+.++++..|+|+.|+|++|+.+..+.
T Consensus        17 ~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e   89 (678)
T KOG0127|consen   17 STGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSE   89 (678)
T ss_pred             cchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccch
Confidence            4678999999999999988754      469999999999999999999999999999999999998776553

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.99  E-value=4.4e-06  Score=95.47  Aligned_cols=64  Identities=19%  Similarity=0.408  Sum_probs=57.9

Q ss_pred             CHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +-.+++.+|..||.|.+|++-      -+||||||+|-+..+|.+|+++|.++-|-||+|.++||+.+..
T Consensus       626 t~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  626 TKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             HHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccchH
Confidence            457899999999999999853      2599999999999999999999999999999999999987643

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.99  E-value=3.5e-06  Score=85.62  Aligned_cols=62  Identities=19%  Similarity=0.326  Sum_probs=57.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +.|++|+++|..||.|.+|.+.  -||+||+|.+..+|.+||..|||++|+|.++.|+|++...
T Consensus        13 ~~~~d~E~~f~~yg~~~d~~mk--~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen   13 ARERDVERFFKGYGKIPDADMK--NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             cchhHHHHHHhhccccccceee--cccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            4689999999999999999985  6799999999999999999999999999999999998653

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

Probab=97.98  E-value=3.3e-06  Score=94.41  Aligned_cols=56  Identities=32%  Similarity=0.459  Sum_probs=53.0

Q ss_pred             CCHHHHHHHhhhcCceeEeee-cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEE
Q 004908            1 MDEQMLHNAMILFGEIERIKS-YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT   56 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt-~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIr   56 (724)
                      |++++|+++|+.||||..|+. ...||..||+|-|+.+|++|+++||+++|.|++|+
T Consensus        87 Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   87 VSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            789999999999999999984 45789999999999999999999999999999999

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=97.98  E-value=8.8e-06  Score=91.58  Aligned_cols=63  Identities=22%  Similarity=0.307  Sum_probs=56.5

Q ss_pred             HHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            3 EQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      -.+|++||++||+|.-.+++.      .|-|+||++.+.++|.++|+.|+-++|.|+-|.|+-|+.+..
T Consensus       419 AtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNEp~  487 (940)
T KOG4661|consen  419 ATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNEPG  487 (940)
T ss_pred             hhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccCcc
Confidence            468999999999998777552      478999999999999999999999999999999999987754

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.97  E-value=1.2e-05  Score=91.94  Aligned_cols=60  Identities=23%  Similarity=0.356  Sum_probs=55.2

Q ss_pred             CHHHHHHHhhhcCceeEeeec---------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            2 DEQMLHNAMILFGEIERIKSY---------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~---------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      +.++|+.+|.+.|.|.+|.+.         .|.|||||+|.+.++|.+|++.|+|+.|+|..|.|.++.
T Consensus       528 t~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  528 TLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             chhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            578999999999999999653         245999999999999999999999999999999999997

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.64  E-value=4.4e-05  Score=79.64  Aligned_cols=60  Identities=23%  Similarity=0.393  Sum_probs=51.9

Q ss_pred             CCHHHHHHHhhhcCce------eEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEI------ERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI------~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      |+++.|-++|.+|-.-      .+-++.+++||+||.|.+.+|+.+|+.+|||+-++.|+|+..=+
T Consensus       202 vnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  202 VNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             ccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            5788999999999544      34447789999999999999999999999999999999987544

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.62  E-value=7.6e-05  Score=81.20  Aligned_cols=65  Identities=25%  Similarity=0.319  Sum_probs=58.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCC-eEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRN-YSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRG-FAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~~~~   65 (724)
                      ||-+-|+.+..+.|+|.+|.+++..| -|.|||++++.|++|+++|||..|--  =+|||+|||+++-
T Consensus       134 ItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  134 ITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             cchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCccee
Confidence            67788999999999999999987666 89999999999999999999999943  4899999998764

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=97.59  E-value=6.8e-05  Score=81.40  Aligned_cols=61  Identities=15%  Similarity=0.262  Sum_probs=55.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      .+|+||+..|+.||+|.+|++.      ..||||||+|.+...-.+||..||-..++|.-|||.-+-
T Consensus       222 LSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  222 LSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             ccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            3699999999999999999854      469999999999999999999999999999999987654

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.55  E-value=0.00013  Score=79.98  Aligned_cols=65  Identities=15%  Similarity=0.352  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ||++.|..+|+-||+|.+|+++. .+--|.|.|.|...|.-|++.|+|..+-|++|+|.|+|...-
T Consensus       310 VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~v  375 (492)
T KOG1190|consen  310 VTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNV  375 (492)
T ss_pred             cchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccc
Confidence            68999999999999999999764 456999999999999999999999999999999999987644

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=97.52  E-value=0.00015  Score=80.08  Aligned_cols=57  Identities=23%  Similarity=0.328  Sum_probs=51.2

Q ss_pred             HHHHHHhh-hcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            4 QMLHNAMI-LFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         4 edLrelFS-~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++||. +-|+|+-|.+.     ++||||.|+|++.|.+++|+|.||-.+++||+|+|.--
T Consensus        59 qdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   59 QDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             HhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            68999986 57999999853     78999999999999999999999999999999998543

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.44  E-value=6.9e-05  Score=76.37  Aligned_cols=57  Identities=33%  Similarity=0.531  Sum_probs=51.1

Q ss_pred             CHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            2 DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ...+|.+.|.++|+++....  .+++|||+|++.++|.+|++.|+|..++|++|++.++
T Consensus       112 ~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  112 SWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             hHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            35899999999999966555  6899999999999999999999999999999999443

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.42  E-value=0.00024  Score=79.76  Aligned_cols=59  Identities=24%  Similarity=0.466  Sum_probs=52.3

Q ss_pred             HHHHHHhhhcCceeEeeec---------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            4 QMLHNAMILFGEIERIKSY---------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~---------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      |+++..+++||.|.+|.+-         .+-|.-||+|++.+++++|.++|+|+.|+||.|...|=-.
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            5778899999999999853         3568999999999999999999999999999999988543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.36  E-value=0.00017  Score=83.14  Aligned_cols=64  Identities=27%  Similarity=0.405  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      |+|+.|-..|..||.|.+|+++         +.|.||||-|-+..||++|++.|+|..+.+..+++.|++.=.
T Consensus       186 v~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~V~  258 (877)
T KOG0151|consen  186 VDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKAVP  258 (877)
T ss_pred             ccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccccc
Confidence            6899999999999999999976         357899999999999999999999999999999999998543

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.27  E-value=0.00049  Score=77.50  Aligned_cols=61  Identities=23%  Similarity=0.233  Sum_probs=53.9

Q ss_pred             HHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++++.+..++||.|..|.+.+ +-||-||.|.++++|..|+.+|||++|.||-|++.|=..+
T Consensus       467 ~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  467 REDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLE  528 (549)
T ss_pred             HHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehh
Confidence            366777789999999999775 4599999999999999999999999999999999986543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.19  E-value=0.0009  Score=69.41  Aligned_cols=66  Identities=24%  Similarity=0.275  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcCceeEeee-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      |+++||+++|..||+++.+-+     .++.|.|=|.|...+||.+|++.+||..++|++|+|+........
T Consensus        95 V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~~~  165 (243)
T KOG0533|consen   95 VIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPSQS  165 (243)
T ss_pred             cchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcccc
Confidence            678999999999999988864     367899999999999999999999999999999999988655443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.16  E-value=0.0015  Score=72.31  Aligned_cols=62  Identities=16%  Similarity=0.193  Sum_probs=52.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +++++|+++|..||+|+...+.      +...||||+|++.+++..||++- =..++|++|.|+--+..
T Consensus       300 a~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  300 ATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             CCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEecccc
Confidence            4788999999999999877643      22279999999999999999998 66789999999876543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.14  E-value=0.00023  Score=74.11  Aligned_cols=59  Identities=27%  Similarity=0.403  Sum_probs=50.5

Q ss_pred             HHHHHHhh-hcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            4 QMLHNAMI-LFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         4 edLrelFS-~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      |+|...|+ +||+|+++++-     .-+|=++|.|...|+|++|++.|||+.|+|++|..++..-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            45555566 99999999743     3478999999999999999999999999999999999853

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.14  E-value=0.00086  Score=72.54  Aligned_cols=59  Identities=22%  Similarity=0.408  Sum_probs=54.4

Q ss_pred             HHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            3 EQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      +++|++...+||.|.+|.++  ...|-+-|.|.+.++|..||+.|+|+.|+||.|+.....
T Consensus       290 kedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence            47889999999999999988  789999999999999999999999999999999876553

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=97.13  E-value=0.00062  Score=75.53  Aligned_cols=59  Identities=20%  Similarity=0.271  Sum_probs=50.9

Q ss_pred             CHHHHHHHhhhcCceeEeeec-CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            2 DEQMLHNAMILFGEIERIKSY-PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~-~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      |=++|++-|..||.|..+.++ +.+.-+.|.|.+.++|++|+..|||..++||.|+|.|.
T Consensus       549 TWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  549 TWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            557899999999999988764 22223399999999999999999999999999999984

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.10  E-value=0.0011  Score=68.69  Aligned_cols=65  Identities=23%  Similarity=0.259  Sum_probs=52.3

Q ss_pred             CHHHHHHHhhhcCceeEeee-cCC------CCeEEEEeCCHHHHHHHHHHhcCCccC---CCcEEEEeccCCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKS-YPS------RNYSFVEFRSVDEARRAKEGLQGRLFN---DPRITIMFSSSELAP   66 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt-~~S------RGFAFVeF~s~EdA~kAIEaLNGk~f~---GRrIrVefAk~~~~p   66 (724)
                      .-.+|+.+|..|---+...+ ..+      +-+|||+|.+..+|.+|+.+|||..|+   +..|+|++||...+.
T Consensus        47 KpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~  121 (284)
T KOG1457|consen   47 KPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTKR  121 (284)
T ss_pred             CHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCccc
Confidence            45689999999966654432 122      359999999999999999999999995   788999999876554

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.09  E-value=0.00045  Score=71.29  Aligned_cols=61  Identities=13%  Similarity=0.234  Sum_probs=55.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ||||.|.++|..-|.|.+|++-     +.| ||||+|+++-...-|++-|||-.+.++.|+|.+-..
T Consensus        21 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   21 VSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            6899999999999999999864     345 999999999999999999999999999999988643

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.01  E-value=0.00076  Score=69.10  Aligned_cols=61  Identities=20%  Similarity=0.341  Sum_probs=53.3

Q ss_pred             CHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            2 DEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +-+++...|+-||.|..|.+      ..+||||||+|.+.+.+.+|+. |||..|.|+.|+|.+.+-.
T Consensus       114 t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  114 TLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTN  180 (231)
T ss_pred             ccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence            34558999999999986653      2479999999999999999999 9999999999999998755

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=96.93  E-value=0.00085  Score=73.91  Aligned_cols=62  Identities=23%  Similarity=0.365  Sum_probs=53.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-CCCC-eEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-PSRN-YSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-~SRG-FAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~   62 (724)
                      |+-+-|+.+|++||.|.+|.++ +.-| -|.|.|.+.+.|..|+.+|+|+-|-+  =.|||+|++-
T Consensus       162 VslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Skl  227 (492)
T KOG1190|consen  162 VSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKL  227 (492)
T ss_pred             eEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhc
Confidence            4567899999999999999987 4455 48999999999999999999999844  3789999875

>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=96.89  E-value=0.0025  Score=57.67  Aligned_cols=57  Identities=19%  Similarity=0.272  Sum_probs=39.5

Q ss_pred             HHHHHhhhc-CceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            5 MLHNAMILF-GEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         5 dLrelFS~F-GeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      -|+.++.-+ |+|.+|    +.|-|.|.|.+.|.|++|...|+|..+.|++|.|.|....+.
T Consensus        22 RL~qLsdNCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~r~   79 (90)
T PF11608_consen   22 RLRQLSDNCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKNRE   79 (90)
T ss_dssp             HHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S--
T ss_pred             HHHHHhhccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCccc
Confidence            477888888 567666    258999999999999999999999999999999999965544

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=96.83  E-value=0.00076  Score=71.98  Aligned_cols=65  Identities=17%  Similarity=0.223  Sum_probs=52.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++||.|++.|..||+|.++.++      ++|||+||+|++.+.-.+++..- -..|+|++|-+.-|.++...
T Consensus        18 ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~-~h~~dgr~ve~k~av~r~~~   88 (311)
T KOG4205|consen   18 TTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNAR-THKLDGRSVEPKRAVSREDQ   88 (311)
T ss_pred             ccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeeccc-ccccCCccccceeccCcccc
Confidence            4799999999999999999865      58999999999988766665543 34578888888877666544

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.58  E-value=0.0038  Score=50.63  Aligned_cols=40  Identities=25%  Similarity=0.404  Sum_probs=35.9

Q ss_pred             HHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHH
Q 004908            3 EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAK   42 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAI   42 (724)
                      .+++.+.|+.||+|+++.....+.+.||+|++..+|++|+
T Consensus        14 ~~~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   14 AEEVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             HHHHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            3567889999999999998777889999999999999984

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=96.48  E-value=0.0026  Score=67.97  Aligned_cols=64  Identities=17%  Similarity=0.269  Sum_probs=53.0

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|++.|.+||.|.++.+      .+.|||+||+|.+.+..+++ ....-..|+|+.+.|.-|-++..
T Consensus       109 ~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv-~~~~f~~~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  109 TTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKV-TLQKFHDFNGKKVEVKRAIPKEV  178 (311)
T ss_pred             CchHHHhhhhhccceeEeeEEeecccccccccceeeEecccccccee-cccceeeecCceeeEeeccchhh
Confidence            589999999999999988863      36899999999988765555 45678899999999999966543

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=96.43  E-value=0.0068  Score=55.28  Aligned_cols=57  Identities=19%  Similarity=0.351  Sum_probs=39.0

Q ss_pred             CHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCC-----ccCCCcEEEE
Q 004908            2 DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR-----LFNDPRITIM   58 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk-----~f~GRrIrVe   58 (724)
                      +-++|+++|+.||+|.-|...++-.-|||.|.+.++|.+|++.+.-.     .+.+..++++
T Consensus        14 ~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen   14 SREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             CHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            46899999999999999998888889999999999999999988765     4556555543

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.29  E-value=0.0059  Score=66.37  Aligned_cols=57  Identities=14%  Similarity=0.405  Sum_probs=48.1

Q ss_pred             HHHhhhcCceeEeeecC-------CCCeE--EEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            7 HNAMILFGEIERIKSYP-------SRNYS--FVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         7 relFS~FGeI~sVkt~~-------SRGFA--FVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++.|.+||+|.+|.+-+       .-+.+  ||+|.+.|||.+||.+.+|..++||.|+..|..-+
T Consensus       138 ~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGTTK  203 (480)
T COG5175         138 HEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTK  203 (480)
T ss_pred             hhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceEeeecCchH
Confidence            47899999999997432       12334  99999999999999999999999999999998643

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.28  E-value=0.0064  Score=65.13  Aligned_cols=61  Identities=26%  Similarity=0.396  Sum_probs=51.2

Q ss_pred             HHHHHHHhhhcCceeEeeecC--C-----CCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSYP--S-----RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~--S-----RGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      |++..+.+.+||.|.+|-++.  +     -=--||+|+.+++|.+|+-.|||+.|+||.++.+|=+-+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~e  367 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLE  367 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHH
Confidence            467788999999999987652  1     124699999999999999999999999999998886543

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

Probab=96.26  E-value=0.011  Score=53.83  Aligned_cols=62  Identities=21%  Similarity=0.320  Sum_probs=46.4

Q ss_pred             CHHHHHHHhhhc--CceeEe------eecCCCCeEEEEeCCHHHHHHHHHHhcCCccC----CCcEEEEeccCC
Q 004908            2 DEQMLHNAMILF--GEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN----DPRITIMFSSSE   63 (724)
Q Consensus         2 dEedLrelFS~F--GeI~sV------kt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~----GRrIrVefAk~~   63 (724)
                      |.++|.+++...  |+..=+      +.....|||||.|.+.++|.+-.+.++|+.+.    .+...|.||+-+
T Consensus        14 t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAriQ   87 (97)
T PF04059_consen   14 TQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYARIQ   87 (97)
T ss_pred             CHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhHhh
Confidence            456677666654  333222      23346899999999999999999999999996    566788998744

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

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.07  E-value=0.0074  Score=68.84  Aligned_cols=54  Identities=22%  Similarity=0.414  Sum_probs=46.0

Q ss_pred             HHHHHhhhcCceeEeee-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccC-CCcEEEE
Q 004908            5 MLHNAMILFGEIERIKS-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFN-DPRITIM   58 (724)
Q Consensus         5 dLrelFS~FGeI~sVkt-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~-GRrIrVe   58 (724)
                      -|.++|+++|+|..+..     ...+||.|++|++..+|++|+..|||+.|+ +.+..|.
T Consensus        80 vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~  139 (698)
T KOG2314|consen   80 VLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVR  139 (698)
T ss_pred             HHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEEee
Confidence            47899999999988863     247899999999999999999999999984 5566664

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.01  E-value=0.014  Score=64.18  Aligned_cols=63  Identities=21%  Similarity=0.334  Sum_probs=57.2

Q ss_pred             CHHHHHHHhhhcCceeEeeecCCC-CeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSYPSR-NYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~SR-GFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +-+.|-++|-.||.|++|+.++.| |-|.|++-+..+-++|+.-||+..+.|.+|.|++++..-
T Consensus       301 N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~  364 (494)
T KOG1456|consen  301 NCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNF  364 (494)
T ss_pred             chhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccc
Confidence            346788999999999999987765 899999999999999999999999999999999998653

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=95.68  E-value=0.0074  Score=68.21  Aligned_cols=65  Identities=17%  Similarity=0.339  Sum_probs=57.2

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +++..++++...||.+.....      ..++||||.+|.+......|+.+|||+.+.++.|.|..|-....
T Consensus       301 l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~  371 (500)
T KOG0120|consen  301 LTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGAS  371 (500)
T ss_pred             cCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccch
Confidence            468899999999999976653      36899999999999999999999999999999999999965543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=95.57  E-value=0.0064  Score=64.08  Aligned_cols=64  Identities=16%  Similarity=0.276  Sum_probs=57.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +++++|+..|..+|+|++|++.      ..+|||||.|.+..++..|+.. +...+.|++++|++......
T Consensus       197 ~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  197 LTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             cchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            4789999999999999999843      4789999999999999999999 99999999999999986644

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=95.48  E-value=0.027  Score=58.20  Aligned_cols=62  Identities=27%  Similarity=0.426  Sum_probs=56.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccC-CCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFN-DPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~-GRrIrVefAk~   62 (724)
                      ++++.|..+|..|.--.+|+... -++.|||+|.+...|.-|..+|+|-.+- ...++|.||++
T Consensus       158 s~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~K  221 (221)
T KOG4206|consen  158 SESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAKK  221 (221)
T ss_pred             hhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccCC
Confidence            36789999999999999999776 4689999999999999999999999996 89999999874

>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=95.35  E-value=0.024  Score=56.71  Aligned_cols=61  Identities=23%  Similarity=0.296  Sum_probs=48.9

Q ss_pred             HHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhc--CCccCCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQ--GRLFNDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLN--Gk~f~GRrIrVefAk~~   63 (724)
                      .+.|+++|..|+.+..+...++=+=..|.|.+.++|.+|+..|+  |..|.|..|+|.|+...
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             HHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            47899999999999999888877778999999999999999999  99999999999999543

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.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=94.83  E-value=0.016  Score=64.43  Aligned_cols=46  Identities=26%  Similarity=0.408  Sum_probs=39.7

Q ss_pred             HHHHHHhhhcCceeEeeecCC-------------------CCeEEEEeCCHHHHHHHHHHhcCCc
Q 004908            4 QMLHNAMILFGEIERIKSYPS-------------------RNYSFVEFRSVDEARRAKEGLQGRL   49 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~S-------------------RGFAFVeF~s~EdA~kAIEaLNGk~   49 (724)
                      |.|.++|+.+|.|..|++-+.                   |-||||+|++.+.|.+|.+.||-..
T Consensus       246 enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e~  310 (484)
T KOG1855|consen  246 ENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPEQ  310 (484)
T ss_pred             HHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchhh
Confidence            679999999999999986432                   5699999999999999999996544

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=94.82  E-value=0.03  Score=61.01  Aligned_cols=66  Identities=18%  Similarity=0.203  Sum_probs=57.0

Q ss_pred             CCHHHHHHHhhhcCceeEee--------------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK--------------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk--------------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +++.+|.+.|..+|+|..=|              +..+||=|-|+|.+.-.|+.||+.++|+.|.|..|+|.+|......
T Consensus        78 ~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~~v  157 (351)
T KOG1995|consen   78 VCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRTGV  157 (351)
T ss_pred             chHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhccCc
Confidence            57888999999999995322              3468999999999999999999999999999999999999876653

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=94.65  E-value=0.037  Score=57.81  Aligned_cols=51  Identities=22%  Similarity=0.345  Sum_probs=42.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFN   51 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f~   51 (724)
                      ++|++|+.+|+.|--...+++.  .+---|||+|++.+.|.+|+..|+|..|-
T Consensus       222 ~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  222 CTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             CCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            6899999999999877666654  33448999999999999999999987763

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=93.98  E-value=0.1  Score=57.15  Aligned_cols=65  Identities=11%  Similarity=0.141  Sum_probs=56.8

Q ss_pred             CCHHHHHHHhhhcCcee--------Eeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIE--------RIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~--------sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ||.+++.++|+++|.|.        .|+++     .-||=|.|.|-..|+...|++.||+..|.|+.|+|+-|+-+..
T Consensus       146 iT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~K  223 (382)
T KOG1548|consen  146 ITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQMK  223 (382)
T ss_pred             ccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhhc
Confidence            68899999999999995        34443     4689999999999999999999999999999999999976644

>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=93.90  E-value=0.12  Score=47.46  Aligned_cols=57  Identities=16%  Similarity=0.209  Sum_probs=44.7

Q ss_pred             HHHHHHhhhcCceeEee-------------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCc-EEEEecc
Q 004908            4 QMLHNAMILFGEIERIK-------------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR-ITIMFSS   61 (724)
Q Consensus         4 edLrelFS~FGeI~sVk-------------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRr-IrVefAk   61 (724)
                      ..+-+.|++||+|.+..             .....++--|+|++..+|.+|+. .||+.|+|.- |-|.|.+
T Consensus        20 ~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   20 NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMVGVKPCD   90 (100)
T ss_dssp             HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEEEEEE-H
T ss_pred             HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEEEEEEcH
Confidence            45678999999998885             34567899999999999999996 5999999864 5577764

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.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=93.70  E-value=0.15  Score=50.01  Aligned_cols=57  Identities=21%  Similarity=0.314  Sum_probs=45.5

Q ss_pred             HHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            4 QMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      .+|-+.|+.||+|.=|+...  +-=+|+|.+-+.|.+|+ .|+|..++|+.|+|..-.++
T Consensus        51 ~~ll~~~~~~GevvLvRfv~--~~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVG--DTMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEET--TCEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEeC--CeEEEEECccHHHHHHH-ccCCcEECCEEEEEEeCCcc
Confidence            36788999999999888764  47799999999998887 59999999999999876644

; PDB: 1UFW_A 2DNR_A.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.45  E-value=0.051  Score=64.59  Aligned_cols=61  Identities=21%  Similarity=0.280  Sum_probs=55.8

Q ss_pred             HHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCcc--CCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF--NDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f--~GRrIrVefAk~~   63 (724)
                      -.-|.-+|+.||+|.++++.+.-..|.|+|.++|.|..|.++|+|+++  .|-+.+|.||+.-
T Consensus       312 SssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  312 SSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             HHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            346889999999999999988888999999999999999999999996  7889999999854

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=92.87  E-value=0.11  Score=62.23  Aligned_cols=63  Identities=21%  Similarity=0.340  Sum_probs=57.5

Q ss_pred             HHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccCCCC
Q 004908            3 EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSSELA   65 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~~~~   65 (724)
                      -..|...|..||.|..|...+..-||+|.|++...|..|.+.|-|..|+|  ++|+|.||....+
T Consensus       469 ~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  469 VSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             HHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence            46788999999999999999888999999999999999999999999987  5799999976544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.12  E-value=0.36  Score=47.90  Aligned_cols=53  Identities=17%  Similarity=0.295  Sum_probs=44.2

Q ss_pred             HHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            6 LHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         6 LrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +..-.+.||+|.+|... +|.-|.|.|+|..+|++|+.+.+- ..-|..+++.|-
T Consensus       107 V~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen  107 VIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             HHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            34567899999999865 788999999999999999999987 456777777664

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=91.38  E-value=0.089  Score=57.07  Aligned_cols=62  Identities=15%  Similarity=0.331  Sum_probs=51.0

Q ss_pred             CHHHHH--HHhhhcCceeEeeecCCC---------CeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            2 DEQMLH--NAMILFGEIERIKSYPSR---------NYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         2 dEedLr--elFS~FGeI~sVkt~~SR---------GFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +|..|+  +-|..||.|.+|.+.+..         -=++|+|.+.|+|.+||...+|..++|+.|+..|+...
T Consensus        91 de~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gttk  163 (327)
T KOG2068|consen   91 DESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGTTK  163 (327)
T ss_pred             chhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCCCc
Confidence            455555  579999999999865411         13799999999999999999999999999999888654

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=90.31  E-value=0.45  Score=40.54  Aligned_cols=56  Identities=23%  Similarity=0.344  Sum_probs=34.1

Q ss_pred             CHHHHHHHhhhcCcee-----EeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            2 DEQMLHNAMILFGEIE-----RIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         2 dEedLrelFS~FGeI~-----sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +..+|-.++..-+.|.     +|++.  ..|+||+-... .|.++++.|++..++|++|+|+.|
T Consensus        14 ~~~~iv~~i~~~~gi~~~~IG~I~I~--~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   14 TPRDIVGAICNEAGIPGRDIGRIDIF--DNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             -HHHHHHHHHTCTTB-GGGEEEEEE---SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             CHHHHHHHHHhccCCCHHhEEEEEEe--eeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4556777777776665     44454  56999998765 699999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=90.13  E-value=0.21  Score=57.82  Aligned_cols=62  Identities=19%  Similarity=0.266  Sum_probs=54.4

Q ss_pred             CHHHHHHHhh-hcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCcc---CCCcEEEEeccCC
Q 004908            2 DEQMLHNAMI-LFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF---NDPRITIMFSSSE   63 (724)
Q Consensus         2 dEedLrelFS-~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f---~GRrIrVefAk~~   63 (724)
                      |.-.|++|.. ..|.|++.++.+=|..+||.|.++++|..-+.+|||..+   +++.|-|+|+..+
T Consensus       457 TlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~d  522 (718)
T KOG2416|consen  457 TLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRAD  522 (718)
T ss_pred             hHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecchh
Confidence            5678999998 677888888777788999999999999999999999998   7788999999754

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=87.69  E-value=0.42  Score=54.23  Aligned_cols=65  Identities=25%  Similarity=0.306  Sum_probs=53.6

Q ss_pred             CHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPG   67 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pg   67 (724)
                      |-++|...|..||+|.+|.+.-+---|.|+|.+..+|-+|. ...|..|+||-|||-|=+....-+
T Consensus       386 t~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnps~~tn  450 (526)
T KOG2135|consen  386 TIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNPSPVTN  450 (526)
T ss_pred             hHhhhhhhhhhcCccccccccCchhhheeeeeccccccchh-ccccceecCceeEEEEecCCcccC
Confidence            34789999999999999997655457899999999996664 468999999999999988755433

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=86.93  E-value=0.96  Score=49.25  Aligned_cols=51  Identities=16%  Similarity=0.291  Sum_probs=43.5

Q ss_pred             HHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcE
Q 004908            4 QMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI   55 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrI   55 (724)
                      ..|-++|++||+|.+......-.+-.|.|.+..+|++|+. -||++|+|..+
T Consensus       211 s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vm  261 (350)
T KOG4285|consen  211 SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVM  261 (350)
T ss_pred             hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhh-hcCeeeccceE
Confidence            3567899999999988876445699999999999999996 59999998764

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=86.52  E-value=0.33  Score=51.56  Aligned_cols=53  Identities=26%  Similarity=0.363  Sum_probs=43.8

Q ss_pred             CHHHHHHHhhhcCceeEeeecCC------------C------CeEEEEeCCHHHHHHHHHHhcCCccCCCc
Q 004908            2 DEQMLHNAMILFGEIERIKSYPS------------R------NYSFVEFRSVDEARRAKEGLQGRLFNDPR   54 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~S------------R------GFAFVeF~s~EdA~kAIEaLNGk~f~GRr   54 (724)
                      +-.-||++|+.||+|-+|.+.+.            +      -=|.|+|.+-..|.+..+.|||..|+|++
T Consensus        87 ~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen   87 DPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIGGKK  157 (278)
T ss_pred             CHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccCCCC
Confidence            34579999999999999975421            1      12789999999999999999999999975

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=84.85  E-value=1.5  Score=52.01  Aligned_cols=59  Identities=19%  Similarity=0.217  Sum_probs=47.1

Q ss_pred             CCHHHHHHHhhhcCcee-Eeee-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEe
Q 004908            1 MDEQMLHNAMILFGEIE-RIKS-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF   59 (724)
Q Consensus         1 VdEedLrelFS~FGeI~-sVkt-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVef   59 (724)
                      |+-+|+-+.|.-|-.+- +|.+     ....|=+-|-|++.|||.+|.+.|+|+.|.+|+|++..
T Consensus       879 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  879 VTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             ccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            34567778888886663 3332     23568999999999999999999999999999999864

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=83.71  E-value=1.6  Score=49.80  Aligned_cols=61  Identities=16%  Similarity=0.244  Sum_probs=47.6

Q ss_pred             CCHHHHHHHhhhcCceeEeee----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||+||++.|+-++ |+++.+    .+..|=|||+|++.||+++|++. |-+.+..|=|-|=-+...
T Consensus        22 at~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen   22 ATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             ccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCCc
Confidence            48999999999986 666653    45679999999999999999874 555666677777666444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	724
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-04
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-06
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-07
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-07
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-07
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	9e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-06
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-06
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-05
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	6e-06
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-06
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-06
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	8e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-05
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-05
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-05
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	3e-05
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-05
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-05
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-05
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-05
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-05
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-05
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	6e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	9e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-04
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-04
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-04
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-04
2div_A	99	TRNA selenocysteine associated protein; structural	2e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-04
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-04
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-04
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	3e-04
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-04
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-04
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-04
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-04
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-04
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-04
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-04
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	7e-04
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-04

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN--DPRITIM 58
               L      FG I  I      +++++++ S+D A+ A   ++G      D R+ + 
Sbjct: 29 TSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD 88

Query: 59 FSSSELAPG 67
          F+ S  + G
Sbjct: 89 FAKSGPSSG 97

>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 = 56.1 bits (135), Expect = 6e-10
 Identities = 13/52 (25%), Positives = 26/52 (50%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFND 52
          +    L   +   G ++ +   P++ YSF  +R+ +E++RA   L G+   D
Sbjct: 39 VSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVD 90

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 55.8 bits (135), Expect = 8e-10
 Identities = 14/60 (23%), Positives = 27/60 (45%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          + +Q++      FG+I  I+ +P + YSFV F + + A  A   + G       +   + 
Sbjct: 37 LTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 12/62 (19%), Positives = 21/62 (33%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
             E  L      FG I   K YP +   F+++ + ++A      L    F    +   + 
Sbjct: 39  ATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG 98

Query: 61  SS 62
             
Sbjct: 99  KE 100

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 55.7 bits (134), Expect = 6e-09
 Identities = 18/120 (15%), Positives = 42/120 (35%), Gaps = 10/120 (8%)

Query: 1   MDEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
           +  Q L     ++G+++R+K  +  +  + V+    ++A+ A   L G   +   I I  
Sbjct: 16  VTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 75

Query: 60  SSSELAPGKDYPGSYSGTKGPRSEMFFGDQI--RPSQLDMLGPNQSMQPNN--FAGHLQP 115
           S       ++      G +       +G+    R  +           P+      ++ P
Sbjct: 76  SKH-----QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 130

>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 = 43.0 bits (101), Expect = 1e-04
 Identities = 12/67 (17%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRN--YSFVEFRSVDEARRAKEGLQGRLFNDPR-ITI 57
           + E+ L       G + +   +  ++   + ++  SV+EA +A   L      +   + +
Sbjct: 132 VSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV 191

Query: 58  MFSSSEL 64
            FS S +
Sbjct: 192 SFSKSTI 198

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 6/88 (6%)

Query: 1   MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
           + E  L +    +GE+E ++             + V F S   A+   + L         
Sbjct: 18  VRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNI 77

Query: 55  ITIMFSSSELAPGKDYPGSYSGTKGPRS 82
           I            K Y    +G+  P++
Sbjct: 78  IHAQLDIKGQQRMKYYELIVNGSYTPQT 105

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 15/59 (25%), Positives = 25/59 (42%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
          M   +L  A   FG I  +   P RN +FV +  ++ A +A   L G      ++ +  
Sbjct: 25 MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 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 = 52.5 bits (127), Expect = 4e-08
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
          + E +L     + G I  IK     +  + NY+FVE+    +A  A + L G+   +  +
Sbjct: 12 ITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIV 71

Query: 56 TIMFSSSELAPGKDYPGSYS 75
           I ++            +++
Sbjct: 72 KINWAFQS--QQSSSDDTFN 89

>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 = 42.5 bits (101), Expect = 1e-04
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 6/67 (8%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
           +D++ L NA   F             +  SR Y FV F S D+A+ A + +QG+  N   
Sbjct: 99  VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 158

Query: 55  ITIMFSS 61
           + I +++
Sbjct: 159 LRINWAA 165

>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 = 53.5 bits (128), Expect = 4e-08
 Identities = 18/120 (15%), Positives = 42/120 (35%), Gaps = 10/120 (8%)

Query: 1   MDEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
           +  Q L     ++G+++R+K  +  +  + V+    ++A+ A   L G   +   I I  
Sbjct: 47  VTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 106

Query: 60  SSSELAPGKDYPGSYSGTKGPRSEMFFGDQI--RPSQLDMLGPNQSMQPNN--FAGHLQP 115
           S       ++      G +       +G+    R  +           P+      ++ P
Sbjct: 107 SKH-----QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 161

>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 = 53.9 bits (130), Expect = 5e-08
 Identities = 13/62 (20%), Positives = 23/62 (37%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          + E+        +GE   +     R + F+   S   A  AK  L G +     + I F+
Sbjct: 34 ITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA 93

Query: 61 SS 62
          + 
Sbjct: 94 TH 95

>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 = 42.8 bits (101), Expect = 2e-04
 Identities = 19/116 (16%), Positives = 38/116 (32%), Gaps = 6/116 (5%)

Query: 1   MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
           +  ++L  A   FG +E+          +    FVEF +   AR+A E      F     
Sbjct: 108 VSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTT- 166

Query: 56  TIMFSSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAG 111
           T      E     D           +++ +  ++ +P +    G  +    + +  
Sbjct: 167 TPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKA 222

>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 = 53.7 bits (128), Expect = 7e-08
 Identities = 31/184 (16%), Positives = 48/184 (26%), Gaps = 6/184 (3%)

Query: 13  FGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS---SSELAP 66
           FG+I  I   +S   R  +FV F+ V  A  A   +QG  F D  + I ++   S  +A 
Sbjct: 37  FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96

Query: 67  GKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHLQPADIRGPSMPMR 126
            K         +  R             +   G    +          P   + P +   
Sbjct: 97  MKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHH 156

Query: 127 SIGAHGGHETLLSGPDFKDFHSMQDPNAKNLDPNWRRPSPSPGIRTSPTQGIRQPLNHAP 186
             G           P          P A           P     +         L + P
Sbjct: 157 MPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLP 216

Query: 187 GSWD 190
              +
Sbjct: 217 EETN 220

>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 = 43.7 bits (102), Expect = 1e-04
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRN-YSFVEFRSVDEARRAKEGLQG-RLFNDPRITIM 58
            +E ML      F   + ++  P R+  +FVEF +  +A  A++ LQG ++  +  + I 
Sbjct: 219 TNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278

Query: 59  FS 60
           F+
Sbjct: 279 FA 280

>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 = 50.0 bits (120), Expect = 9e-08
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 2   DEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            E+ L +    F E +         +   R  +F+ F + + A +A   + G       +
Sbjct: 38  TERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL 97

Query: 56  TIMFSSSE 63
            I F  ++
Sbjct: 98  VIEFGKNK 105

>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 = 49.2 bits (118), Expect = 1e-07
 Identities = 12/60 (20%), Positives = 26/60 (43%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
            E+M+             +    R+Y+FV F + ++A  A + L G++ +   I +  +
Sbjct: 27 TSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKE-GLQGRLFNDPRITIMF 59
          E  L N    FGEI  I     +  +F++F +   A  A E      + N  R+ + +
Sbjct: 26 ETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW 83

>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 = 48.7 bits (116), Expect = 3e-07
 Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 5/71 (7%)

Query: 13 FGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPG 72
          FG + R+        + VEF    EAR+A   L    F+   + +     E AP   +  
Sbjct: 34 FGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYL-----EWAPIGVFGA 88

Query: 73 SYSGTKGPRSE 83
          +         +
Sbjct: 89 APQKKDSQHEQ 99

>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 = 48.0 bits (115), Expect = 3e-07
 Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 3/76 (3%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          + E+ +      +G+   +  +  + + F+   +   A  AK  L        ++ + F+
Sbjct: 27 ITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA 86

Query: 61 SSELAPGKDYPGSYSG 76
                     G  SG
Sbjct: 87 CH---SASLTSGPSSG 99

>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 = 50.5 bits (120), Expect = 4e-07
 Identities = 17/114 (14%), Positives = 32/114 (28%), Gaps = 3/114 (2%)

Query: 1   MDEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
           M+   + N   L+G +E++K        + VE        RA   L        ++ +  
Sbjct: 17  MNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV 76

Query: 60  SSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDMLGPNQSMQPNNFAGHL 113
           S           G   G+     + F   +              +Q  +   H 
Sbjct: 77  SKQPAIMPGQSYGLEDGS--CSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHF 128

>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 = 49.5 bits (119), Expect = 4e-07
 Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 6/67 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          M ++ L+      G I   +      +  S  Y+FV+F S  +++RA + L G    + R
Sbjct: 15 MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74

Query: 55 ITIMFSS 61
          + + ++ 
Sbjct: 75 LKVSYAR 81

>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 = 51.1 bits (123), Expect = 5e-07
 Identities = 6/62 (9%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          +  Q +H+ +  +  ++       +  +FV   + ++A  A          +  +++   
Sbjct: 34 VTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ 92

Query: 61 SS 62
           +
Sbjct: 93 PT 94

>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 = 47.3 bits (113), Expect = 8e-06
 Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 6/68 (8%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
           + +Q     +  FG +ER        +  S+ Y F E+   D A RAK  L G+      
Sbjct: 107 LTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRT 166

Query: 55  ITIMFSSS 62
           + + ++ +
Sbjct: 167 LYVHWTDA 174

>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 = 47.7 bits (114), Expect = 5e-07
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           + E++L  A   FG++ER+K    ++Y+F+ F   D A +A E + G+      I I+F+
Sbjct: 23  VTEEILEKAFSQFGKLERVKK--LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA 80

Query: 61  SSELAPGKDYPGSYSGTKGPRS 82
                  K+         GP S
Sbjct: 81  KPPDQKRKERKAQRQAASGPSS 102

>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 = 50.0 bits (120), Expect = 5e-07
 Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 6/68 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          + E ML+      G I  I+      +  S  Y++V F+   +A RA + +   +     
Sbjct: 27 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 86

Query: 55 ITIMFSSS 62
          + IM+S  
Sbjct: 87 VRIMWSQR 94

>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 = 44.2 bits (105), Expect = 4e-05
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 4/91 (4%)

Query: 1   MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
           +D + L++    FG I   K       S+ Y FV F + + A RA E + G L ND ++ 
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174

Query: 57  IMFSSSELAPGKDYPGSYSGTKGPRSEMFFG 87
           +    S      +               + G
Sbjct: 175 VGRFKSRKEREAELGARAKEFYPYDVPDYAG 205

>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 = 48.6 bits (116), Expect = 7e-07
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 7/81 (8%)

Query: 2   DEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            E+ ++      G+I++I          +  + FVE+ S  +A  A   + G   +D  I
Sbjct: 52  TEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII 111

Query: 56  TIMFSSSELAPGKDYPGSYSG 76
              + +     G+ Y    SG
Sbjct: 112 RTDWDAGF-KEGRQYGRGRSG 131

>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 = 47.2 bits (113), Expect = 7e-07
 Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 7/78 (8%)

Query: 3   EQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIM 58
           E ++       G  +  K       +  Y FVEF    +A  A   + GR      + + 
Sbjct: 29  EVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN 88

Query: 59  FSSSELAPGKDYPGSYSG 76
           ++++   P     G  SG
Sbjct: 89  WATT---PSSQKSGPSSG 103

>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 = 51.8 bits (123), Expect = 8e-07
 Identities = 95/614 (15%), Positives = 150/614 (24%), Gaps = 204/614 (33%)

Query: 1   MDEQMLHNAMILFGEIERIKS---------YPSRNYSFVEFRSVDEARRAKEGLQGRLF- 50
             E       IL    +              P    S  E   +  ++ A  G   RLF 
Sbjct: 11  TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL-RLFW 69

Query: 51  ----NDPRITIMFSSSELAPGKDYPGSYSG----TKGP--RSEMFFGDQIRPSQLDML-G 99
                   +   F    L    +Y    S      + P   + M+        Q D L  
Sbjct: 70  TLLSKQEEMVQKFVEEVLRI--NYKFLMSPIKTEQRQPSMMTRMYI------EQRDRLYN 121

Query: 100 PNQSMQPNNFAGHLQPADIRGPSM---PMRSIGAHG----GHETL----------LSGPD 142
            NQ     N +       +R   +   P +++   G    G   +              D
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181

Query: 143 FK----DFHSMQDPNA-----KNL----DPNW-RRPSPSPGIRTSPTQGIRQPLNHAPGS 188
           FK    +  +   P       + L    DPNW  R   S  I+      I+  L     S
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK-LRIHSIQAELRRLLKS 240

Query: 189 W----------DVYDA---NQFQRDSKRL---RVDGSMPIDDATFPSRK---IDDH--GL 227
                      +V +A   N F    K L   R    +  D  +  +     +D H   L
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR-FKQV-TDFLSAATTTHISLDHHSMTL 298

Query: 228 VLDQSYGL-GSITGGPASGAFVNVQGRNRLSPVASKV---TAGGFG---RNPID-SDFIW 279
             D+   L                     L                   R+ +   D  W
Sbjct: 299 TPDEVKSLLLKYLDCRPQ----------DLPREVLTTNPRRLSIIAESIRDGLATWDN-W 347

Query: 280 R--------GIIAKG----GTPVCRAR---CVPF---------------GKGIESELPEV 309
           +         II            R        F                  I+S++  V
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV 407

Query: 310 VNCSARTGL------------------------DMLAKH------YAEAIGFDIVFFLPD 339
           VN   +  L                        +  A H      Y     FD    +P 
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP 467

Query: 340 SEDD-FASYTEFLRY-LGSKNRAGVAKFDDGTTLFLVPPSD--FLSKVLKVVG-PERLYG 394
             D  F S+   + + L +       +      +FL    D  FL + ++         G
Sbjct: 468 YLDQYFYSH---IGHHLKNIEHPE--RMTLFRMVFL----DFRFLEQKIRHDSTAWNASG 518

Query: 395 VVLKLPQQAMVPPQTVDKQNIPPPHAEYGLTRPKEEHVLPVDYNRFSHDDSKVQSKMHFP 454
            +L   QQ       +           Y      + ++   D       +  V + + F 
Sbjct: 519 SILNTLQQ-------LKF---------Y------KPYICDND----PKYERLVNAILDFL 552

Query: 455 HASEPLIAHSSSMD 468
              E  +  S   D
Sbjct: 553 PKIEENLICSKYTD 566

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 46.8 bits (112), Expect = 9e-07
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 13 FGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPG 72
          +G I +I       + F++F +    R A E     +    ++ +  SSS   P  D+  
Sbjct: 35 YGHIMQINI--KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHGD 92

>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 = 46.5 bits (111), Expect = 1e-06
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 13 FGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE 63
          FG+I  I   +S   R  +FV F+ V  A  A   +QG  F D  + I ++ ++
Sbjct: 36 FGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 89

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 4/56 (7%)

Query: 1  MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFND 52
             +ML +     G +        +  S+    V+F S + A RA   + G   + 
Sbjct: 20 FTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSG 75

>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 = 47.6 bits (114), Expect = 2e-06
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 6/67 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          M ++   +     GEIE  K      +  S  Y FV +    +A +A   L G       
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 73

Query: 55 ITIMFSS 61
          I + ++ 
Sbjct: 74 IKVSYAR 80

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 46.4 bits (110), Expect = 3e-06
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 3/54 (5%)

Query: 13  FGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE 63
            G+I  I    S  +   +++ F + + A+   E  QG  F    + I FS + 
Sbjct: 57  QGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110

>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 = 45.3 bits (108), Expect = 3e-06
 Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 6/67 (8%)

Query: 2  DEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
           E+ L      +G I  +       S  SR ++FV F +VD+A+ AKE   G   +  RI
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87

Query: 56 TIMFSSS 62
           +   SS
Sbjct: 88 RVSGPSS 94

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 48.2 bits (114), Expect = 3e-06
 Identities = 16/61 (26%), Positives = 25/61 (40%)

Query: 3   EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS 62
           E  +       G+I+RI+   S+N  FV+F+    A  AKE +  +    P         
Sbjct: 157 ESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRR 216

Query: 63  E 63
           E
Sbjct: 217 E 217

>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 = 48.4 bits (116), Expect = 4e-06
 Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 1   MDEQMLHNAMILFGEIE---RIKSYP---SRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
             ++ + + +     +    R+ S     SR +++++  S ++AR   E L G       
Sbjct: 129 YTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT 188

Query: 55  ITIMFSSSELAPGKDYPGSYSGTK 78
           +    S+      +    +  G +
Sbjct: 189 LVTKVSNPLEKSKRTDSATLEGRE 212

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 9/68 (13%), Positives = 21/68 (30%), Gaps = 4/68 (5%)

Query: 1   MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
            ++  ++      G I  +        +  ++ +EF   D A  A       +  +  I 
Sbjct: 53  YNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIV 112

Query: 57  IMFSSSEL 64
              +   L
Sbjct: 113 SHLTECTL 120

>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 = 41.9 bits (99), Expect = 4e-04
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 8/66 (12%)

Query: 2   DEQMLHNAMILFGEIERIK-------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
           DE +L  +   FG IE+I           +   +F+ F + D A RA + +   L  +  
Sbjct: 224 DENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNRE 282

Query: 55  ITIMFS 60
           I++  +
Sbjct: 283 ISVSLA 288

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 44.4 bits (105), Expect = 6e-06
 Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 2/64 (3%)

Query: 2  DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR--LFNDPRITIMF 59
           E  L  A+  FG I  +   P +  + VEF  V  A  A                 + +
Sbjct: 34 VEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNY 93

Query: 60 SSSE 63
          S+S+
Sbjct: 94 STSQ 97

>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 = 44.1 bits (105), Expect = 6e-06
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 6/53 (11%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQG 47
          +D+++LH A I FG+I  I+      +   R ++FVEF   ++A  A + +  
Sbjct: 19 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 71

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 46.5 bits (111), Expect = 8e-06
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 2   DEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            E  +  A   FG I+ I       +   + ++FVE+   + A+ A E +   +     I
Sbjct: 41  GEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI 100

Query: 56  TIMFSSS 62
            +   S+
Sbjct: 101 KVGRPSN 107

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A* Length = 345

 Score = 47.5 bits (112), Expect = 8e-06
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRL---FNDPRITI 57
           +    L   +   G ++ +   P++ YSF  +R+ +E++RA   L G+        +IT+
Sbjct: 32  VSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL 91

Query: 58  MFSSSELAPGKDYP 71
             +  E    K+  
Sbjct: 92  YLNFVEKVQWKELR 105

>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 = 43.7 bits (104), Expect = 8e-06
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 7/63 (11%)

Query: 2  DEQMLHNAMILFGEI---ERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          DE++L++    FG I    +I   P    S+ Y+F+ F S D +  A E + G+   +  
Sbjct: 18 DEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRP 77

Query: 55 ITI 57
          IT+
Sbjct: 78 ITV 80

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 44.3 bits (105), Expect = 1e-05
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 6/88 (6%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
           +  + +  A   FG I   +      +  S+ Y FV F +  +A  A + + G+     +
Sbjct: 27  ITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ 86

Query: 55  ITIMFSSSELAPGKDYPGSYSGTKGPRS 82
           I   +++ +    K    S +   GP S
Sbjct: 87  IRTNWATRKPPAPKSTYESNTKQSGPSS 114

>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 = 43.8 bits (104), Expect = 1e-05
 Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 6/66 (9%)

Query: 2  DEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
           E +L    +  G +          +   + Y FVEF S ++A  A + +         I
Sbjct: 28 SEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI 87

Query: 56 TIMFSS 61
           +  +S
Sbjct: 88 RVNKAS 93

>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 = 43.9 bits (104), Expect = 1e-05
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 13  FGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPG 72
           +G +        + Y+FV++ +   AR A  G  GR+     + I  +     P  D  G
Sbjct: 52  YGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE---PKPDRSG 106

Query: 73  SYSG 76
             SG
Sbjct: 107 PSSG 110

>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 = 43.9 bits (104), Expect = 1e-05
 Identities = 13/95 (13%), Positives = 40/95 (42%), Gaps = 4/95 (4%)

Query: 1   MDEQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI 57
           +  + +++    +G I +I    +  +R  ++V +  + +A+ A + L G   ++  + +
Sbjct: 20  ITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVV 79

Query: 58  MFSSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRP 92
           ++ ++  A  K         +    +  +G    P
Sbjct: 80  LYYNANRAFQK-MDTKKKEEQLKLLKEKYGINTDP 113

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 44.3 bits (104), Expect = 1e-05
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 1   MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
           +   +L+      G+++RI  +  +   + VEF SV  A++AK  L G        T+  
Sbjct: 37  ITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI 96

Query: 60  SSSEL 64
             +  
Sbjct: 97  EYARP 101

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 2/62 (3%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR--LFNDPRITIMFS 60
          E  L  A+  FG I  +   P +  + VEF ++D A+                +    +S
Sbjct: 29 EADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS 88

Query: 61 SS 62
          +S
Sbjct: 89 TS 90

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 44.4 bits (105), Expect = 1e-05
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 6/53 (11%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQG 47
           +D+++LH A I FG+I  I+      +   R ++FVEF   ++A  A + +  
Sbjct: 75  VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 127

>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 = 42.9 bits (102), Expect = 1e-05
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 6/66 (9%)

Query: 2  DEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
              +  A   FG I   +      +  S+ Y FV F +  +A  A + + G+     +I
Sbjct: 19 TTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78

Query: 56 TIMFSS 61
             +++
Sbjct: 79 RTNWAT 84

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 2  DEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           +  L  A   +G +  +  +     ++FVEF    +A  A  GL G++    R+ +   
Sbjct: 13 GKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV--- 69

Query: 61 SSELAPGKDYPGSYSGTKGPRSE 83
            EL+ G      +      R  
Sbjct: 70 --ELSTGMPRRSRFDRPPARRKL 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 = 43.5 bits (103), Expect = 2e-05
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 1   MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
             +  L      FG+I  ++       S+ + FV F +  +A RA+E L G +    +I 
Sbjct: 41  FRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100

Query: 57  I 57
           +
Sbjct: 101 V 101

>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 = 42.6 bits (101), Expect = 2e-05
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 5/67 (7%)

Query: 1  MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
          + E++L+   +  G + ++          +++ FV F+  +    A   L G       I
Sbjct: 28 VREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87

Query: 56 TIMFSSS 62
           +   SS
Sbjct: 88 NVSGPSS 94

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 43.1 bits (102), Expect = 3e-05
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           + E  L+     FG ++ +K      ++FVEF   + A +A E + G+ F +  + +++S
Sbjct: 43  VQESELNEIFGPFGPMKEVK--ILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100

>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 = 43.7 bits (103), Expect = 3e-05
 Identities = 8/70 (11%), Positives = 22/70 (31%), Gaps = 11/70 (15%)

Query: 2   DEQMLHNAMILFGEIE-----------RIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF 50
            E+ L      + +              +K    +  +F+   +   A +A +   G + 
Sbjct: 58  QEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVL 117

Query: 51  NDPRITIMFS 60
               + + F+
Sbjct: 118 FGKPMVVQFA 127

>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 = 42.2 bits (100), Expect = 3e-05
 Identities = 10/48 (20%), Positives = 17/48 (35%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
          +    L             +      Y+FV++   + A RA E L G+
Sbjct: 20 VTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 67

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 42.7 bits (101), Expect = 3e-05
 Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 2/53 (3%)

Query: 13 FGEIERIKSYPSRNYS--FVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE 63
           G +  I    +      +V+  S+  A  A   L GR F    IT  +    
Sbjct: 41 HGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLP 93

>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 = 43.2 bits (102), Expect = 3e-05
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 6/65 (9%)

Query: 2   DEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            E+ L      +G I  +       S  SR ++FV F +VD+A+ AKE   G   +  RI
Sbjct: 59  TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118

Query: 56  TIMFS 60
            + FS
Sbjct: 119 RVDFS 123

>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 = 43.1 bits (102), Expect = 3e-05
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
             E+ +H+    +GEI+ I       +   + Y+ VE+ +  EA+ A EGL G+      
Sbjct: 34  ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP 93

Query: 55  ITIMFSSSELAPGKDYPGSYSGTKGPRS 82
           I++ +      P     G    ++ P  
Sbjct: 94  ISVDWCFVRGPPKGKRRGGRRRSRSPDR 121

>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 = 42.3 bits (100), Expect = 3e-05
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 13 FGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS 62
          +G I +I       + F++F +    R A E     +    ++ +  SSS
Sbjct: 47 YGHIMQINI--KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS 94

>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 = 42.2 bits (100), Expect = 4e-05
 Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 6/54 (11%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGR 48
          +D+++LH A I FG+I  I+      +   R ++FVEF   ++A  A + +   
Sbjct: 24 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES 77

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 42.1 bits (99), Expect = 4e-05
 Identities = 13/69 (18%), Positives = 32/69 (46%), Gaps = 3/69 (4%)

Query: 1  MDEQMLHNAMILFGEIER---IKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI 57
          +  ++L + ++ +G +E    + +        V + S D+AR+A + L G    +  + +
Sbjct: 27 LQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKV 86

Query: 58 MFSSSELAP 66
           +   E+A 
Sbjct: 87 AYIPDEMAA 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 = 41.9 bits (99), Expect = 4e-05
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 9/69 (13%)

Query: 1  MDEQMLHNAMILFGEIERIK---------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
            E+ L       G I+               S  + FVE++  ++A++A + LQG   +
Sbjct: 17 TTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD 76

Query: 52 DPRITIMFS 60
            ++ +  S
Sbjct: 77 GHKLEVRIS 85

>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 = 42.2 bits (100), Expect = 5e-05
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 1  MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
          +D + L++    FG I   K       S+ Y FV F + + A RA E + G L ND ++ 
Sbjct: 17 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 76

Query: 57 I 57
          +
Sbjct: 77 V 77

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 43.4 bits (103), Expect = 5e-05
 Identities = 12/61 (19%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 1   MDEQMLHNAMILFGEIERI-KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
           + E  L        EI  + +   S+  +++EF+S  +A +  E  QG   +   +++ +
Sbjct: 111 ITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170

Query: 60  S 60
           +
Sbjct: 171 T 171

>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 = 42.6 bits (101), Expect = 9e-05
 Identities = 11/68 (16%), Positives = 22/68 (32%), Gaps = 6/68 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
               L  A+        +      +  +R + +V+F S ++  +A E L G       I
Sbjct: 25 KSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEI 83

Query: 56 TIMFSSSE 63
           +      
Sbjct: 84 KLEKPKGR 91

>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 = 41.4 bits (98), Expect = 5e-05
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 6/57 (10%)

Query: 1  MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFN 51
            +Q L      +G+I   K+         + Y FV+F S   A++A   L+     
Sbjct: 17 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ 73

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 41.8 bits (98), Expect = 6e-05
 Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 9/65 (13%)

Query: 3   EQMLHNAMILFGEIERIKSYPSRNYS-------FVEFRSVDEARRAKEGLQGRLFNDPRI 55
           E++       +GE+E +      N         +V+FR  ++A +A   L  R FN   I
Sbjct: 41  EEVFTEMEEKYGEVEEMNVC--DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI 98

Query: 56  TIMFS 60
               S
Sbjct: 99  HAELS 103

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 42.0 bits (99), Expect = 6e-05
 Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 10/70 (14%)

Query: 13  FGEIERIKSYPSRNYS----------FVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS 62
           FG + R+  Y  +             FVEF    E  +A + L GR F   ++       
Sbjct: 49  FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ 108

Query: 63  ELAPGKDYPG 72
           E     D   
Sbjct: 109 ERFDNSDLSA 118

>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 = 40.9 bits (97), Expect = 6e-05
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 6/67 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          +D++ L NA   F             +  SR Y FV F S D+A+ A + +QG+  N   
Sbjct: 13 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 72

Query: 55 ITIMFSS 61
          + I +++
Sbjct: 73 LRINWAA 79

>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 = 41.1 bits (97), Expect = 9e-05
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 1  MDEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGR 48
          + E  L        EI  +     S+  +++EF+S  +A +  E  QG 
Sbjct: 28 ITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 76

>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 Length = 105

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 8/59 (13%)

Query: 13 FGEIERIKSYPSRNYS--------FVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE 63
          +G ++ I+     +          FVEF SV + ++A +GL GR F +  +   +   +
Sbjct: 39 YGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPD 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 = 41.1 bits (97), Expect = 1e-04
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 6/54 (11%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGR 48
            E  L      FG I RI       +  S+ ++F+ F   ++A RA  G+ G 
Sbjct: 27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF 80

>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 = 40.2 bits (95), Expect = 1e-04
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 7/64 (10%)

Query: 1  MDEQMLHNAMILFGEIERIK-------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDP 53
          + +  +      +G+I+ I         + S+ Y++VEF + DEA +A + + G   +  
Sbjct: 16 VTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQ 75

Query: 54 RITI 57
           IT 
Sbjct: 76 EITA 79

>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 = 42.1 bits (99), Expect = 1e-04
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
             E  +      +GEI+ I       +  S+ Y+ VE+ +  +A  AKE L G       
Sbjct: 84  AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT 143

Query: 55  ITIMFS 60
           I + + 
Sbjct: 144 IQVDWC 149

>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 = 40.7 bits (96), Expect = 1e-04
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 1  MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
            +  L      FG+I  ++       S+ + FV F +  +A RA+E L G +    +I 
Sbjct: 27 FRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 86

Query: 57 I 57
          +
Sbjct: 87 V 87

>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 = 40.7 bits (96), Expect = 1e-04
 Identities = 15/62 (24%), Positives = 22/62 (35%), Gaps = 5/62 (8%)

Query: 1  MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
          MDEQ L N +  FG++   +     S  SR   F    S ++         G+    P  
Sbjct: 37 MDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG 96

Query: 56 TI 57
            
Sbjct: 97 VS 98

>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 = 40.6 bits (95), Expect = 2e-04
 Identities = 14/82 (17%), Positives = 24/82 (29%), Gaps = 1/82 (1%)

Query: 1   MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
              Q L + M   G++             VEF   ++   A   L    F        + 
Sbjct: 27  GSWQDLKDHMREAGDVCYAD-VYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI 85

Query: 61  SSELAPGKDYPGSYSGTKGPRS 82
             ++   +      S + GP S
Sbjct: 86  RVKVDGPRSPSYGRSRSSGPSS 107

>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 = 40.3 bits (95), Expect = 2e-04
 Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 12/84 (14%)

Query: 1   MDEQMLHNAMILFGEIERI--KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIM 58
             E+ L         I+    ++  S+ Y+F+EF S ++A+ A      R      I + 
Sbjct: 27  ATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRL- 85

Query: 59  FSSSELAPGKDYPGSYSGTKGPRS 82
               EL   +  P S     GP S
Sbjct: 86  ----ELQGPRGSPNS-----GPSS 100

>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 = 40.4 bits (95), Expect = 2e-04
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 7/66 (10%)

Query: 1  MDEQMLHNAMILFGE-IERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDP 53
          MDE  +  A    GE +  +K      +     Y FVEF  +  A +    + G+     
Sbjct: 21 MDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGA 80

Query: 54 RITIMF 59
               F
Sbjct: 81 TPAKRF 86

>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 = 40.2 bits (95), Expect = 2e-04
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 6/53 (11%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQG 47
          + E ML      FG+I+ I       +  S+ Y F+ F   + ARRA E L G
Sbjct: 17 ITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG 69

>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 = 40.4 bits (95), Expect = 2e-04
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 7/88 (7%)

Query: 1   MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            +E+ML       G I  +      +  SR ++F+ F +  +A+ A + + G+  +   I
Sbjct: 19  TNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI 78

Query: 56  TIMFSS--SELAPGKDYPGSYSGTKGPR 81
            +  +   S  + G+  P + S  + P 
Sbjct: 79  KVEQAKKPSFQSGGRRRPPASSRNRSPS 106

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 40.8 bits (95), Expect = 2e-04
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 4/64 (6%)

Query: 1   MDEQMLHNAMILFGEIERIKSYP--SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT-- 56
           +   +LH     FG + +I ++   ++  + +++     A+ AK  L G+   +   T  
Sbjct: 40  VTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR 99

Query: 57  IMFS 60
           I FS
Sbjct: 100 IDFS 103

>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 = 39.7 bits (93), Expect = 2e-04
 Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 15/84 (17%)

Query: 1  MDEQMLHNAMILFG--EIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIM 58
           + Q +H+   L    +++      ++  +FV   + ++A+ A +      F    + + 
Sbjct: 17 SNCQEVHD---LLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV- 72

Query: 59 FSSSELAPGKDYPGSYSGTKGPRS 82
              +L P      S     GP S
Sbjct: 73 ----QLQPTDALLCS-----GPSS 87

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
            E+ +H+    +GEI+ I       +   + Y+ VE+ +  EA+ A EGL G+      
Sbjct: 35 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP 94

Query: 55 ITI 57
          I++
Sbjct: 95 ISV 97

>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 = 39.5 bits (93), Expect = 3e-04
 Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 8/76 (10%)

Query: 2  DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS 61
            Q L +     G +        ++Y+FV      +A+ A   L G+     RI +    
Sbjct: 22 TSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINV---- 75

Query: 62 SELA-PGKDYPGSYSG 76
           EL+  G+   G  SG
Sbjct: 76 -ELSTKGQKKSGPSSG 90

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.0 bits (94), Expect = 3e-04
 Identities = 19/87 (21%), Positives = 28/87 (32%), Gaps = 5/87 (5%)

Query: 1   MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
           +  + L     + G + R          SR    V F    EA +A     G+L  D  +
Sbjct: 27  VGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM 86

Query: 56  TIMFSSSELAPGKDYPGSYSGTKGPRS 82
            +      L  G  +P       GP S
Sbjct: 87  HVKMDERALPKGDFFPPERPQQSGPSS 113

>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 = 40.6 bits (95), Expect = 3e-04
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 2   DEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           ++  L  A   +G +  +  +     ++FVEF    +A  A   L GR     R+ +  S
Sbjct: 86  NKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145

>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 Length = 112

 Score = 40.1 bits (94), Expect = 3e-04
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 13 FGEIERIKSYP--SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
          FG+I ++  +       + V FR  +EA    + L GR F   +IT   
Sbjct: 50 FGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98

>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 = 39.1 bits (92), Expect = 3e-04
 Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 13 FGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPG 72
          +G +        ++Y+FV     ++A  A  GL    F   R+ +  S+S     +   G
Sbjct: 34 YGPVIECDI--VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS---RLRTASG 88

Query: 73 SYSG 76
            SG
Sbjct: 89 PSSG 92

>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 = 39.6 bits (93), Expect = 4e-04
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 6/57 (10%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
          + E ML      FG IE I+      +  S+ Y F+ F   + A++A E L G    
Sbjct: 38 ITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA 94

>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 = 39.1 bits (92), Expect = 4e-04
 Identities = 7/57 (12%), Positives = 21/57 (36%), Gaps = 6/57 (10%)

Query: 1  MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
          +    L+     +G++ ++       +  S+  +F+ F   D A+     +  +   
Sbjct: 28 LTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF 84

>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 = 39.1 bits (92), Expect = 5e-04
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 1  MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
          +D++ L  A   FG I   K       S+ + FV F S +EA +A   + GR+     + 
Sbjct: 27 IDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY 86

Query: 57 I 57
          +
Sbjct: 87 V 87

>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 = 39.2 bits (92), Expect = 5e-04
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 6/63 (9%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
             E  +      +GEI+ I       +  S+ Y+ VE+ +  +A  AKE L G       
Sbjct: 38  AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT 97

Query: 55  ITI 57
           I +
Sbjct: 98  IQV 100

>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 = 40.7 bits (96), Expect = 5e-04
 Identities = 11/63 (17%), Positives = 17/63 (26%), Gaps = 8/63 (12%)

Query: 1  MDEQMLHNAMILFGEIERIK--------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFND 52
            E+ L      +G +  I            S+   FV F +   A  A+  L       
Sbjct: 15 WSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLP 74

Query: 53 PRI 55
             
Sbjct: 75 GMH 77

>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 = 40.8 bits (96), Expect = 5e-04
 Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 6/67 (8%)

Query: 1   MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
           +++  +   +  FG ++         +  S+ Y+F E+  ++   +A  GL G    D +
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 55  ITIMFSS 61
           + +  +S
Sbjct: 186 LLVQRAS 192

>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 = 39.1 bits (92), Expect = 5e-04
 Identities = 9/65 (13%), Positives = 23/65 (35%), Gaps = 6/65 (9%)

Query: 2  DEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
              L      +G +  +       +   R ++FV F    +A+ A+  + G   +   +
Sbjct: 26 SPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL 85

Query: 56 TIMFS 60
           +  +
Sbjct: 86 RVQVA 90

>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 = 41.8 bits (97), Expect = 6e-04
 Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 6/102 (5%)

Query: 2   DEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
            E  L     ++G I+RI      +S   R Y+F+E+    +   A +   G+  +  R+
Sbjct: 115 TESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 174

Query: 56  TIMFSSSELAPGKDYPGSYSGTKGPRSEMFFGDQIRPSQLDM 97
            +         G        G  G R      +     + D 
Sbjct: 175 LVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDT 216

>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 = 40.3 bits (95), Expect = 6e-04
 Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 12/71 (16%)

Query: 2  DEQMLHNAMILFGEIERIKSYP-----------SRNYSFVEFRSVDEARRAKEGLQGRLF 50
           E+ + +       +  +   P            +N++F+EFRSVDE  +A     G +F
Sbjct: 17 TEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIF 75

Query: 51 NDPRITIMFSS 61
              + I    
Sbjct: 76 QGQSLKIRRPH 86

>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 = 39.7 bits (93), Expect = 7e-04
 Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 10/88 (11%)

Query: 1   MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
           +DE  L      +G IE +K         SR Y FV+F+S   A++A  GL G    + R
Sbjct: 54  VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113

Query: 55  ITIMFSSSELAPGKDYPGSYSGTKGPRS 82
           + +    +  A G   PG          
Sbjct: 114 LKV----ALAASGHQRPGIAGAVGDGNG 137

>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 = 38.5 bits (90), Expect = 8e-04
 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 9/68 (13%)

Query: 13  FGEIERIK---SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA-PGK 68
           +G I  I          ++FVEF    +A  A  G  G  ++  R+ +     E    G+
Sbjct: 46  YGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV-----EFPRSGR 100

Query: 69  DYPGSYSG 76
                 S 
Sbjct: 101 GTGSGPSS 108

>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 = 38.3 bits (89), Expect = 9e-04
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 3  EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKE--GLQGRLFNDPRITIMFS 60
          E  +    + FG++  I     +N +F+E  + + A               +  I I +S
Sbjct: 29 ETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS 88

Query: 61 SS 62
          + 
Sbjct: 89 NH 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	724
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.61
1x5p_A	97	Negative elongation factor E; structure genomics,	99.6
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.6
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.6
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.59
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.58
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.58
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.57
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.56
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.56
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.56
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.56
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.56
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.56
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.56
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.56
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.55
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.55
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.55
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.55
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.54
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.54
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.54
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.54
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.54
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.54
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.54
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.54
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.53
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.53
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.53
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.53
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.53
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.53
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.53
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.53
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.53
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.53
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.52
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.52
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.52
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.52
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.52
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.52
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.52
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.52
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.52
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.52
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.51
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.51
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.51
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.51
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.51
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.51
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.51
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.51
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.5
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.5
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.5
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.5
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.5
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.5
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.5
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.5
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.5
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.49
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.49
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.49
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.49
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.49
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.49
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.49
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.49
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.49
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.49
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.48
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.48
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.48
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.48
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.48
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.48
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.48
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.48
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.47
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.47
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.47
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.47
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.47
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.47
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.46
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.46
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.46
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.46
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.46
2div_A	99	TRNA selenocysteine associated protein; structural	99.45
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.45
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.45
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.45
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.44
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.44
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.44
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.44
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.44
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.44
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.44
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.44
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.43
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.42
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.42
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.42
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.42
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.41
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.41
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.41
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.41
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.41
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.41
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.41
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.41
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.41
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.41
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.4
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.4
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.4
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.4
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.4
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.4
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.4
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.4
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.39
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.39
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.39
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.38
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.37
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.36
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.36
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.35
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.35
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.35
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.35
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.34
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.34
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.34
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.02
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.34
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.33
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.33
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.33
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.33
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.33
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.33
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.33
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.32
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.32
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.32
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.32
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.32
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.31
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.31
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.3
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.29
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.29
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.29
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.29
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.28
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.27
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.27
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.27
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.26
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.26
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.25
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.24
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.24
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.24
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.24
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.23
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.22
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.22
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.21
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.2
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.2
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.19
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.19
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.19
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.16
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.1
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.08
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.05
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.98
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.95
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.71
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.52
1ow1_A	195	Smart/HDAC1 associated repressor protein; beta-alp	97.73
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.64
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.28
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.42
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.36
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.72
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	89.34
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	86.36
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	83.05

>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=99.61  E-value=1.8e-15  Score=126.63  Aligned_cols=66  Identities=21%  Similarity=0.389  Sum_probs=62.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccC--CCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN--DPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~--GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.+.||||||+|.+.++|++|++.|||..|+  |++|+|+||+++...
T Consensus        29 ~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~~~   96 (97)
T 1why_A           29 TSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS   96 (97)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCCC
T ss_pred             CCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCCCC
Confidence            689999999999999999999888999999999999999999999999999  999999999987553

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.5e-15  Score=127.37  Aligned_cols=66  Identities=23%  Similarity=0.403  Sum_probs=62.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++...
T Consensus        25 ~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~   90 (97)
T 1x5p_A           25 MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML   90 (97)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCCC
T ss_pred             CCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCCC
Confidence            689999999999999999999999999999999999999999999999999999999999876543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.60  E-value=8.1e-16  Score=134.64  Aligned_cols=61  Identities=16%  Similarity=0.307  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      +||++|+++|.+||+|.++++..+||||||+|.+.+||++|+++|||..++||+|+|++|+
T Consensus        19 ~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           19 IDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            6899999999999999999999999999999999999999999999999999999999995

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.60  E-value=8.6e-16  Score=131.61  Aligned_cols=62  Identities=26%  Similarity=0.431  Sum_probs=58.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||++
T Consensus        31 ~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           31 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            6899999999999999999854      4689999999999999999999999999999999999975

>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=99.59  E-value=2.8e-15  Score=130.91  Aligned_cols=65  Identities=22%  Similarity=0.261  Sum_probs=60.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCC--ccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR--LFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk--~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++.+.||||||+|++.++|.+|++.|||.  .|+|++|+|+||+.+..
T Consensus        27 ~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           27 VVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             CCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCccc
Confidence            689999999999999999999999999999999999999999999875  49999999999986544

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.58  E-value=2.2e-15  Score=133.05  Aligned_cols=63  Identities=24%  Similarity=0.259  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCc--cCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRL--FNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~--f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|++|++.+.||||||+|++.++|.+|++.|||..  |+|++|+|+||+.+
T Consensus        33 ~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           33 VVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             CCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            6899999999999999999999999999999999999999999999986  78999999999865

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=2.1e-15  Score=134.04  Aligned_cols=66  Identities=17%  Similarity=0.258  Sum_probs=61.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcC--CccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQG--RLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNG--k~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.+.||||||+|++.++|++|++.|+|  ..|+|++|+|+||+.+...
T Consensus        28 vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~   95 (105)
T 1sjq_A           28 VTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK   95 (105)
T ss_dssp             SCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCC
Confidence            68999999999999999999999999999999999999999999874  7899999999999876544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.57  E-value=1.5e-15  Score=127.70  Aligned_cols=63  Identities=19%  Similarity=0.292  Sum_probs=60.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++||+|++|++.++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++
T Consensus        39 ~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           39 ATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             CCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             cCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            689999999999999999999999999999999999999999999999999999999999863

>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=99.57  E-value=3e-15  Score=125.73  Aligned_cols=65  Identities=12%  Similarity=0.264  Sum_probs=62.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++.+.||||||+|.+.++|++|++.|||..|+|++|+|+||+.+..
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           27 ITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             CCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             CCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999987544

>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=99.56  E-value=6.8e-15  Score=125.80  Aligned_cols=66  Identities=21%  Similarity=0.464  Sum_probs=62.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|.+|++.+.||||||+|.+.++|.+|++.|||..|+|++|+|+||+.+...
T Consensus        37 ~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           37 LTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM  102 (109)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSS
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCC
Confidence            689999999999999999999988999999999999999999999999999999999999877654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.56  E-value=2.3e-15  Score=126.73  Aligned_cols=67  Identities=19%  Similarity=0.330  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcC-ceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhc-CCccCCCcEEEEeccCCCCCC
Q 004908            1 MDEQMLHNAMILFG-EIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQ-GRLFNDPRITIMFSSSELAPG   67 (724)
Q Consensus         1 VdEedLrelFS~FG-eI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLN-Gk~f~GRrIrVefAk~~~~pg   67 (724)
                      +||++|+++|++|| +|++|++.      ++||||||+|.+.++|.+|++.|+ |..|+|++|+|+||+++....
T Consensus        13 ~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~~~   87 (91)
T 2lxi_A           13 ATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKIN   87 (91)
T ss_dssp             CCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCCCS
T ss_pred             CCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCCCC
Confidence            68999999999999 89999853      579999999999999999999985 567999999999998765543

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.56  E-value=3.1e-15  Score=130.87  Aligned_cols=64  Identities=17%  Similarity=0.186  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|++.++|++|++.|||+.|+|++|+|++|+...
T Consensus        18 ~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~~   87 (110)
T 3s8s_A           18 VRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQ   87 (110)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTTH
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            6899999999999999999863      578999999999999999999999999999999999997553

>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=99.56  E-value=9.1e-15  Score=127.07  Aligned_cols=64  Identities=19%  Similarity=0.189  Sum_probs=61.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|.+|++.++||||||+|.+.++|++|++.|||..|+|++|+|+||+...
T Consensus        22 ~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A           22 TLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            5899999999999999999999999999999999999999999999999999999999998653

>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=99.56  E-value=9e-15  Score=123.28  Aligned_cols=66  Identities=18%  Similarity=0.316  Sum_probs=61.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.+    +||||||+|.+.++|.+|++.|||..|+|++|+|+||+.....
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           27 VTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCC
T ss_pred             CCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCccc
Confidence            68999999999999999999764    6899999999999999999999999999999999999876554

>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=2.9e-15  Score=131.44  Aligned_cols=65  Identities=17%  Similarity=0.131  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCC--ccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR--LFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk--~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++|++.+.||||||+|++.++|.+|++.|||.  .|+|++|+|+||+....
T Consensus        28 ~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~   94 (102)
T 1x4d_A           28 NLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR   94 (102)
T ss_dssp             SHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTT
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCCC
Confidence            579999999999999999999999999999999999999999999975  49999999999986543

>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=99.56  E-value=3.6e-15  Score=129.74  Aligned_cols=64  Identities=31%  Similarity=0.472  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.    .+||||||+|.+.++|++|+++|||..|+|++|+|++|+.+.
T Consensus        17 ~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~   84 (115)
T 4f25_A           17 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   84 (115)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCC
T ss_pred             CCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcc
Confidence            6899999999999999999865    358999999999999999999999999999999999997654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.3e-14  Score=119.98  Aligned_cols=64  Identities=19%  Similarity=0.267  Sum_probs=60.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.  ||||||+|.+.++|++|++.|||..|+|++|+|+||++....
T Consensus        20 ~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           20 ATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKA   83 (90)
T ss_dssp             CCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCC
T ss_pred             CCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCC
Confidence            6899999999999999999987  899999999999999999999999999999999999876554

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.2e-14  Score=120.37  Aligned_cols=66  Identities=29%  Similarity=0.443  Sum_probs=60.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+.+...
T Consensus        17 ~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           17 ITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG   88 (95)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCC
T ss_pred             CCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCC
Confidence            6899999999999999999864      36899999999999999999999999999999999999876654

>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=99.55  E-value=1.4e-14  Score=122.64  Aligned_cols=64  Identities=30%  Similarity=0.583  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.  ||||||+|.+.++|.+|++.|||..|+|++|+|+||++....
T Consensus        23 ~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           23 VTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            6899999999999999999986  789999999999999999999999999999999999876554

>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=3.3e-15  Score=121.38  Aligned_cols=61  Identities=25%  Similarity=0.408  Sum_probs=59.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHh-cCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGL-QGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaL-NGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|.+|++.++||||||+|.+.++|.+|++.| ||..|+|++|+|+||+
T Consensus        24 ~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           24 ITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            589999999999999999999999999999999999999999999 9999999999999986

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.1e-14  Score=124.26  Aligned_cols=66  Identities=21%  Similarity=0.370  Sum_probs=60.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.   .+||||||+|++.++|++|++.|||..|+|++|+|+||+..+..
T Consensus        34 ~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  102 (109)
T 1x4a_A           34 IRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT  102 (109)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCCC
Confidence            6899999999999999999875   36899999999999999999999999999999999999876554

>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=99.54  E-value=9e-15  Score=123.05  Aligned_cols=65  Identities=14%  Similarity=0.278  Sum_probs=59.9

Q ss_pred             CCHHHHH----HHhhhcCceeEeeecCC---CCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLH----NAMILFGEIERIKSYPS---RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLr----elFS~FGeI~sVkt~~S---RGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+    ++|++||+|++|++...   ||||||+|.+.++|.+|++.|||..|+|++|+|++|++...
T Consensus        21 ~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~   92 (96)
T 2dgx_A           21 LSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGASG   92 (96)
T ss_dssp             SCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSSC
T ss_pred             CCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            5899999    99999999999997633   89999999999999999999999999999999999986654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.4e-14  Score=121.55  Aligned_cols=66  Identities=23%  Similarity=0.434  Sum_probs=60.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.+      +||||||+|.+.++|.+|++.|||..|+|++|+|+||++....
T Consensus        24 ~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   95 (102)
T 1x5s_A           24 TNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   95 (102)
T ss_dssp             CCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            68999999999999999998753      6899999999999999999999999999999999999876543

>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=1.4e-14  Score=124.74  Aligned_cols=76  Identities=21%  Similarity=0.267  Sum_probs=65.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSY   74 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~   74 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.||| .|+|++|+|+||+....+.+..+.+.
T Consensus        29 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~~~~~~~~~~~~  107 (116)
T 2cqd_A           29 TTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFA  107 (116)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTCCCCCCCCCCS
T ss_pred             CCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccCCCccccCCCcc
Confidence            6899999999999999999865      3689999999999999999999999 89999999999987766655545554


Q ss_pred             CCC
Q 004908           75 SGT   77 (724)
Q Consensus        75 sG~   77 (724)
                      .|.
T Consensus       108 ~g~  110 (116)
T 2cqd_A          108 IGV  110 (116)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            443

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.54  E-value=6.4e-15  Score=119.81  Aligned_cols=63  Identities=21%  Similarity=0.374  Sum_probs=57.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++||+|.+|++..      +||||||+|.+.++|++|++.|||..|+|++|+|+||+++
T Consensus        18 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           18 ITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             CCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            68999999999999999998643      5799999999999999999999999999999999999865

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=7.6e-15  Score=122.43  Aligned_cols=66  Identities=23%  Similarity=0.402  Sum_probs=60.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.         ++||||||+|.+.++|++|++.|||..|+|++|+|+||+....+
T Consensus        17 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (98)
T 2cpf_A           17 TTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKP   91 (98)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCCC
Confidence            6899999999999999999865         45799999999999999999999999999999999999876554

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=1.7e-14  Score=121.72  Aligned_cols=66  Identities=20%  Similarity=0.447  Sum_probs=60.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-------CCCeEEEEeCCHHHHHHHHHHh-cCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-------SRNYSFVEFRSVDEARRAKEGL-QGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-------SRGFAFVeF~s~EdA~kAIEaL-NGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.+       +||||||+|.+.++|.+|++.| ||..|+|++|+|+||+++...
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~  100 (107)
T 2cph_A           27 ANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV  100 (107)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCC
T ss_pred             CCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCC
Confidence            68999999999999999998754       3899999999999999999999 999999999999999876543

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=9.3e-15  Score=132.08  Aligned_cols=66  Identities=17%  Similarity=0.258  Sum_probs=61.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcC--CccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQG--RLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNG--k~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.+.||||||+|++.++|.+|++.|||  ..|+|++|+|+||+.+...
T Consensus        43 vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~  110 (119)
T 2ad9_A           43 VTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELK  110 (119)
T ss_dssp             CCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCC
Confidence            68999999999999999999998999999999999999999999984  6899999999999876554

>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=99.54  E-value=1.9e-14  Score=121.25  Aligned_cols=66  Identities=23%  Similarity=0.421  Sum_probs=61.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++..    +||||||+|.+.++|++|++.|||..|+|++|+|+||+.+...
T Consensus        27 ~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           27 FRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMT   96 (103)
T ss_dssp             CCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCC
Confidence            68999999999999999999763    4899999999999999999999999999999999999877654

>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=99.54  E-value=8.4e-15  Score=127.55  Aligned_cols=66  Identities=17%  Similarity=0.216  Sum_probs=60.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhc--CCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQ--GRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLN--Gk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.+.||||||+|++.++|.+|++.|+  |..|+|++|+|+||+.+...
T Consensus        27 ~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~   94 (101)
T 2cq1_A           27 VTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELK   94 (101)
T ss_dssp             CCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCc
Confidence            6899999999999999999999999999999999999999999874  67899999999999866543

>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=99.54  E-value=7.7e-15  Score=132.22  Aligned_cols=65  Identities=20%  Similarity=0.348  Sum_probs=61.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCcc-----CCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF-----NDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f-----~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++|.+..+||||||+|++.++|++|+++|||++|     .|++|.|+||+.-..
T Consensus        39 ~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~p~  108 (114)
T 2cq2_A           39 VSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQW  108 (114)
T ss_dssp             CCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccCcc
Confidence            68999999999999999999988999999999999999999999999998     799999999986544

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.54  E-value=8.8e-15  Score=118.06  Aligned_cols=63  Identities=30%  Similarity=0.446  Sum_probs=58.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+++
T Consensus        13 ~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           13 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             CCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            5899999999999999999865      34899999999999999999999999999999999999865

>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=99.54  E-value=2.1e-14  Score=119.95  Aligned_cols=66  Identities=17%  Similarity=0.337  Sum_probs=60.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+.+...
T Consensus        20 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (99)
T 1whw_A           20 SSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             CCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCccc
Confidence            6899999999999999999864      36799999999999999999999999999999999999877654

>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=2.1e-14  Score=123.27  Aligned_cols=66  Identities=20%  Similarity=0.353  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|+.||+|++|++..      +||||||+|.+.++|++|++.|||..|+|++|+|+||+.....
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           27 ITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA   98 (115)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCC
Confidence            68999999999999999998653      4799999999999999999999999999999999999876554

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=1.1e-14  Score=122.71  Aligned_cols=66  Identities=26%  Similarity=0.450  Sum_probs=61.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.    ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++...
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2d9p_A           27 IDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEER   96 (103)
T ss_dssp             CCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccC
Confidence            6899999999999999999976    56899999999999999999999999999999999999876543

>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=1.1e-14  Score=122.16  Aligned_cols=66  Identities=26%  Similarity=0.446  Sum_probs=60.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||++....
T Consensus        24 ~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2cqb_A           24 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   95 (102)
T ss_dssp             CCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCC
Confidence            6899999999999999999864      36899999999999999999999999999999999999876554

>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=1.2e-14  Score=118.09  Aligned_cols=64  Identities=23%  Similarity=0.387  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|.+|++.       +++|||||+|.+.++|.+|++.|||..|+|++|+|++|++..
T Consensus        16 ~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           16 VTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             CCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence            6899999999999999999863       278999999999999999999999999999999999997653

>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=1.2e-14  Score=119.98  Aligned_cols=61  Identities=13%  Similarity=0.263  Sum_probs=57.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+|||
T Consensus        28 ~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           28 LTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             SCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            5899999999999999999864      468999999999999999999999999999999999986

>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=99.53  E-value=5.3e-15  Score=132.43  Aligned_cols=65  Identities=11%  Similarity=0.156  Sum_probs=60.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcC--CccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQG--RLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNG--k~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++.++||||||+|++.++|.+|++.|||  ..|+|++|+|+||+....
T Consensus        38 ~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~  104 (112)
T 1x4f_A           38 YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK  104 (112)
T ss_dssp             CCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSS
T ss_pred             CCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccccc
Confidence            58999999999999999999999999999999999999999999865  569999999999986544

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.53  E-value=2.7e-14  Score=120.66  Aligned_cols=66  Identities=20%  Similarity=0.268  Sum_probs=60.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCcc---CCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLF---NDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f---~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..+   +|++|+|.||+.+...
T Consensus        25 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           25 LDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG   99 (106)
T ss_dssp             CCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCC
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccccc
Confidence            6899999999999999999865      3689999999999999999999999998   9999999999876543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.53  E-value=1.4e-14  Score=121.57  Aligned_cols=64  Identities=20%  Similarity=0.324  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|.+|++.  ||||||+|.+.++|.+|++.|||..|+|++|+|+||+....+
T Consensus        23 ~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   86 (96)
T 2kvi_A           23 VSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARP   86 (96)
T ss_dssp             CCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC-
T ss_pred             CCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCCC
Confidence            5899999999999999999984  899999999999999999999999999999999999876654

>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=1.2e-14  Score=117.83  Aligned_cols=61  Identities=28%  Similarity=0.511  Sum_probs=57.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+
T Consensus        19 ~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           19 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            5899999999999999999863      368999999999999999999999999999999999986

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.52  E-value=9.1e-15  Score=120.37  Aligned_cols=66  Identities=20%  Similarity=0.247  Sum_probs=60.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.+    +||||||+|.+.++|++|++.|||..|+|++|+|+||+....+
T Consensus        20 ~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~   89 (92)
T 2dgv_A           20 FTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGP   89 (92)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCSSC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCCC
Confidence            58999999999999999998653    6899999999999999999999999999999999999876553

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.52  E-value=1.4e-14  Score=121.72  Aligned_cols=66  Identities=21%  Similarity=0.390  Sum_probs=61.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.+ +||||||+|.+.++|.+|++.|||..|+|++|+|+||+.....
T Consensus        12 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A           12 AGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCS
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCc
Confidence            68999999999999999999876 5999999999999999999999999999999999999876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=3.6e-14  Score=118.83  Aligned_cols=65  Identities=12%  Similarity=0.220  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++ |||..|+|++|+|+||+++...
T Consensus        22 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~~   92 (99)
T 2dgs_A           22 CGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDSK   92 (99)
T ss_dssp             CCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCccc
Confidence            6899999999999999999875      368999999999999999999 9999999999999999876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.3e-14  Score=120.27  Aligned_cols=66  Identities=27%  Similarity=0.492  Sum_probs=60.4

Q ss_pred             CCHHHHHHHhhhcCceeEe-eec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERI-KSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sV-kt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|.+| ++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+++...
T Consensus        17 ~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   89 (96)
T 1x5t_A           17 IDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   89 (96)
T ss_dssp             CCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCC
Confidence            6899999999999999999 754      35899999999999999999999999999999999999876554

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.52  E-value=1.8e-14  Score=120.40  Aligned_cols=65  Identities=22%  Similarity=0.346  Sum_probs=60.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||++...
T Consensus        14 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           14 QTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            6899999999999999999864      3589999999999999999999999999999999999987653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.7e-14  Score=121.91  Aligned_cols=64  Identities=27%  Similarity=0.428  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||+|.+|++.      .+||||||+|.+.++|.+|++.|||..|+|++|+|+||+++.
T Consensus        35 ~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           35 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             CCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            6899999999999999999864      358999999999999999999999999999999999998654

>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=99.52  E-value=6e-15  Score=122.50  Aligned_cols=65  Identities=18%  Similarity=0.237  Sum_probs=55.5

Q ss_pred             CCHHHHHHHhhhcC--ceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFG--EIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FG--eI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||  +|.+|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|.+|++...
T Consensus        13 ~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           13 TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH   85 (90)
T ss_dssp             CCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-----
T ss_pred             CCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCcc
Confidence            68999999999999  99999853      4689999999999999999999999999999999999986644

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=2.4e-14  Score=120.74  Aligned_cols=66  Identities=20%  Similarity=0.219  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+.+...
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           27 VSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcC
Confidence            6899999999999999999864      36799999999999999999999999999999999999876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=2.2e-14  Score=120.30  Aligned_cols=66  Identities=15%  Similarity=0.288  Sum_probs=60.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.     ++||||||+|.+.++|.+|++.|||..|+|++|+|+||++....
T Consensus        29 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   99 (100)
T 2do4_A           29 CTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS   99 (100)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSCC
T ss_pred             CCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCCC
Confidence            6899999999999999999865     35699999999999999999999999999999999999876543

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.52  E-value=2.4e-14  Score=120.80  Aligned_cols=66  Identities=23%  Similarity=0.342  Sum_probs=60.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCC---CcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFND---PRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~G---RrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++..     +||||||+|.+.++|++|++.|||..|.|   ++|+|+||+.+...
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~  100 (105)
T 2dnh_A           27 QSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES  100 (105)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCccc
Confidence            68999999999999999998763     48999999999999999999999999998   99999999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=1.8e-14  Score=121.49  Aligned_cols=66  Identities=14%  Similarity=0.305  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+..+..
T Consensus        25 ~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dnm_A           25 TSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD   96 (103)
T ss_dssp             CCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCSC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCCC
Confidence            6899999999999999999864      46899999999999999999999999999999999999876543

>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=99.51  E-value=2.4e-14  Score=121.44  Aligned_cols=62  Identities=19%  Similarity=0.315  Sum_probs=58.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|.+|++  .||||||+|.+.++|.+|++.|||..|+|++|+|+||+...
T Consensus        35 ~t~~~L~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           35 VSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEE--CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            589999999999999999998  49999999999999999999999999999999999998653

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.51  E-value=3e-14  Score=120.95  Aligned_cols=66  Identities=14%  Similarity=0.343  Sum_probs=61.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhc------CCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQ------GRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLN------Gk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|+.||+|++|++.      ++||||||+|.+.++|.+|++.||      |..|+|++|+|+||+++...
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           27 SEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccC
Confidence            6899999999999999999865      469999999999999999999999      99999999999999876554

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=1.4e-14  Score=119.51  Aligned_cols=62  Identities=32%  Similarity=0.474  Sum_probs=58.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+.
T Consensus        27 ~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            6899999999999999999864      4589999999999999999999999999999999999985

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=1.2e-14  Score=122.42  Aligned_cols=66  Identities=23%  Similarity=0.406  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++...
T Consensus        27 ~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS   98 (103)
T ss_dssp             CCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCS
T ss_pred             CCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCC
Confidence            6899999999999999999864      35799999999999999999999999999999999999876554

>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=3.7e-14  Score=117.65  Aligned_cols=64  Identities=23%  Similarity=0.415  Sum_probs=59.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.  |+||||+|.+.++|.+|++.|||..|+|++|+|+||+.+...
T Consensus        22 ~t~~~l~~~F~~~G~v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   85 (92)
T 2dgt_A           22 CTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT   85 (92)
T ss_dssp             CCHHHHHHHHHTTSCCCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCSC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCCC
Confidence            6899999999999999999987  779999999999999999999999999999999999876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=4.3e-14  Score=120.78  Aligned_cols=66  Identities=21%  Similarity=0.260  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++..     +||||||+|.+.++|++|++.|||..|+|++|+|+||+.....
T Consensus        27 ~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   97 (114)
T 2do0_A           27 VGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPK   97 (114)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCCCC
Confidence            68999999999999999998653     4899999999999999999999999999999999999865443

>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=99.51  E-value=1.5e-14  Score=119.98  Aligned_cols=65  Identities=18%  Similarity=0.149  Sum_probs=58.4

Q ss_pred             CCHHHHHHHhhhcCc-eeEeeecCCCCeEEEEeCCHHHHHHHHHHhcC-CccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGE-IERIKSYPSRNYSFVEFRSVDEARRAKEGLQG-RLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGe-I~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNG-k~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+ |..+.+ .+||||||+|.+.++|++|++.||| ..|+|++|+|+||+++...
T Consensus        20 ~t~~~l~~~F~~~G~vv~~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   86 (93)
T 2cqh_A           20 VTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   86 (93)
T ss_dssp             CCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CCHHHHHHHHHHcCCceEEEEE-cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcccc
Confidence            689999999999999 555554 5899999999999999999999999 9999999999999876544

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.50  E-value=3.5e-14  Score=129.01  Aligned_cols=65  Identities=23%  Similarity=0.312  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCe-EEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNY-SFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGF-AFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~~~~   65 (724)
                      |+|++|+++|++||+|++|++++.+|| |||+|.+.++|.+|+++|||..|.|  ++|+|+||+...-
T Consensus        37 vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           37 ITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            689999999999999999998755697 9999999999999999999999988  6899999987643

>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=2e-14  Score=124.57  Aligned_cols=64  Identities=23%  Similarity=0.485  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.  ||||||+|.+.++|++|++.|||..|+|++|+|+||+.....
T Consensus        43 ~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~r  106 (108)
T 2jvo_A           43 VQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR  106 (108)
T ss_dssp             CCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC--
T ss_pred             CCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCCCC
Confidence            6899999999999999999987  999999999999999999999999999999999999876543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=3.9e-14  Score=118.79  Aligned_cols=65  Identities=17%  Similarity=0.263  Sum_probs=58.3

Q ss_pred             CCHHHHHHHhhhcCcee-EeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIE-RIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~-sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|+.||+|. .|.+.++||||||+|.+.++|.+|++.|||..|+|++|+|+||++++.
T Consensus        31 ~t~~~l~~~F~~~G~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   96 (97)
T 2e5j_A           31 ARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD   96 (97)
T ss_dssp             CCHHHHHHHHHHTTCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCCC
T ss_pred             CcHHHHHHHHHhcCCEEEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            68999999999999996 333457899999999999999999999999999999999999987643

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.50  E-value=6.5e-14  Score=122.53  Aligned_cols=66  Identities=20%  Similarity=0.361  Sum_probs=60.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++..     +||||||+|.+.++|++|++.|||..|+|++|+|+||++....
T Consensus        19 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           19 TNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQ   89 (116)
T ss_dssp             CCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSCS
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCCC
Confidence            68999999999999999998754     5799999999999999999999999999999999999876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=3.7e-14  Score=117.18  Aligned_cols=63  Identities=21%  Similarity=0.313  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++|++.  |+||||+|.+.++|++|++.|||..|+|++|+|+||++...
T Consensus        21 ~t~~~l~~~F~~~G~v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A           21 CTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCHHHHHHHHHcCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            6899999999999999999987  77999999999999999999999999999999999987644

>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=1.5e-14  Score=124.88  Aligned_cols=65  Identities=11%  Similarity=0.239  Sum_probs=59.4

Q ss_pred             CCHHHHH---HHhhhcCceeEeeec---------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLH---NAMILFGEIERIKSY---------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLr---elFS~FGeI~sVkt~---------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+   ++|++||+|++|++.         ++||||||+|.+.++|++|++.|||..|+|++|+|+||+.+..
T Consensus        27 ~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           27 LADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC  103 (111)
T ss_dssp             TCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCSC
T ss_pred             CCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEecccccc
Confidence            5899999   999999999999865         3458999999999999999999999999999999999987653

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.50  E-value=1.9e-14  Score=123.20  Aligned_cols=63  Identities=17%  Similarity=0.367  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++  +||||||+|++.++|++|++.|||..|+|++|+|+||+..+.
T Consensus        40 ~t~~~l~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  102 (110)
T 1wf1_A           40 VKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP  102 (110)
T ss_dssp             CCHHHHHHHHGGGSCCSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCCS
T ss_pred             CCHHHHHHHHHhCCCeEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCCC
Confidence            589999999999999999999  799999999999999999999999999999999999985543

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.50  E-value=1.9e-14  Score=119.02  Aligned_cols=62  Identities=19%  Similarity=0.301  Sum_probs=58.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|++|++..     +||||||+|.+.++|.+|++.|||..|+|++|+|+||+.
T Consensus        28 ~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           28 VREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            58999999999999999998753     479999999999999999999999999999999999974

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.50  E-value=1.4e-14  Score=124.73  Aligned_cols=62  Identities=19%  Similarity=0.295  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCc--eeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCc----cCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGE--IERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRL----FNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGe--I~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~----f~GRrIrVefAk~   62 (724)
                      +||++|+++|++||.  |.+|++      .++||||||+|.+.++|.+|++.|||..    |+||+|+|+||+.
T Consensus        21 ~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           21 TVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             CCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             CCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            689999999999996  567764      3579999999999999999999999984    8999999999985

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.50  E-value=3.5e-14  Score=125.49  Aligned_cols=66  Identities=32%  Similarity=0.480  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|+.||+|++|++.      ++||||||+|.+.++|.+|+++|||..|+|++|+|+||+.....
T Consensus        54 ~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  125 (139)
T 1u6f_A           54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            6899999999999999999864      35899999999999999999999999999999999999876543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.50  E-value=2.9e-14  Score=131.20  Aligned_cols=65  Identities=20%  Similarity=0.365  Sum_probs=60.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-CCCCe-EEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-PSRNY-SFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-~SRGF-AFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~~~~   65 (724)
                      |||++|+++|++||+|.+|++. +.||| |||+|.+.++|++|+++|||+.|.|  ++|+|+||+...-
T Consensus        40 vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           40 VTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             CCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             CCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            6899999999999999999875 46788 9999999999999999999999998  8999999997654

>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=99.49  E-value=4e-14  Score=135.02  Aligned_cols=65  Identities=20%  Similarity=0.316  Sum_probs=59.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~~~~   65 (724)
                      |||++|+++|++||+|++|+++  +.||||||+|++.++|++|+++|||+.|.|  ++|+|+||+.+..
T Consensus        58 vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~l  126 (164)
T 1sjr_A           58 VTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  126 (164)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSSC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCcc
Confidence            6899999999999999999975  357899999999999999999999999965  9999999997643

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.49  E-value=2.4e-14  Score=126.94  Aligned_cols=63  Identities=19%  Similarity=0.023  Sum_probs=58.7

Q ss_pred             CCHHHHHHHhhhcC-ceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFG-EIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FG-eI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++|| +|+.|++.  ++||||||+|++.++|++|++.|||..|+|++|+|++|+..
T Consensus        40 ~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           40 CSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            68999999999999 99999874  58999999999999999999999999999999999999754

>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=2.5e-14  Score=123.46  Aligned_cols=63  Identities=24%  Similarity=0.434  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++||+|++|++..    +||||||+|.+.++|++|++.|||..|+|++|+|+||+.+
T Consensus        41 ~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           41 FRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             CCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            68999999999999999999753    5899999999999999999999999999999999999865

>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=99.49  E-value=2.9e-14  Score=118.40  Aligned_cols=65  Identities=26%  Similarity=0.391  Sum_probs=60.2

Q ss_pred             CCHHHHH----HHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLH----NAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLr----elFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+    ++|++||+|.+|++.   ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++..
T Consensus        20 ~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   91 (97)
T ss_dssp             SCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             CCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCCc
Confidence            5889999    999999999999875   5789999999999999999999999999999999999987653

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.49  E-value=4.4e-14  Score=121.54  Aligned_cols=66  Identities=20%  Similarity=0.350  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+++...
T Consensus        37 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~  108 (115)
T 2cpz_A           37 FGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS  108 (115)
T ss_dssp             CCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcC
Confidence            6899999999999999999864      35699999999999999999999999999999999999876543

>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=99.49  E-value=2.9e-14  Score=120.67  Aligned_cols=61  Identities=15%  Similarity=0.237  Sum_probs=57.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|++|++.     ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+
T Consensus        41 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           41 VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            6899999999999999999865     468999999999999999999999999999999999986

>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=7.9e-14  Score=121.68  Aligned_cols=65  Identities=15%  Similarity=0.239  Sum_probs=60.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++..     +||||||+|.+.++|++|++.|||..|+|++|+|+||.....
T Consensus        47 ~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  116 (124)
T 2kt5_A           47 VSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID  116 (124)
T ss_dssp             CCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTC
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            68999999999999999998753     789999999999999999999999999999999999987554

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.49  E-value=3.9e-14  Score=123.91  Aligned_cols=62  Identities=21%  Similarity=0.315  Sum_probs=57.4

Q ss_pred             CHHHHHHHhhhcCceeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +|++|+++|++||+|++|++.       ++||||||+|.+.++|.+|+++|||+.|+||+|+|+||...
T Consensus        26 ~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~~   94 (105)
T 2pe8_A           26 LEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLD   94 (105)
T ss_dssp             CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             HHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCHH
Confidence            589999999999999999864       46899999999999999999999999999999999999753

>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=5.1e-14  Score=126.03  Aligned_cols=64  Identities=31%  Similarity=0.494  Sum_probs=59.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+.++
T Consensus        58 ~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            6899999999999999999864      578999999999999999999999999999999999998754

>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=99.49  E-value=4.2e-14  Score=120.01  Aligned_cols=66  Identities=18%  Similarity=0.293  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCc-eeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhc--CCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGE-IERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQ--GRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGe-I~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLN--Gk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+ |++|++.       ++||||||+|.+.++|.+|++.||  +..|+|++|+|+||+++..+
T Consensus        20 ~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~~   95 (109)
T 2dis_A           20 KKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   95 (109)
T ss_dssp             SCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             CCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCCc
Confidence            689999999999999 9999876       689999999999999999999996  59999999999999876554

>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=5.6e-14  Score=122.30  Aligned_cols=66  Identities=27%  Similarity=0.455  Sum_probs=60.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.      .++|||||+|.+.++|++|++.|||..|+|++|+|+||+....+
T Consensus        34 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           34 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP  105 (126)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSSC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCC
Confidence            6899999999999999999864      34899999999999999999999999999999999999866544

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.48  E-value=4.8e-14  Score=120.13  Aligned_cols=65  Identities=25%  Similarity=0.355  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++.      .+||||||+|.+.++|.+|++.|||..|+|++|+|+||+.+..
T Consensus        38 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  108 (110)
T 1oo0_B           38 AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  108 (110)
T ss_dssp             CCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESSC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCCC
Confidence            5899999999999999999864      3579999999999999999999999999999999999986543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.48  E-value=1.9e-14  Score=122.47  Aligned_cols=61  Identities=15%  Similarity=0.289  Sum_probs=57.0

Q ss_pred             CHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCC-CcEEEEeccC
Q 004908            2 DEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFND-PRITIMFSSS   62 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G-RrIrVefAk~   62 (724)
                      +|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+| ++|+|.+|++
T Consensus        25 ~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           25 LKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             HHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHH
T ss_pred             HHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECch
Confidence            689999999999999999853      478999999999999999999999999999 9999999975

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=5e-14  Score=118.61  Aligned_cols=66  Identities=21%  Similarity=0.322  Sum_probs=60.6

Q ss_pred             CCHHHHHHHhhh-cCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCc-cCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMIL-FGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRL-FNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~-FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~-f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++ ||+|++|++.     ++||||||+|.+.++|.+|++.|||.. |+|++|+|+||+++...
T Consensus        21 ~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   93 (104)
T 2dhg_A           21 VDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASR   93 (104)
T ss_dssp             CCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSC
T ss_pred             CCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcC
Confidence            689999999999 9999999865     358999999999999999999999999 99999999999876554

>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=99.48  E-value=8.7e-14  Score=119.30  Aligned_cols=64  Identities=19%  Similarity=0.187  Sum_probs=60.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCC-----CcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFND-----PRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G-----RrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++... |||||+|++.++|++|++.|||..|+|     +.|+|++|+++..
T Consensus        27 ~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           27 GSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSP   95 (108)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSC
T ss_pred             CCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCC
Confidence            689999999999999999998765 999999999999999999999999999     9999999987544

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=3.2e-14  Score=119.52  Aligned_cols=65  Identities=22%  Similarity=0.365  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|.+|++.      .+||||||+|.+.++|.+|++.|||..|+|++|+|+||+.+..
T Consensus        20 ~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   90 (104)
T 1p1t_A           20 ATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKN   90 (104)
T ss_dssp             SCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTH
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCccc
Confidence            5899999999999999999865      2489999999999999999999999999999999999987654

>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=99.48  E-value=5.6e-14  Score=126.25  Aligned_cols=64  Identities=23%  Similarity=0.366  Sum_probs=60.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.+ +||||||+|.+.++|.+|++.|||..|+|++|+|+||++++
T Consensus        85 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           85 GNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             CSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            58999999999999999999875 49999999999999999999999999999999999998764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=5.9e-14  Score=126.88  Aligned_cols=65  Identities=20%  Similarity=0.285  Sum_probs=58.1

Q ss_pred             CCHHHHH----HHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLH----NAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLr----elFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+    ++|++||+|.+|.+.   ++||||||+|.+.++|.+|++.|||..|.|++|+|+||+.+..
T Consensus        41 ~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           41 VPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS  112 (127)
T ss_dssp             SCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCCH
T ss_pred             CCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcch
Confidence            4677765    799999999999864   6799999999999999999999999999999999999986543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.47  E-value=2.7e-14  Score=123.05  Aligned_cols=61  Identities=21%  Similarity=0.427  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+|||
T Consensus        52 ~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           52 FTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             CCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            6899999999999999999864      458999999999999999999999999999999999986

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=1e-13  Score=116.35  Aligned_cols=63  Identities=25%  Similarity=0.522  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhc--CceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILF--GEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~F--GeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++|  |+|.+|++.  ||||||+|.+.++|.+|++.|||..|+|++|+|+||++...
T Consensus        27 ~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           27 TSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             CCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             CCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            6899999999999  999999874  89999999999999999999999999999999999987654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.47  E-value=4.9e-14  Score=118.33  Aligned_cols=61  Identities=20%  Similarity=0.319  Sum_probs=56.7

Q ss_pred             CCHHHHHHHhhhcCceeE--------eeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIER--------IKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~s--------Vkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|++        |++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+
T Consensus        25 ~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           25 VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             CCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             CCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            689999999999999999        8754      357999999999999999999999999999999999985

>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=99.47  E-value=5.4e-14  Score=121.67  Aligned_cols=64  Identities=27%  Similarity=0.434  Sum_probs=59.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++.
T Consensus        38 ~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           38 ITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            6899999999999999999864      357999999999999999999999999999999999998653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=7.3e-14  Score=119.51  Aligned_cols=66  Identities=15%  Similarity=0.250  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhhcCcee--------Eeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIE--------RIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~--------sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|.        +|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+.+...
T Consensus        27 ~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           27 VTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             CCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             CCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCC
Confidence            68999999999999999        57754      35899999999999999999999999999999999999876554

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.47  E-value=9.7e-14  Score=124.79  Aligned_cols=66  Identities=17%  Similarity=0.388  Sum_probs=60.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|.||+..+.+
T Consensus        82 ~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           82 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             CCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            6899999999999999999854      47899999999999999999999999999999999999876544

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=8.4e-14  Score=117.82  Aligned_cols=64  Identities=14%  Similarity=0.258  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|+.|| |++|++.       ++||||||+|.+.++|++|+ +|||..|+|++|+|+||+.+...
T Consensus        27 ~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           27 VTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             CCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCC
T ss_pred             CCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCC
Confidence            68999999999999 9999863       45899999999999999999 99999999999999999876553

>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=99.46  E-value=7.7e-14  Score=121.82  Aligned_cols=61  Identities=25%  Similarity=0.438  Sum_probs=56.2

Q ss_pred             HHHHHHHhhhcCceeEeeec--------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSY--------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~--------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +++|+++|++||+|++|++.        ++||||||+|++.++|.+|+++|||+.|+||+|+|+|+..+
T Consensus        29 ~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPD   97 (105)
T ss_dssp             HHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECHH
T ss_pred             HHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCHH
Confidence            58999999999999999964        36899999999999999999999999999999999998643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=7.9e-14  Score=117.15  Aligned_cols=66  Identities=21%  Similarity=0.305  Sum_probs=58.6

Q ss_pred             CCHHHHHHHhhhcCceeEee--ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK--SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk--t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|.-++  ..++||||||+|.+.++|++|++.|||..|+|++|+|+||+.+...
T Consensus        27 ~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   94 (101)
T 2fc9_A           27 ATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP   94 (101)
T ss_dssp             CCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCCC
T ss_pred             CCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCC
Confidence            68999999999999994333  2357999999999999999999999999999999999999877554

>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=4.1e-14  Score=118.01  Aligned_cols=63  Identities=17%  Similarity=0.198  Sum_probs=57.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++||+|+++++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+..
T Consensus        27 ~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           27 VSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             CCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             CCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            6899999999999999877643      46899999999999999999999999999999999999854

>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=4.5e-14  Score=116.79  Aligned_cols=63  Identities=11%  Similarity=0.207  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++| +|++|++.++||||||+|.+.++|++|++.|||..|+|++|+|+||..+.
T Consensus        17 ~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A           17 SNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            6899999999999 99999988899999999999999999999999999999999999997653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=6.3e-14  Score=117.06  Aligned_cols=65  Identities=22%  Similarity=0.406  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCcee-Eeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCc----EEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIE-RIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR----ITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~-sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRr----IrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|. +|++.      ++||||||+|.+.++|++|++.|||..|+|+.    |+|+||+....
T Consensus        21 ~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~~   96 (99)
T 2div_A           21 MDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGP   96 (99)
T ss_dssp             CCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCSS
T ss_pred             CCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCCC
Confidence            68999999999999999 99864      35699999999999999999999999999999    99999987654

>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=99.45  E-value=1.4e-13  Score=118.09  Aligned_cols=65  Identities=15%  Similarity=0.333  Sum_probs=59.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||.|.+|++.   .+||||||+|.+.++|.+|++.|||..|+|++|+|+||++...
T Consensus        20 ~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   87 (115)
T 3lqv_A           20 ITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRA   87 (115)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHH
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChh
Confidence            6899999999999999999874   4689999999999999999999999999999999999976543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.45  E-value=7.4e-14  Score=111.28  Aligned_cols=59  Identities=17%  Similarity=0.250  Sum_probs=55.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|++|++ |||..|+|++|+|.+|
T Consensus        11 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           11 TTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            5899999999999999999854      468999999999999999998 9999999999999987

>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=99.45  E-value=7e-14  Score=114.13  Aligned_cols=62  Identities=16%  Similarity=0.380  Sum_probs=57.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|+.||+|++|++.      ++||||||+|.+.++|++|+ .|||..|+|++|+|++|+..
T Consensus        18 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           18 ATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             CCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            5899999999999999999854      45899999999999999999 99999999999999999864

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=1.1e-13  Score=118.44  Aligned_cols=66  Identities=18%  Similarity=0.232  Sum_probs=58.7

Q ss_pred             CCHHHHHHHhhhcCcee----Eee--ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIE----RIK--SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~----sVk--t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|+    .++  +.++||||||+|.+.++|.+|++.|||..|+|++|+|+||+.....
T Consensus        37 ~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  108 (115)
T 2cpx_A           37 VTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR  108 (115)
T ss_dssp             CCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCC
T ss_pred             CCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCC
Confidence            68999999999999994    444  3467899999999999999999999999999999999999876543

>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=4.2e-14  Score=117.02  Aligned_cols=62  Identities=19%  Similarity=0.159  Sum_probs=56.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|++|+.
T Consensus        27 ~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           27 VSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             CCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             CCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            6899999999999999877643      4689999999999999999999999999999999999874

>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=99.44  E-value=1.4e-13  Score=119.35  Aligned_cols=63  Identities=24%  Similarity=0.324  Sum_probs=57.8

Q ss_pred             HHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            3 EQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      |++|+++|++||+|++|.+.  .+||||||+|.+.++|.+|++.|||+.|+|++|+|+||++...
T Consensus        40 e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             HHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             HHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            68999999999999999764  4799999999999999999999999999999999999976543

>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=99.44  E-value=3.7e-14  Score=116.62  Aligned_cols=65  Identities=15%  Similarity=0.257  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.+ |.+|++.|||..|+|++|+|++|.....+
T Consensus        13 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~~   83 (90)
T 2ki2_A           13 ATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKSL   83 (90)
T ss_dssp             SSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC------
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCCC
Confidence            5899999999999999999864      46899999999999 99999999999999999999999876543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=1.7e-13  Score=119.86  Aligned_cols=63  Identities=19%  Similarity=0.263  Sum_probs=57.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++. ++||||||+|++.++|++|++.++|  +.|++|+|+||+....
T Consensus        29 ~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           29 YSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            5799999999999999999975 7899999999999999999999665  6899999999986643

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.44  E-value=8.5e-14  Score=119.10  Aligned_cols=62  Identities=18%  Similarity=0.262  Sum_probs=57.5

Q ss_pred             CHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCC-cEEEEeccCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDP-RITIMFSSSE   63 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GR-rIrVefAk~~   63 (724)
                      +|++|+++|++||+|.+|++.    ++||||||+|.+.++|.+|++.|||..|+|+ +|+|++|+..
T Consensus        34 t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           34 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF  100 (105)
T ss_dssp             HHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCC
T ss_pred             HHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchH
Confidence            579999999999999999865    4689999999999999999999999999999 9999999743

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.44  E-value=4.9e-14  Score=117.11  Aligned_cols=65  Identities=18%  Similarity=0.295  Sum_probs=59.2

Q ss_pred             CCHHHHHHHhhhcCceeEee-ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk-t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|+.||+|..|. ..++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++..
T Consensus        28 ~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           28 ITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             CCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            68999999999999999883 345789999999999999999999999999999999999986644

>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=99.44  E-value=1.4e-13  Score=124.43  Aligned_cols=65  Identities=20%  Similarity=0.262  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++|++.      .+||||||+|.+.++|++|++.|||..|+|++|+|+||+....
T Consensus        51 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           51 TTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            6899999999999999999864      3579999999999999999999999999999999999986543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.43  E-value=1.5e-13  Score=120.36  Aligned_cols=60  Identities=28%  Similarity=0.519  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||
T Consensus        75 ~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           75 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             CCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            5899999999999999999864      46899999999999999999999999999999999987

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.42  E-value=6.9e-14  Score=113.82  Aligned_cols=57  Identities=19%  Similarity=0.300  Sum_probs=52.9

Q ss_pred             CHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCC-cEEEE
Q 004908            2 DEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDP-RITIM   58 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GR-rIrVe   58 (724)
                      +|++|+++|++||+|.+|++.    ++||||||+|.+.++|.+|++.|||..|+|+ +|+|+
T Consensus        20 t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V~   81 (81)
T 2krb_A           20 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN   81 (81)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCCC
T ss_pred             HHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEeC
Confidence            579999999999999999865    4689999999999999999999999999999 99874

>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=99.42  E-value=2.1e-13  Score=130.33  Aligned_cols=64  Identities=19%  Similarity=0.303  Sum_probs=60.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      |||++|+++|++||+|.+|++.+ .||||||+|.+.++|++|++.|||..|.|++|+|.||+.+.
T Consensus        17 ~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A           17 MNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            68999999999999999999875 58999999999999999999999999999999999998653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.42  E-value=2e-13  Score=115.36  Aligned_cols=64  Identities=16%  Similarity=0.283  Sum_probs=58.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++|| |++|++.      ++||||||+|.+.++|++|+ +|||..|+|++|+|+||+.....
T Consensus        27 ~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           27 TVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             CCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCCC
T ss_pred             CCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCCC
Confidence            68999999999997 9999864      35799999999999999999 99999999999999999876543

>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=99.42  E-value=1.2e-13  Score=118.57  Aligned_cols=63  Identities=21%  Similarity=0.329  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||+|++|++.      ++||||||+|.+.++|++|+ .|||..|+|++|+|+||+.+.
T Consensus        37 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~  105 (114)
T 2cq4_A           37 IRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEK  105 (114)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHHH
T ss_pred             CCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCCc
Confidence            6899999999999999999864      57899999999999999999 999999999999999997653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.41  E-value=1.7e-13  Score=119.05  Aligned_cols=64  Identities=19%  Similarity=0.366  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|+.||+|++|++.      .+||||||+|.+.++|.+|+ +|||..|+|++|+|+||+....
T Consensus        48 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~  117 (124)
T 2jwn_A           48 STAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMP  117 (124)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCCS
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCCC
Confidence            6899999999999999999864      45899999999999999999 8999999999999999986543

>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=99.41  E-value=5e-13  Score=116.52  Aligned_cols=62  Identities=19%  Similarity=0.207  Sum_probs=55.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCc-----EEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR-----ITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRr-----IrVefAk~~   63 (724)
                      ++|++|+++|++||+|++|++... |||||+|++.++|++||++|||..|+|++     |+|+.++..
T Consensus        28 ~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~   94 (115)
T 3beg_B           28 GSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   94 (115)
T ss_dssp             CCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC--
T ss_pred             CCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCCC
Confidence            689999999999999999998755 99999999999999999999999999999     666666543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=5.9e-14  Score=114.26  Aligned_cols=62  Identities=24%  Similarity=0.275  Sum_probs=57.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++.|||..|+|+.|+|.+++.
T Consensus        17 ~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~s   84 (85)
T 1x4e_A           17 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPSS   84 (85)
T ss_dssp             CCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCCC
Confidence            6899999999999999999864      3589999999999999999999999999999999988763

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.41  E-value=3.1e-13  Score=116.81  Aligned_cols=65  Identities=17%  Similarity=0.198  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|+.||+|++|++.      ++||||||+|.+.++|.+|++.| |..|+|++|+|++|+.+...
T Consensus        37 ~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           37 TTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPRRAQ  107 (109)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCCCCC
T ss_pred             CCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCCCCC
Confidence            6899999999999999999864      46899999999999999999987 59999999999999876554

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.41  E-value=1.8e-13  Score=115.84  Aligned_cols=62  Identities=15%  Similarity=0.269  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.|| |++|++.       ++||||||+|.+.++|.+|+ +|||..|+|++|+|++|+.+.
T Consensus        31 ~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           31 VTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             CSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCSC
T ss_pred             CCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCCC
Confidence            58999999999999 9999864       35899999999999999999 999999999999999998653

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=3.1e-13  Score=115.79  Aligned_cols=63  Identities=24%  Similarity=0.400  Sum_probs=57.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCcc--------CCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLF--------NDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f--------~GRrIrVefAk~~   63 (724)
                      ++|++|+++|+.||+|++|++.     ++||||||+|.+.++|++|++.|||+.|        .|++|+|.||++.
T Consensus        37 ~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           37 MDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             CCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            6899999999999999999864     3589999999999999999999999999        5788999999854

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.41  E-value=1.5e-13  Score=122.52  Aligned_cols=65  Identities=14%  Similarity=0.185  Sum_probs=58.8

Q ss_pred             CCHHHHHHHhhhcCceeEe-----------eecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERI-----------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sV-----------kt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|.+|           ++.++||||||+|.+.++|.+|++.|||..|+|++|+|+||+....
T Consensus        57 ~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~  132 (143)
T 3egn_A           57 VQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP  132 (143)
T ss_dssp             CCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCSCC
T ss_pred             CCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            6899999999999999764           3457899999999999999999999999999999999999986543

>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=99.41  E-value=2e-13  Score=118.81  Aligned_cols=58  Identities=26%  Similarity=0.387  Sum_probs=52.5

Q ss_pred             HHHHHHHh-hhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            3 EQMLHNAM-ILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         3 EedLrelF-S~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +++|+++| ++||+|++|++.+     +||||||+|.+.++|.+|+++|||+.|+||+|+|+|+
T Consensus        40 ~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           40 FEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            35666677 9999999999753     6899999999999999999999999999999999997

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=2.3e-13  Score=117.17  Aligned_cols=65  Identities=18%  Similarity=0.235  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++. ||..|+|++|+|+||+++...
T Consensus        39 ~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~~  109 (116)
T 1x4b_A           39 TTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREES  109 (116)
T ss_dssp             CCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCccC
Confidence            6899999999999999999864      3589999999999999999999 999999999999999876554

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.41  E-value=1.9e-13  Score=122.98  Aligned_cols=66  Identities=17%  Similarity=0.388  Sum_probs=60.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+..+.+
T Consensus        59 ~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             CHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            5799999999999999999864      46899999999999999999999999999999999999876554

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.40  E-value=1e-13  Score=122.77  Aligned_cols=64  Identities=14%  Similarity=0.298  Sum_probs=57.7

Q ss_pred             CCHHHHHHHhhhcCceeE--eeec------CCCCeEEEEeCCHHHHHHHHHHhcCC----ccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIER--IKSY------PSRNYSFVEFRSVDEARRAKEGLQGR----LFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~s--Vkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk----~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++  |++.      ++||||||+|.+. +|.+|++.|||.    .|+|++|+|+||+..+.
T Consensus        35 ~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           35 STMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             CCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            689999999999999966  7643      5789999999999 999999999999    99999999999986543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=2e-13  Score=114.58  Aligned_cols=66  Identities=18%  Similarity=0.302  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcCceeEee---ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK---SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk---t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|+.|+.|.-++   +.++||||||+|.+.++|++|++.|||..|+|++|+|+||+++...
T Consensus        27 ~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           27 TTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             CCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSS
T ss_pred             cCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCC
Confidence            68999999999998776664   2356899999999999999999999999999999999999876654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=3.4e-13  Score=116.97  Aligned_cols=61  Identities=18%  Similarity=0.308  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|++||+|++|++.     .+||||||+|.+.++|.+|++ |||..|+|+.|+|.+++.
T Consensus        23 ~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           23 ATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             CCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            6899999999999999999875     379999999999999999999 999999999999999853

>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=3.5e-13  Score=113.19  Aligned_cols=64  Identities=17%  Similarity=0.224  Sum_probs=57.1

Q ss_pred             CCHHHHHHHhhhcCceeE-----eeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIER-----IKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~s-----Vkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|+.||+|.+     ..+.++||||||+|.+.++|++|++ |||..|+|++|+|++|+++..
T Consensus        29 ~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           29 KSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             SCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCCC
T ss_pred             CCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCCC
Confidence            689999999999998866     2345789999999999999999999 999999999999999986543

>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=99.40  E-value=2.6e-13  Score=121.21  Aligned_cols=61  Identities=20%  Similarity=0.222  Sum_probs=56.5

Q ss_pred             HHHHHHHhhhcCceeEeeecC--CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSYP--SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~--SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +++|+++|++||+|++|++.+  +||||||+|.+.++|.+|+++|||+.|+||.|+|+|+...
T Consensus        31 ~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~~~   93 (114)
T 3s6e_A           31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLP   93 (114)
T ss_dssp             HHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEECHH
T ss_pred             HHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEcHH
Confidence            579999999999999999764  5899999999999999999999999999999999999643

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.40  E-value=1.9e-13  Score=126.56  Aligned_cols=63  Identities=19%  Similarity=0.309  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcC--ceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFG--EIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FG--eI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||  +|.+|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|.+|++.
T Consensus        67 ~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           67 TTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             CCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             CCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            68999999999999  99999864      46899999999999999999999999999999999999753

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=1.5e-13  Score=116.22  Aligned_cols=65  Identities=14%  Similarity=0.209  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|++.++|.+|++. ||..|+|++|+|++|+++...
T Consensus        28 ~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~~   98 (105)
T 2dh8_A           28 TTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQ   98 (105)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCCC
Confidence            6899999999999999999864      3579999999999999999999 999999999999999866543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=2.9e-13  Score=111.79  Aligned_cols=64  Identities=16%  Similarity=0.241  Sum_probs=58.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|+.| +|.+|++.     ++||||||+|.+.++|.+|++ |||..|+|++|+|.+|+.+..+
T Consensus        22 ~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~~s   90 (91)
T 2dgw_A           22 VTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGPSS   90 (91)
T ss_dssp             CCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCCCC
T ss_pred             CCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCCCC
Confidence            6899999999999 99999864     358999999999999999999 9999999999999999877554

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.39  E-value=1.9e-13  Score=136.78  Aligned_cols=65  Identities=23%  Similarity=0.417  Sum_probs=58.8

Q ss_pred             CHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCcc------------CCCcEEEEeccCCCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF------------NDPRITIMFSSSELAP   66 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f------------~GRrIrVefAk~~~~p   66 (724)
                      +|++|+++|++||+|++|++.++||||||+|.+.++|++|+++|||+.|            +|++|+|.||+.+..+
T Consensus       156 tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          156 IESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             HHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             cHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence            5999999999999999999999999999999999999999999999999            8999999999977654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.39  E-value=4.4e-13  Score=123.29  Aligned_cols=66  Identities=12%  Similarity=0.265  Sum_probs=60.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.+      +||||||+|.+.++|.+|++.|||..|+|++|+|+||+....+
T Consensus       137 ~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             CCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             CCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            58999999999999999998653      4899999999999999999999999999999999999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.39  E-value=3.7e-13  Score=118.04  Aligned_cols=62  Identities=31%  Similarity=0.468  Sum_probs=57.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +++++|+++|++||+|.+|++.      .+||||||+|.+.++|.+|++.|||..|+|++|+|.||++
T Consensus        99 ~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A           99 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             CCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            5899999999999999999864      4589999999999999999999999999999999999974

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.38  E-value=2.8e-13  Score=127.87  Aligned_cols=63  Identities=32%  Similarity=0.491  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|++|++.    .+||||||+|.+.++|.+|+++|||..|+|++|+|+||+++
T Consensus       115 ~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          115 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             cHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            6899999999999999999865    36899999999999999999999999999999999999764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.37  E-value=2.7e-13  Score=107.90  Aligned_cols=59  Identities=17%  Similarity=0.244  Sum_probs=55.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|++|++.|| ..|+|++|+|++|
T Consensus        12 ~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           12 TTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            5899999999999999999864      458999999999999999999999 9999999999997

>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=99.36  E-value=9.5e-13  Score=110.92  Aligned_cols=64  Identities=19%  Similarity=0.306  Sum_probs=57.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++  +|..|+|++|+|+||+.+...
T Consensus        27 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~~~   96 (103)
T 2cqg_A           27 TTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQSQ   96 (103)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCCcC
Confidence            6899999999999999999864      357999999999999999999  478999999999999876554

>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=99.36  E-value=6.3e-13  Score=121.96  Aligned_cols=66  Identities=24%  Similarity=0.354  Sum_probs=59.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +++++|+++|++||+|.+|++..      +||||||+|.+.++|.+|++.|||..|+|++|+|.||+.....
T Consensus        84 ~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A           84 AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             CCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            68999999999999999998753      4799999999999999999999999999999999999866543

>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=99.35  E-value=1e-12  Score=127.15  Aligned_cols=62  Identities=27%  Similarity=0.441  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCC-CeEEEEeCCHHHHHHHHHHhcCCccC-CCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSR-NYSFVEFRSVDEARRAKEGLQGRLFN-DPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SR-GFAFVeF~s~EdA~kAIEaLNGk~f~-GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|++|++.+.| |||||+|.+.++|.+|++.|||..|+ |++|+|+|||+
T Consensus       219 ~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          219 TNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             CCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence            5899999999999999999988765 99999999999999999999999999 99999999984

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.35  E-value=8.3e-13  Score=107.36  Aligned_cols=58  Identities=26%  Similarity=0.486  Sum_probs=55.7

Q ss_pred             CCHHHHHHHhhhc----C-------ceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEe
Q 004908            1 MDEQMLHNAMILF----G-------EIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF   59 (724)
Q Consensus         1 VdEedLrelFS~F----G-------eI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVef   59 (724)
                      ++|++|+++|+.|    |       +|.+|++.+.||||||+|.+.++|.+|+ .|||..|+|++|+|+.
T Consensus        18 ~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           18 ITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             CCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             CCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            5899999999999    8       9999999999999999999999999999 9999999999999974

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.35  E-value=4.4e-13  Score=106.51  Aligned_cols=59  Identities=19%  Similarity=0.306  Sum_probs=54.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++. +|..|+|++|+|.+|
T Consensus        11 ~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           11 TPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            5899999999999999999863      4689999999999999999995 999999999999986

>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=99.35  E-value=8.1e-13  Score=115.96  Aligned_cols=77  Identities=25%  Similarity=0.311  Sum_probs=65.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSY   74 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~   74 (724)
                      ++|++|+++|+.||+|.+|++.+      +||||||+|.+.++|.+|++.|||..++|++|+|.++++.....+....|+
T Consensus        14 ~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v   93 (167)
T 1fxl_A           14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYV   93 (167)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCGGGTTCEEEE
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcccCCCCcEEE
Confidence            68999999999999999998653      459999999999999999999999999999999999987654433444555


Q ss_pred             CCC
Q 004908           75 SGT   77 (724)
Q Consensus        75 sG~   77 (724)
                      .++
T Consensus        94 ~nl   96 (167)
T 1fxl_A           94 SGL   96 (167)
T ss_dssp             ESC
T ss_pred             CCC
Confidence            555

>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=1.2e-12  Score=116.22  Aligned_cols=62  Identities=19%  Similarity=0.228  Sum_probs=55.4

Q ss_pred             CCHHH----HHHHhhhc-CceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQM----LHNAMILF-GEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEed----LrelFS~F-GeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +++++    |+++|++| |+|.+|.    .|||||+|.+.|+|.+|+++|||..|.||+|+|.||+.++..
T Consensus        21 ~~~~~lk~~L~~lF~~yGG~Vl~Vt----gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           21 KDGKSVSNRLRRLSDNCGGKVLSIT----GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNREL   87 (96)
T ss_dssp             SCHHHHHHHHHHHHHTTTCCEEECC----TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCCC
T ss_pred             CCHHHHHHHHHHHHHHcCCeeEEEe----cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCcce
Confidence            45666    67999999 5999993    399999999999999999999999999999999999987664

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=2.4e-12  Score=106.94  Aligned_cols=64  Identities=19%  Similarity=0.360  Sum_probs=57.8

Q ss_pred             CCHHHHHHHhhhcCceeEee-ecC--CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK-SYP--SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk-t~~--SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|++|+ +..  ..|.|||+|.+.++|.+|++.|||..|+|++|+|+||+++.
T Consensus        27 ~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           27 LQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             SCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            58999999999999999995 543  44669999999999999999999999999999999998763

>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=99.34  E-value=8.1e-13  Score=107.97  Aligned_cols=59  Identities=15%  Similarity=0.263  Sum_probs=53.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++ ++|..|+|++|+|.+|
T Consensus        23 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           23 TSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            6899999999999999999864      358999999999999999995 5888999999999986

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.02  E-value=9.1e-14  Score=120.02  Aligned_cols=66  Identities=18%  Similarity=0.269  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcCceeE--------eeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIER--------IKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~s--------Vkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|.+        |++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++...
T Consensus        19 ~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           19 VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF   98 (116)
Confidence            589999999999999998        6643      46899999999999999999999999999999999999876543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=1.2e-12  Score=109.22  Aligned_cols=64  Identities=13%  Similarity=0.221  Sum_probs=56.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCC-eEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRN-YSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRG-FAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|.+|.+.+..| ||||+|.+.++|.+|++ |||..|+|++|+|++|..+..
T Consensus        20 ~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A           20 VDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             CCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCC
Confidence            68999999999999999994433222 99999999999999999 999999999999999975543

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.33  E-value=8.5e-13  Score=118.34  Aligned_cols=60  Identities=25%  Similarity=0.373  Sum_probs=55.1

Q ss_pred             HHHHHHHhhhcCceeEeeecC----------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            3 EQMLHNAMILFGEIERIKSYP----------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~----------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      |++|+++|++||+|++|++.+          +||||||+|.+.++|.+|+++|||+.|+||.|+|+|+..
T Consensus        39 eedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             HHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCh
Confidence            689999999999999998542          459999999999999999999999999999999999864

>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=99.33  E-value=1.4e-12  Score=115.44  Aligned_cols=62  Identities=21%  Similarity=0.291  Sum_probs=57.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +++++|+++|++||+|++|++.      .+||||||+|.+.++|.+|++ |||..|+|++|+|.||+++
T Consensus        99 ~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A           99 VRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            5899999999999999999854      468999999999999999998 9999999999999999864

>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=99.33  E-value=1.1e-12  Score=117.50  Aligned_cols=63  Identities=19%  Similarity=0.325  Sum_probs=58.4

Q ss_pred             CCHHHHHHHhhhcCceeEee-ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIK-SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk-t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++||+|..|. ..++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++
T Consensus       111 ~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          111 ITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             CCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            58999999999999999983 3468999999999999999999999999999999999999865

>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=99.33  E-value=1.5e-12  Score=115.08  Aligned_cols=77  Identities=22%  Similarity=0.272  Sum_probs=65.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSY   74 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~   74 (724)
                      ++|++|+++|+.||+|.+|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|.|+++.....+..-.|+
T Consensus        15 ~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v   94 (168)
T 1b7f_A           15 MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYV   94 (168)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSSTTTTCEEEE
T ss_pred             CCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcccCCCCCEEE
Confidence            6899999999999999999854      2579999999999999999999999999999999999987655434444555


Q ss_pred             CCC
Q 004908           75 SGT   77 (724)
Q Consensus        75 sG~   77 (724)
                      .++
T Consensus        95 ~nl   97 (168)
T 1b7f_A           95 TNL   97 (168)
T ss_dssp             ESC
T ss_pred             eCC
Confidence            554

>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=99.33  E-value=9.4e-13  Score=117.09  Aligned_cols=61  Identities=20%  Similarity=0.469  Sum_probs=56.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|++|++.+      +||||||+|.+.++|.+|++.|||..|+|++|+|+||.
T Consensus       106 ~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          106 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            58999999999999999998643      47999999999999999999999999999999999984

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.33  E-value=1.1e-12  Score=119.14  Aligned_cols=65  Identities=18%  Similarity=0.423  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +++++|+++|++||+|++|++..      +||||||+|.+.++|.+|++.|||..|+|++|+|+||+++..
T Consensus       126 ~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             CCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            58999999999999999998653      389999999999999999999999999999999999987654

>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=99.33  E-value=6.7e-13  Score=129.53  Aligned_cols=63  Identities=17%  Similarity=0.270  Sum_probs=58.4

Q ss_pred             CCHHHHHHHhhhcC--ceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFG--EIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FG--eI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      |||++|+++|++||  +|++|++.      ++||||||+|.+.++|++||+.|||..|+|++|+|.||++.
T Consensus        80 ~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C           80 TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             CCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCHH
T ss_pred             CCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCCC
Confidence            68999999999999  99999864      46899999999999999999999999999999999999653

>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=99.32  E-value=1.7e-12  Score=110.81  Aligned_cols=63  Identities=17%  Similarity=0.124  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCceeE-eee-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIER-IKS-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~s-Vkt-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||.|.+ |++     .++||||||+|++.++|++|++. ||..|+||.|+|.+++.+.
T Consensus        27 ~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           27 CSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             CCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTT
T ss_pred             CCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHH
Confidence            689999999999999987 764     35789999999999999999998 9999999999999997543

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=4.2e-13  Score=117.64  Aligned_cols=62  Identities=13%  Similarity=0.116  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||.|.++.+      .++||||||+|.+.++|++|++ |||..|+|+.|+|.+|+.+
T Consensus        37 ~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~  104 (124)
T 1wel_A           37 AENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKK  104 (124)
T ss_dssp             CCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHH
T ss_pred             CCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCHH
Confidence            689999999999999987432      2468999999999999999999 9999999999999999754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.32  E-value=2.2e-12  Score=121.52  Aligned_cols=64  Identities=16%  Similarity=0.256  Sum_probs=59.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||+|++|++.     ++||||||+|.+.++|.+|++.|||..|+|++|+|+||....
T Consensus       100 ~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A          100 VSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             CCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSGG
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            6899999999999999999874     468999999999999999999999999999999999997653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.32  E-value=1.8e-12  Score=118.93  Aligned_cols=63  Identities=22%  Similarity=0.331  Sum_probs=59.5

Q ss_pred             CCHHHHHHHhhhcC-ceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccC-CCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFG-EIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFN-DPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FG-eI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~-GRrIrVefAk~~   63 (724)
                      ++|++|+++|++|| +|++|++.+ .||||||+|.+.++|.+|++.|||+.|+ |++|+|.||++.
T Consensus       132 ~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          132 VSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            58999999999999 999999854 8999999999999999999999999999 999999999864

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.32  E-value=3.5e-12  Score=111.83  Aligned_cols=65  Identities=25%  Similarity=0.398  Sum_probs=59.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|.+|++.     +++|||||+|.+.++|.+|++.|||..+.|++|+|.++.....
T Consensus        12 ~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~   81 (166)
T 3md3_A           12 ITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQ   81 (166)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCC
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCC
Confidence            6899999999999999999864     4679999999999999999999999999999999999976544

>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=99.31  E-value=2.6e-12  Score=113.91  Aligned_cols=61  Identities=21%  Similarity=0.318  Sum_probs=55.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccC---CCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFN---DPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~---GRrIrVefAk   61 (724)
                      +||++|+++|++||+|++|++.+     +||||||+|.+.++|.+|++.|||..+.   |++|+|.||.
T Consensus       107 ~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          107 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            58999999999999999998653     4899999999999999999999998876   4999999984

>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=99.31  E-value=3.5e-12  Score=121.62  Aligned_cols=63  Identities=22%  Similarity=0.331  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcC-ceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccC-CCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFG-EIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFN-DPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FG-eI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~-GRrIrVefAk~~   63 (724)
                      ++|++|+++|++|| +|++|++.+ .||||||+|.+.++|.+|++.|||+.|+ |++|+|.||++.
T Consensus       163 ~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          163 VSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            58999999999999 999999854 8999999999999999999999999999 999999999864

>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=99.30  E-value=1.2e-12  Score=113.56  Aligned_cols=63  Identities=11%  Similarity=0.122  Sum_probs=57.6

Q ss_pred             CCHHHHHHHhhhcCce-eEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEI-ERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI-~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|+.||.| .+|++.     ++||||||+|.+.++|.+|++. ||..|+|++|+|.+|+.+.
T Consensus        27 ~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           27 ITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLED   95 (114)
T ss_dssp             SCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHHH
T ss_pred             CCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHHH
Confidence            6899999999999999 888864     4799999999999999999998 9999999999999997653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.29  E-value=1.1e-12  Score=115.03  Aligned_cols=62  Identities=15%  Similarity=0.119  Sum_probs=56.8

Q ss_pred             CCHHHHHHHhhhcCc---eeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGE---IERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGe---I~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||.   |++|++.     ++||||||+|++.++|++|++ |||..|+||.|+|.+|+.+
T Consensus        29 ~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~   98 (118)
T 2db1_A           29 CSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRT   98 (118)
T ss_dssp             CCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECHH
T ss_pred             CCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCHH
Confidence            689999999999999   8888854     468999999999999999999 9999999999999999654

>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=99.29  E-value=3.6e-12  Score=107.02  Aligned_cols=60  Identities=22%  Similarity=0.305  Sum_probs=51.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-CCCCeEEEEeCCHHHHHHHHHHhcCCccC--CCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-PSRNYSFVEFRSVDEARRAKEGLQGRLFN--DPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-~SRGFAFVeF~s~EdA~kAIEaLNGk~f~--GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++. .+||||||+|++.++|+    +|+|..+.  |++|+|.+|+++.
T Consensus        23 ~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~----~~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A           23 MTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ----SLCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             CCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHH----HHTTCEEEETTEEEEEEECC---
T ss_pred             CCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHH----HHcCCCcccCCEEEEEEEcCCCC
Confidence            6899999999999999999976 47999999999999998    47888764  9999999998654

>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=99.29  E-value=4e-12  Score=112.31  Aligned_cols=60  Identities=17%  Similarity=0.323  Sum_probs=55.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefA   60 (724)
                      ++|++|+++|++||+|++|++.+      +||||||+|.+.++|.+|++.|||+.|+|  ++|+|.||
T Consensus       101 ~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          101 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            58999999999999999998653      46999999999999999999999999988  99999997

>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=99.29  E-value=4.3e-12  Score=111.34  Aligned_cols=60  Identities=28%  Similarity=0.420  Sum_probs=55.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCc--EEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPR--ITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRr--IrVefA   60 (724)
                      +++++|+++|++||+|++|++..      +||||||+|.+.++|.+|++.|||+.|+|+.  |+|.||
T Consensus       100 ~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          100 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            58999999999999999998642      4799999999999999999999999999975  999987

>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=99.28  E-value=5.7e-12  Score=121.92  Aligned_cols=65  Identities=26%  Similarity=0.394  Sum_probs=59.2

Q ss_pred             CCHHHHH----HHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLH----NAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLr----elFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+    ++|++||+|++|++.   ++||||||+|.+.++|.+|++.|||..|.|++|+|+||+.+..
T Consensus        21 ~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   92 (282)
T 3pgw_A           21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   92 (282)
T ss_pred             CCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCcc
Confidence            5889966    999999999999954   5899999999999999999999999999999999999976543

>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=99.27  E-value=1.9e-12  Score=111.15  Aligned_cols=62  Identities=13%  Similarity=0.083  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCc---eeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGE---IERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGe---I~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||.   |.+|++.     ++||||||+|.+.++|++|++ |||..|+||.|+|.+|+.+
T Consensus        23 ~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           23 CTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNE   92 (107)
T ss_dssp             CCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCHH
T ss_pred             CCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCHH
Confidence            689999999999999   8888864     578999999999999999999 9999999999999999754

>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=99.27  E-value=2.2e-12  Score=110.99  Aligned_cols=63  Identities=14%  Similarity=0.132  Sum_probs=55.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||.| +|++.     ++||||||+|++.++|++|+ +|||..|+||.|+|..+.....
T Consensus        27 ~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~~~~~~   94 (102)
T 1wez_A           27 ATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAGT   94 (102)
T ss_dssp             CCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEECCCCC
T ss_pred             CCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEECCCCCC
Confidence            6899999999999954 88754     46899999999999999999 5899999999999999976544

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.27  E-value=7.9e-12  Score=114.93  Aligned_cols=64  Identities=22%  Similarity=0.351  Sum_probs=58.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|+.||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|.++....
T Consensus        40 ~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~  109 (216)
T 2qfj_A           40 LGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIG  109 (216)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCG
T ss_pred             CCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCcc
Confidence            6899999999999999999864      368999999999999999999999999999999999986543

>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=99.27  E-value=6e-12  Score=111.90  Aligned_cols=76  Identities=21%  Similarity=0.312  Sum_probs=66.0

Q ss_pred             CCHHHHHHHhhhc----C-------ceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCC
Q 004908            1 MDEQMLHNAMILF----G-------EIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKD   69 (724)
Q Consensus         1 VdEedLrelFS~F----G-------eI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~   69 (724)
                      +||++|+++|++|    |       .|.++++.++||||||+|.+.++|.+|+ .|||..|+|++|+|.+++........
T Consensus        16 ~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~~~~~~   94 (172)
T 2g4b_A           16 ITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGA   94 (172)
T ss_dssp             CCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSCCCCTTT
T ss_pred             cCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcccCCCCCC
Confidence            6899999999999    7       8889999999999999999999999999 99999999999999999866554334


Q ss_pred             CCCCCCCC
Q 004908           70 YPGSYSGT   77 (724)
Q Consensus        70 ~p~y~sG~   77 (724)
                      ...|+.++
T Consensus        95 ~~l~v~nl  102 (172)
T 2g4b_A           95 HKLFIGGL  102 (172)
T ss_dssp             TCEEEECC
T ss_pred             CEEEEEcC
Confidence            44566555

>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=99.26  E-value=7.9e-12  Score=119.17  Aligned_cols=64  Identities=20%  Similarity=0.326  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCC-CCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPS-RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~S-RGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|++|++.+. ||||||+|.+.++|++|++.|||..|+|++|+|+||+...
T Consensus        47 ~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  111 (229)
T 2adc_A           47 VTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN  111 (229)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCcc
Confidence            689999999999999999998754 6999999999999999999999999999999999998653

>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=99.26  E-value=6.2e-12  Score=131.53  Aligned_cols=62  Identities=21%  Similarity=0.393  Sum_probs=57.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCcc---CCC--cEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF---NDP--RITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f---~GR--rIrVefAk~   62 (724)
                      +||++|+++|++||+|++|++.++||||||+|++.+||++||++|||+++   .|+  .|.|+|+.+
T Consensus        32 ~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~~   98 (345)
T 3tht_A           32 VSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK   98 (345)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECSS
T ss_pred             CCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEeec
Confidence            69999999999999999999989999999999999999999999999998   355  688899853

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.25  E-value=6e-12  Score=115.54  Aligned_cols=64  Identities=20%  Similarity=0.326  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCC-CCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPS-RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~S-RGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|.+|++.+. ||||||+|.+.++|.+|++.|||..|+|++|+|.||+...
T Consensus        16 ~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A           16 VTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             CCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            589999999999999999997654 7999999999999999999999999999999999998654

>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=99.24  E-value=2.9e-12  Score=117.19  Aligned_cols=62  Identities=15%  Similarity=0.097  Sum_probs=56.7

Q ss_pred             CCHHHHHHHhhhcCc---eeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGE---IERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGe---I~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||+   |++|++.     ++||||||+|++.++|++|++ |||+.|+||.|+|.+|+.+
T Consensus        56 ~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           56 CSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             CCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHH
T ss_pred             CCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChH
Confidence            689999999999999   8888754     568999999999999999999 9999999999999998643

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.24  E-value=1.9e-12  Score=108.84  Aligned_cols=62  Identities=19%  Similarity=0.353  Sum_probs=56.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||+|++|++..     +||||||+|.+.++|++|++  ||..|+|++|+|.+|....
T Consensus        21 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~~   87 (102)
T 2xs2_A           21 MDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQ   87 (102)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEECC
T ss_pred             CCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcCc
Confidence            68999999999999999998653     68999999999999999999  9999999999999997543

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.24  E-value=2.9e-12  Score=117.74  Aligned_cols=63  Identities=19%  Similarity=0.116  Sum_probs=57.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++|| |++|++.     ++||||||+|++.++|++|+ +|||..|+||.|+|..++....
T Consensus        58 ~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           58 ATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             CCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            68999999999999 7788864     57999999999999999999 8999999999999999986544

>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=99.24  E-value=9.7e-12  Score=120.98  Aligned_cols=63  Identities=21%  Similarity=0.361  Sum_probs=60.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|.+|++.++||||||+|.+.++|.+|++.|||..|.|++|+|.|++..
T Consensus        34 ~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~~   96 (261)
T 3sde_A           34 ITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHG   96 (261)
T ss_dssp             CCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecccC
Confidence            689999999999999999999999999999999999999999999999999999999999754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.23  E-value=8.9e-12  Score=117.60  Aligned_cols=64  Identities=25%  Similarity=0.382  Sum_probs=59.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..+.|+.|+|.++....
T Consensus        27 ~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~   96 (213)
T 4f02_A           27 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDP   96 (213)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCT
T ss_pred             CCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccccc
Confidence            6899999999999999999864      468999999999999999999999999999999999997654

>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=99.22  E-value=1.7e-11  Score=130.39  Aligned_cols=65  Identities=20%  Similarity=0.408  Sum_probs=60.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      |||++|+++|++||+|++|+++      .++|||||+|.+.++|.+||++|||..|+|+.|+|+||+....
T Consensus       114 ~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          114 TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             CCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            6899999999999999999865      3689999999999999999999999999999999999986544

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=1.3e-11  Score=108.83  Aligned_cols=61  Identities=10%  Similarity=0.096  Sum_probs=56.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.| .|++|++.     ++||||||+|.+.++|++|+ .|||..|+||.|+|..|+.+
T Consensus        28 ~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           28 AMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             CCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            6899999999999 89999864     47899999999999999999 79999999999999988654

>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=99.22  E-value=1e-11  Score=120.72  Aligned_cols=62  Identities=26%  Similarity=0.456  Sum_probs=57.5

Q ss_pred             CCHHHHHHHhhhcCceeEeee-------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS-------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt-------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +|+++|+++|++||+|++|++       ..+||||||+|.+.++|.+|+ .|||+.|+|++|+|.||+++
T Consensus       223 ~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             CCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            589999999999999999986       446899999999999999999 99999999999999999865

>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=99.21  E-value=1e-11  Score=112.59  Aligned_cols=65  Identities=20%  Similarity=0.268  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.      .+||||||+|.+.++|.+|++. +|..|+|+.|+|.||.++...
T Consensus       116 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             CCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            5899999999999999999865      3589999999999999999987 899999999999999876543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=3.1e-11  Score=104.62  Aligned_cols=58  Identities=16%  Similarity=0.311  Sum_probs=50.0

Q ss_pred             CCHHHHHHHhhhcCceeEeee---------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKS---------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt---------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ++|++|+++|++||+|. +.+         .++||||||+|.+.++|++|+++|++  ++|+.|.+..+.
T Consensus        20 ~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~~~~~~   86 (114)
T 2dnl_A           20 IDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYLCVSSP   86 (114)
T ss_dssp             CCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEEEECCS
T ss_pred             CCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEEeccCC
Confidence            68999999999999999 653         25699999999999999999999964  778888877654

>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=99.20  E-value=2e-11  Score=108.21  Aligned_cols=77  Identities=19%  Similarity=0.178  Sum_probs=63.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec--------CCCCeEEEEeCCHHHHHHHHHHhcCCccC---CCcEEEEeccCCCCCC-C
Q 004908            1 MDEQMLHNAMILFGEIERIKSY--------PSRNYSFVEFRSVDEARRAKEGLQGRLFN---DPRITIMFSSSELAPG-K   68 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~--------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~---GRrIrVefAk~~~~pg-k   68 (724)
                      +||++|+++|++||+|.+|++.        ++||||||+|.+.++|.+|++.|||..+.   ++.|+|.+++...... .
T Consensus        15 ~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (175)
T 3nmr_A           15 WSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVE   94 (175)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCSCGG
T ss_pred             CCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccccccCC
Confidence            6899999999999999999864        46899999999999999999999999886   6889999987665432 1


Q ss_pred             CCCCCCCCC
Q 004908           69 DYPGSYSGT   77 (724)
Q Consensus        69 ~~p~y~sG~   77 (724)
                      ....|+.++
T Consensus        95 ~~~l~v~nl  103 (175)
T 3nmr_A           95 DRKLFIGMI  103 (175)
T ss_dssp             GSEEEEESC
T ss_pred             CCeEEEcCC
Confidence            333455554

>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=99.19  E-value=8.7e-12  Score=102.59  Aligned_cols=62  Identities=21%  Similarity=0.313  Sum_probs=53.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-CCCCeEEEEeCCHHHHHHHHHHhcCCcc--CCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-PSRNYSFVEFRSVDEARRAKEGLQGRLF--NDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-~SRGFAFVeF~s~EdA~kAIEaLNGk~f--~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++. .+||||||+|.+.++|++    |+|..+  +|++|+|.+|+++...
T Consensus        17 ~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~----~~~~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           17 MTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQS----LCGEDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             SCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHH----TTTCEEEETTEEEEEECCCCCCCC
T ss_pred             CCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHH----HhcCCceeCCEEEEEEecCCCCCC
Confidence            6899999999999999999975 479999999999999974    566655  8999999999866543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.19  E-value=1.7e-11  Score=111.30  Aligned_cols=63  Identities=24%  Similarity=0.429  Sum_probs=58.6

Q ss_pred             CCHHHHHHHhhhc----C-------ceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILF----G-------EIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~F----G-------eI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|+.|    |       .|.++++.++||||||+|.+.++|++|+ .|||..|+|++|+|.+++...
T Consensus        16 ~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~~   89 (198)
T 2yh0_A           16 ITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQ   89 (198)
T ss_dssp             CCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCCC
T ss_pred             CCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCCC
Confidence            6899999999999    6       7888888899999999999999999999 899999999999999997653

>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=99.19  E-value=1.4e-11  Score=119.29  Aligned_cols=63  Identities=13%  Similarity=0.202  Sum_probs=58.7

Q ss_pred             CHHHHHHHhhhcCceeEeeecC-----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            2 DEQMLHNAMILFGEIERIKSYP-----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~-----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ||++|+++|++||.|++|++.+     ++|||||+|.+.++|.+|++.|||..|+|++|+|.||++..
T Consensus       198 ~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          198 DVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             CHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             CHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            8999999999999999998653     58999999999999999999999999999999999998654

>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=99.16  E-value=2.8e-11  Score=109.71  Aligned_cols=64  Identities=16%  Similarity=0.240  Sum_probs=56.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++. +|..|+|+.|+|.++.....
T Consensus        25 ~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~   94 (196)
T 1l3k_A           25 TTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSRED   94 (196)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC---
T ss_pred             CCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCccc
Confidence            6899999999999999999864      3589999999999999999977 99999999999999976543

>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=99.16  E-value=3.3e-11  Score=114.41  Aligned_cols=60  Identities=25%  Similarity=0.372  Sum_probs=56.1

Q ss_pred             HHHHHHHhhhcCceeEeeec----------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            3 EQMLHNAMILFGEIERIKSY----------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~----------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +++|++.|++||+|++|++.          ++|||+||+|.+.++|.+|+++|||+.|+||.|+|+|+..
T Consensus       143 ~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          143 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             HHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            67999999999999999864          5789999999999999999999999999999999999854

>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=99.13  E-value=6.5e-11  Score=114.65  Aligned_cols=62  Identities=10%  Similarity=0.220  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.|| |.+|++.++||||||+|.+.++|.+|++.|||..|.|++|+|+++...
T Consensus        34 ~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~~   95 (284)
T 3smz_A           34 VTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD   95 (284)
T ss_dssp             CCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCCC
Confidence            68999999999999 999999999999999999999999999999999999999999997543

>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=99.10  E-value=7.4e-11  Score=105.74  Aligned_cols=64  Identities=16%  Similarity=0.204  Sum_probs=56.5

Q ss_pred             CCHHHHHHHhhhcCceeE-----eeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIER-----IKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~s-----Vkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|+.||.|..     +++.++||||||+|.+.++|.+|+ +|||..|.|++|+|.+++....
T Consensus        25 ~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~~~~~   93 (175)
T 1fje_B           25 KSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDS   93 (175)
T ss_dssp             SCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCCCSSC
T ss_pred             CCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCCCccc
Confidence            589999999999997654     446679999999999999999999 5999999999999999986543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.09  E-value=2.7e-11  Score=109.10  Aligned_cols=62  Identities=18%  Similarity=0.118  Sum_probs=55.0

Q ss_pred             CCHHHHHHHhhhcCce----eEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEI----ERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI----~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|    ++|++.     ++||||||+|.+.++|++|++. ||+.|+||.|+|..|+.+
T Consensus        35 ~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~~  105 (123)
T 2dha_A           35 ATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTAA  105 (123)
T ss_dssp             CCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECHH
T ss_pred             CCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCHH
Confidence            6899999999999986    577653     5689999999999999999997 999999999999998643

>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=99.08  E-value=4.9e-11  Score=108.31  Aligned_cols=60  Identities=20%  Similarity=0.150  Sum_probs=53.5

Q ss_pred             CCHHHHHHHhhhcCcee--Eeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIE--RIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~--sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|+.| .|.  +|++.     ++||||||+|++.++|++|++. +|..|+||.|+|..|..
T Consensus        54 ~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~  120 (126)
T 2hgm_A           54 CTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQ  120 (126)
T ss_dssp             CCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEECH
T ss_pred             CCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECCH
Confidence            6899999999999 566  88754     5799999999999999999985 88999999999999864

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.07  E-value=3.9e-11  Score=112.39  Aligned_cols=62  Identities=13%  Similarity=0.322  Sum_probs=53.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCC----HHH----HHHHHH--HhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRS----VDE----ARRAKE--GLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s----~Ed----A~kAIE--aLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|+.||+|.+|+++      .+||||||+|.+    .++    |.+|++  +|||..|+|++|+|++=+.
T Consensus        18 tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           18 IQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             CCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECCT
T ss_pred             CCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECcc
Confidence            6899999999999999999843      689999999996    433    899999  8999999999999998653

>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=99.07  E-value=1.5e-10  Score=112.61  Aligned_cols=65  Identities=15%  Similarity=0.208  Sum_probs=58.0

Q ss_pred             CCHHHHHHHhhhcC-ceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFG-EIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FG-eI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +++++|+++|+.|| +|.+|++.     .+||||||+|.+.++|.+|++.|||..|+|++|+|.||.+...
T Consensus       129 ~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          129 YTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             CCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             CCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            58999999999999 99999865     3789999999999999999999999999999999999986544

>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=99.06  E-value=8.8e-11  Score=111.74  Aligned_cols=61  Identities=16%  Similarity=0.256  Sum_probs=55.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +++++|+++|++||+|.+|++.     .+||||||+|++.++|.+|++.++ ..|+|++|+|.+++.
T Consensus       121 ~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          121 ATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             CCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             CCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            5899999999999999999864     368999999999999999998775 499999999999864

>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=99.05  E-value=1.7e-10  Score=110.24  Aligned_cols=60  Identities=15%  Similarity=0.209  Sum_probs=53.4

Q ss_pred             CCHHHHHHHhhhcCce--eEeeecC----CCCeEEEEeCCHHHHHHHHHHhcCCccCCC----cEEEEec
Q 004908            1 MDEQMLHNAMILFGEI--ERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDP----RITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI--~sVkt~~----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GR----rIrVefA   60 (724)
                      +||++|+++|++||.|  ++|++++    .+|||||+|.+.++|.+|++.|||..|+|+    ++.|.||
T Consensus       135 ~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          135 VTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            6899999999999999  8998764    358999999999999999999999999998    4666665

>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=99.05  E-value=1.5e-10  Score=102.43  Aligned_cols=62  Identities=15%  Similarity=0.224  Sum_probs=55.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++.  +..++|+.|+|.++....
T Consensus        15 ~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~~   82 (167)
T 2cjk_A           15 TTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIPRD   82 (167)
T ss_dssp             CCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCCHH
T ss_pred             CCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccchh
Confidence            6899999999999999999864      4689999999999999999995  679999999999987543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=5.2e-10  Score=98.60  Aligned_cols=57  Identities=25%  Similarity=0.316  Sum_probs=52.9

Q ss_pred             HHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            4 QMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      .+|.++|+.||+|..|++...|  +||+|++.++|.+|++ |||..++||+|+|++++++
T Consensus        30 ~~L~~~F~~~G~Vi~vr~~~d~--~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           30 DELLQQFASFGEVILIRFVEDK--MWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             HHHHHHHHTTCCEEEEEECSSS--EEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCS
T ss_pred             HHHHHHHHhCCCeEEEEEecCC--EEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCC
Confidence            5799999999999999998654  8999999999999999 9999999999999999865

>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=98.95  E-value=6.4e-10  Score=108.22  Aligned_cols=64  Identities=22%  Similarity=0.283  Sum_probs=56.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhc-CCccC---CCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQ-GRLFN---DPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLN-Gk~f~---GRrIrVefAk~~~   64 (724)
                      +|+++|+++|+.||+|++|++.     ++||||||+|.+.++|.+|++.|| |..+.   |++|+|.++....
T Consensus       108 ~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          108 VSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             CCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            6899999999999999999864     458999999999999999999995 55555   9999999997653

>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=98.71  E-value=8.8e-09  Score=91.57  Aligned_cols=55  Identities=16%  Similarity=0.204  Sum_probs=51.0

Q ss_pred             HHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            4 QMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      .+|.+.|+.||+|..|++...|  +||+|.+.++|.+||+ |||..++||.|+|.+-.
T Consensus        39 ~~L~~~F~~~G~Vilvr~v~d~--~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           39 TELMQTLGSYGTIVLVRINQGQ--MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTE--EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHHHCCCEEEEEEecCc--EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            4689999999999999998777  9999999999999999 99999999999998754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.52  E-value=2.1e-07  Score=85.12  Aligned_cols=61  Identities=16%  Similarity=0.140  Sum_probs=56.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCC-HHHHHHHHHHhc--CCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRS-VDEARRAKEGLQ--GRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s-~EdA~kAIEaLN--Gk~f~GRrIrVefAk   61 (724)
                      +++++|+++|+.||+|..|.+.+.+-.|||+|.+ .++|.+|+++||  |..|+|..++++...
T Consensus        31 ~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           31 TCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             CCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             CCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            5789999999999999999999888899999999 899999999994  888999999997754

>1ow1_A Smart/HDAC1 associated repressor protein; beta-alpha-barrel, SPOC domain,, transcription; 1.80A {Homo sapiens} SCOP: b.131.1.3

Probab=97.73  E-value=3.4e-05  Score=76.19  Aligned_cols=110  Identities=24%  Similarity=0.457  Sum_probs=79.2

Q ss_pred             ceeeeeec-cCCcceeeeEeeeccccccc-cCC-----ceeecccccch-----hHHHHHhhhccCceEEEEeCCCch--
Q 004908          277 FIWRGIIA-KGGTPVCRARCVPFGKGIES-ELP-----EVVNCSARTGL-----DMLAKHYAEAIGFDIVFFLPDSED--  342 (724)
Q Consensus       277 ~~W~G~iA-KgG~pvC~arC~~~gk~~~~-~~P-----~~ldctaRT~l-----d~l~khy~~a~~~~vvff~P~s~~--  342 (724)
                      ..|+|.|+ |.=.-.+++.|+-....+.- -+|     ..|-+|-|--|     |-|.+.-....++-++.-|||+.+  
T Consensus        38 ~~WqG~L~LKn~~f~v~mh~v~Gn~~l~~~~L~~~~~~~~LRItQRmRLd~~qLe~V~rRi~~~~~~cilLAlp~~~~~~  117 (195)
T 1ow1_A           38 IVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGGPPLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQE  117 (195)
T ss_dssp             EEEEEEEEETTEEEEEEEEEEEECHHHHHHHSCCC---CCEEECEEEECSHHHHHHHHHHTSSTTTEEEEEEEECCSSHH
T ss_pred             hhceeeeeeecchhhhEEEEEeCcHHHHHHhCCCCCCCCceeeehhhccChHHHHHHHHHHhCCCCceEEEEecCCCCch
Confidence            78999986 66666677777766422211 122     34567777655     455666656677778888898843  


Q ss_pred             hh-----hhHHHHHHhhccccccceEeecC------CcEEEEeCCChhhhcceee
Q 004908          343 DF-----ASYTEFLRYLGSKNRAGVAKFDD------GTTLFLVPPSDFLSKVLKV  386 (724)
Q Consensus       343 D~-----~~y~eFl~YL~~K~rAgV~K~~~------~ttLFLVPPSdf~~~vLkV  386 (724)
                      |.     .-.+.|++||.+|+.||||-+..      .-+|++.||.+|+.+.|+=
T Consensus       118 d~~~q~~~L~~~fV~YL~qKqAAGIisl~~~~s~~~~~vlhiFPPCeFs~~~L~~  172 (195)
T 1ow1_A          118 DVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSR  172 (195)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHTEEEEEEECCTTCCSCCEEEEEECSSHHHHHHHHH
T ss_pred             hhHhhhhHHHHHHHHHHHhCccceEEecCCCCCCCcceEEEEcCCcHHHHHHHHH
Confidence            22     33567999999999999999985      4789999999999988765

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.64  E-value=7.5e-05  Score=68.71  Aligned_cols=59  Identities=17%  Similarity=0.116  Sum_probs=56.0

Q ss_pred             CCHHHHHHHhhhc-----CceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEe
Q 004908            1 MDEQMLHNAMILF-----GEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF   59 (724)
Q Consensus         1 VdEedLrelFS~F-----GeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVef   59 (724)
                      |+++-++.+..+|     |.|++|.+.+.-|=|+|+|+|+..|-+|.-+|||.+|+||+|+|.=
T Consensus        33 vndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           33 VSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             CCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            5788999999999     9999999999999999999999999999999999999999999853

>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=97.16  E-value=0.00036  Score=63.11  Aligned_cols=59  Identities=12%  Similarity=0.163  Sum_probs=53.8

Q ss_pred             HHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            4 QMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +.++++|..|+++......++=.=.-|.|.+.++|.+|...|||..|+|++|+|-||..
T Consensus        25 ~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A           25 AKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             HHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             HHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            57899999999999988777655668999999999999999999999999999999983

>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=96.28  E-value=0.0011  Score=59.34  Aligned_cols=40  Identities=8%  Similarity=-0.045  Sum_probs=37.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHh-cCCccCCCcEEEEeccCC
Q 004908           23 PSRNYSFVEFRSVDEARRAKEGL-QGRLFNDPRITIMFSSSE   63 (724)
Q Consensus        23 ~SRGFAFVeF~s~EdA~kAIEaL-NGk~f~GRrIrVefAk~~   63 (724)
                      +-+|+++|+|.+.++|++|+++| ||..++| .|+|++++..
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            56899999999999999999999 9999999 9999998754

>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=95.42  E-value=0.0066  Score=54.31  Aligned_cols=37  Identities=11%  Similarity=-0.130  Sum_probs=30.4

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEe
Q 004908           23 PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF   59 (724)
Q Consensus        23 ~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVef   59 (724)
                      +++|||||+|.+.++|++|++.+++....+..+.+..
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~   47 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDD   47 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEET
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccC
Confidence            6899999999999999999999998665555555443

>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=95.36  E-value=0.024  Score=52.27  Aligned_cols=55  Identities=20%  Similarity=0.312  Sum_probs=46.3

Q ss_pred             HHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCC-CcEEEEe
Q 004908            4 QMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFND-PRITIMF   59 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G-RrIrVef   59 (724)
                      ..+-+.|++||+|.+.......++-.|.|.+..+|++|+.. ||+.|+| -.|-|..
T Consensus        38 ~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           38 SYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKP   93 (119)
T ss_dssp             HHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEE
T ss_pred             HHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEE
Confidence            45678999999999998755678999999999999999987 9999986 4455544

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.72  E-value=0.04  Score=60.33  Aligned_cols=44  Identities=25%  Similarity=0.370  Sum_probs=34.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCC-eEEEEeCCHHHHHHHHHH
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRN-YSFVEFRSVDEARRAKEG   44 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRG-FAFVeF~s~EdA~kAIEa   44 (724)
                      ++|.+|.+.|+.||.|.++...+.+| ||.|+|.+.+++..+++.
T Consensus        64 ~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           64 ISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             ---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             CCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            47899999999999999999998888 999999999988866544

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=89.34  E-value=0.3  Score=45.87  Aligned_cols=57  Identities=14%  Similarity=0.197  Sum_probs=45.2

Q ss_pred             HHHHHHhhhcCceeE-eee----------------c---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            4 QMLHNAMILFGEIER-IKS----------------Y---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         4 edLrelFS~FGeI~s-Vkt----------------~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      ..+-+.|++||.|.+ +..                +   ...++-.|+|.+..+|.+|+. .||+.|+|.-|-|..-+
T Consensus        21 ~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           21 NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeEeCcEEEEEEECC
Confidence            456689999999976 211                1   146788999999999999996 59999999888887654

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=86.36  E-value=3.7  Score=37.28  Aligned_cols=64  Identities=13%  Similarity=0.184  Sum_probs=49.3

Q ss_pred             CCHHHHHHHhhhc-----CceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCC
Q 004908            1 MDEQMLHNAMILF-----GEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGK   68 (724)
Q Consensus         1 VdEedLrelFS~F-----GeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk   68 (724)
                      ++++.|+-.|+.=     |+|++|+..+  +=|+|+|.+.+.|++.++.- -..|+|-+|.| +....+.+.|
T Consensus        20 ~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k~-~H~L~~~~LsV-~P~~~~~~~r   88 (104)
T 2dhx_A           20 VPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQA-DHELHGAQLSL-RPAPPRAPAR   88 (104)
T ss_dssp             SCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTCS-CCBSSSSBCEE-EECCCCCCCC
T ss_pred             CChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcCC-cceecCeEEEE-EcCCCCCcce
Confidence            4688899999882     8999999876  78999999999998877651 23677789998 4444555545

>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=83.05  E-value=2.7  Score=36.89  Aligned_cols=62  Identities=11%  Similarity=0.310  Sum_probs=48.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC--------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCc-----EEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP--------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPR-----ITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~--------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRr-----IrVefAk~   62 (724)
                      +||+++.+.+++..++.-..-.+        .-.-|+|.|.+.|++.+-.+.++|..|.+.+     -.|+||--
T Consensus        13 LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~VE~AP~   87 (91)
T 1uw4_A           13 LTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPF   87 (91)
T ss_dssp             CCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECEEEECSS
T ss_pred             CCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeEEEEcCC
Confidence            58999999999999876554221        1246999999999999999999999995542     35777743

---

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	724
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	7e-05
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-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-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.002

>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 = 46.5 bits (110), Expect = 3e-07
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 6/66 (9%)

Query: 1  MDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          + E ML+      G I  I       +  S  Y++V F+   +A RA + +   +     
Sbjct: 12 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 71

Query: 55 ITIMFS 60
          + IM+S
Sbjct: 72 VRIMWS 77

>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 = 45.3 bits (107), Expect = 8e-07
 Identities = 8/62 (12%), Positives = 23/62 (37%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          + E+ +      +G+   +  +  + + F+   +   A  AK  L        ++ + F+
Sbjct: 20 ITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA 79

Query: 61 SS 62
            
Sbjct: 80 CH 81

>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 = 45.8 bits (108), Expect = 1e-06
 Identities = 11/71 (15%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPS---RNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI 57
          +  + +++    +G I +I+   +   R  ++V +  + +A+ A + L G    +  + +
Sbjct: 19 ITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVV 78

Query: 58 MFSSSELAPGK 68
          ++ ++  A  K
Sbjct: 79 LYYNANRAFQK 89

>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 = 44.2 bits (104), Expect = 2e-06
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 7/76 (9%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSR------NYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
            E+ ++      G+I++I     +       + FVE+ S  +A  A   + G   +D  
Sbjct: 19 TTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 78

Query: 55 ITIMFSSSELAPGKDY 70
          I   + +     G+ Y
Sbjct: 79 IRTDWDAGF-KEGRQY 93

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 3e-06
 Identities = 14/60 (23%), Positives = 27/60 (45%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
          + +Q++      FG+I  I+ +P + YSFV F + + A  A   + G       +   + 
Sbjct: 30 LTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG 89

>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 = 43.4 bits (102), Expect = 3e-06
 Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 5/67 (7%)

Query: 1  MDEQMLHNAMILFGEIERIK-----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
          + +  +      FG +++       S  S   + V F    +A +A +   G   +   +
Sbjct: 12 VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 71

Query: 56 TIMFSSS 62
           I   +S
Sbjct: 72 NIQLVTS 78

>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 = 40.7 bits (95), Expect = 3e-05
 Identities = 10/63 (15%), Positives = 21/63 (33%), Gaps = 6/63 (9%)

Query: 1  MDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          + +  L      +G I +        +   R  +FV +   +EA+ A   L   +     
Sbjct: 18 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGS 77

Query: 55 ITI 57
            +
Sbjct: 78 QPL 80

>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 = 40.0 bits (93), Expect = 5e-05
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 9/75 (12%)

Query: 1  MDEQMLHNAMILFGEI---------ERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
            E+ L       G I          +     S  + FVE++  ++A++A + LQG   +
Sbjct: 10 TTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD 69

Query: 52 DPRITIMFSSSELAP 66
            ++ +  S     P
Sbjct: 70 GHKLEVRISERATKP 84

>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 = 40.3 bits (94), Expect = 7e-05
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 3  EQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
           + L      FG+I ++  +       + V FR  +EA    + L GR F   +IT    
Sbjct: 33 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>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 = 39.9 bits (93), Expect = 7e-05
 Identities = 13/71 (18%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 1  MDEQMLHNAMILFGEIERIK-------SYPSRNYSFVEFRSVDEARRAKEGL-QGRLFND 52
           +++ +      FGE++ ++       +   R + FV+F +  +A++A   L        
Sbjct: 20 ANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG 79

Query: 53 PRITIMFSSSE 63
           R+ + ++ SE
Sbjct: 80 RRLVLEWADSE 90

>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 = 39.7 bits (92), Expect = 1e-04
 Identities = 13/54 (24%), Positives = 26/54 (48%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
          +    L   +   G ++ +   P++ YSF  +R+ +E++RA   L G+   D  
Sbjct: 32 VSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDL 85

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 6/63 (9%)

Query: 1  MDEQMLHNAMILFGEIER------IKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
            E+ L      +G I         +S  SR ++FV F +VD+A+ AKE   G   +  R
Sbjct: 21 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 80

Query: 55 ITI 57
          I +
Sbjct: 81 IRV 83

>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 = 38.1 bits (88), Expect = 4e-04
 Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 5/65 (7%)

Query: 1   MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRI 55
             E++       +GE+E +              +V+FR  ++A +A   L  R FN   I
Sbjct: 39  FFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI 98

Query: 56  TIMFS 60
               S
Sbjct: 99  HAELS 103

>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 = 37.7 bits (87), Expect = 6e-04
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 1  MDEQMLHNAMILFGEIER---IKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI 57
          + ++     ++   EI R       P     FVEF SV + ++A +GL GR F +  +  
Sbjct: 31 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90

Query: 58 MFSSSE 63
           +   +
Sbjct: 91 KYCDPD 96

>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 = 36.9 bits (85), Expect = 7e-04
 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 8/68 (11%)

Query: 1  MDEQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN--D 52
          M ++ L      +G I          +  SR   F+ F    EA  A +GL G+  +   
Sbjct: 18 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT 77

Query: 53 PRITIMFS 60
            IT+ F+
Sbjct: 78 EPITVKFA 85

>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 = 36.3 bits (83), Expect = 0.002
 Identities = 7/60 (11%), Positives = 18/60 (30%)

Query: 1  MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
                 +    + +    + + S     + F +   A  A+  L    F    + + F+
Sbjct: 22 ETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFA 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	724
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.67
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.6
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.59
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.58
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.58
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.57
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.57
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.57
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.57
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.57
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.57
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.56
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.55
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.55
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.55
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.55
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.55
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.54
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.54
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.54
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.54
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.53
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.53
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.53
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.53
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.53
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.52
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.52
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.51
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.51
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.51
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.5
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.5
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.5
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.5
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.5
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.5
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	99.49
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.46
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.46
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.46
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.45
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.45
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.45
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.44
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.44
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.42
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.42
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.42
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.41
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.41
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.4
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.4
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.4
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.39
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.39
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.37
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.37
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.36
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.36
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.35
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.35
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.34
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.32
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.3
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.3
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.3
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.25
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.25
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.24
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.22
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.2
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.18
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.13
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.11
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.99
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.54
d1ow1a_	170	SMART/HDAC1 associated repressor protein, SHARP {H	97.23
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.17
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.88
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	81.23

>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=99.67  E-value=4.1e-17  Score=133.28  Aligned_cols=64  Identities=23%  Similarity=0.431  Sum_probs=61.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|.+|++.+.||||||+|.+.++|.+|+++|||..|+|++|+|+||++++
T Consensus        15 ~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1          15 MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            6899999999999999999999999999999999999999999999999999999999998653

>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=99.64  E-value=1.2e-16  Score=135.43  Aligned_cols=65  Identities=22%  Similarity=0.483  Sum_probs=62.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|++|++.+.||||||+|.+.++|.+|++.|||+.|+|++|+|+||++.+.
T Consensus        30 ~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p~   94 (96)
T d1x4ga1          30 LTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD   94 (96)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999987543

>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=8.3e-16  Score=130.40  Aligned_cols=64  Identities=19%  Similarity=0.189  Sum_probs=61.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|++|++.+.||||||+|.+.++|.+|++.|||..|.|++|+|+||....
T Consensus        22 ~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          22 TLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            6899999999999999999999999999999999999999999999999999999999997653

>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=99.60  E-value=1e-15  Score=129.75  Aligned_cols=64  Identities=20%  Similarity=0.322  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      |||++|+++|++||+|++|++.+ .||||||+|++.++|.+|++.|||..|+|++|+|+||+...
T Consensus        15 ~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1          15 VTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            68999999999999999999764 57999999999999999999999999999999999997554

>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=99.59  E-value=7.9e-16  Score=127.84  Aligned_cols=64  Identities=13%  Similarity=0.263  Sum_probs=61.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|.+|++.+.||||||+|++.++|.+|++.|||..|+|++|+|+||....
T Consensus        20 ~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          20 ITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            6899999999999999999999999999999999999999999999999999999999998653

>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=99.58  E-value=9e-16  Score=124.71  Aligned_cols=62  Identities=24%  Similarity=0.396  Sum_probs=58.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||++
T Consensus        14 ~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          14 MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            6899999999999999999853      3689999999999999999999999999999999999985

>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=5.7e-16  Score=126.40  Aligned_cols=63  Identities=25%  Similarity=0.401  Sum_probs=58.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++.|||+.|+|++|+|.||+.+
T Consensus        12 ~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~d   80 (80)
T d1cvja1          12 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD   80 (80)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCCC
T ss_pred             CCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            6899999999999999999964      35799999999999999999999999999999999999753

>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=99.58  E-value=6.8e-16  Score=131.48  Aligned_cols=62  Identities=18%  Similarity=0.357  Sum_probs=58.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||+|++|++  .||||||+|++.++|++|+++|||+.|+|++|+|+||+..+
T Consensus        28 ~~~~~L~~~F~~~G~i~~~~i--~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          28 VKKSDVEAIFSKYGKIVGCSV--HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             CCHHHHHHSSTTSSCEEEEEE--ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCHHHHHHHHhhcCCEEEEEE--eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            468899999999999999998  58999999999999999999999999999999999998653

>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=6.2e-16  Score=126.70  Aligned_cols=64  Identities=19%  Similarity=0.155  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCC-ccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGR-LFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk-~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||.|.++++.+.||||||+|.+.++|.+|++.|||+ .|+|++|+|+||.++.
T Consensus        13 ~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1          13 VTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            689999999999999999999899999999999999999999999997 5999999999998654

>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=99.57  E-value=2.4e-15  Score=126.87  Aligned_cols=66  Identities=20%  Similarity=0.366  Sum_probs=62.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|++|++.+.|+||||+|.+.++|.+|++.|||..|.|  ++|+|+||+.++..
T Consensus        29 ~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~~s   96 (97)
T d1whya_          29 TSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS   96 (97)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCCC
T ss_pred             CCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCCCC
Confidence            6899999999999999999999999999999999999999999999999987  58999999977654

>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=99.57  E-value=1.1e-15  Score=123.98  Aligned_cols=62  Identities=24%  Similarity=0.385  Sum_probs=58.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      ++|++|+++|++||+|++|++.      +.||||||+|.+.++|++|++.|||..|+|++|+|+||++
T Consensus        14 ~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            6899999999999999999854      4679999999999999999999999999999999999985

>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=99.57  E-value=1.8e-15  Score=123.21  Aligned_cols=62  Identities=16%  Similarity=0.245  Sum_probs=58.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|++||+|++|++.     ++||||||+|.+.++|.+|++.|||+.|+|++|+|++|..
T Consensus        12 ~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_          12 VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             CCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            6899999999999999999864     5789999999999999999999999999999999999863

>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=99.57  E-value=1e-15  Score=125.33  Aligned_cols=65  Identities=22%  Similarity=0.370  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++|++.         ++||||||+|.+.++|.+|++.|||..|+|++|+|+||++...
T Consensus        10 ~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~~k   83 (85)
T d2cpfa1          10 TTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK   83 (85)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSC
T ss_pred             CCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            6899999999999999999854         2589999999999999999999999999999999999975543

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=3.4e-15  Score=125.92  Aligned_cols=66  Identities=17%  Similarity=0.337  Sum_probs=60.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|.+|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|++|+.+...
T Consensus        20 ~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~   91 (99)
T d1whwa_          20 SSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             CCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCcc
Confidence            6899999999999999999853      47899999999999999999999999999999999999876544

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.8e-15  Score=125.64  Aligned_cols=65  Identities=23%  Similarity=0.438  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|++|++.    .+||||||+|.+.++|.+|++.|||..|+|++|+|+||+++..
T Consensus        23 ~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~~   91 (93)
T d2cq3a1          23 FRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   91 (93)
T ss_dssp             CCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             CCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCCC
Confidence            6899999999999999999865    3689999999999999999999999999999999999987643

>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=99.57  E-value=1.2e-15  Score=126.79  Aligned_cols=63  Identities=25%  Similarity=0.388  Sum_probs=58.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||+.+
T Consensus        19 ~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          19 AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             CCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            6899999999999999999854      36899999999999999999999999999999999999864

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=3e-15  Score=125.93  Aligned_cols=65  Identities=20%  Similarity=0.468  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-------CCCCeEEEEeCCHHHHHHHHHHh-cCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-------PSRNYSFVEFRSVDEARRAKEGL-QGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaL-NGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|+.||+|++|++.       ++||||||+|.+.++|.+|++.| ||..|+|++|+|+||+.+..
T Consensus        20 ~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~~   92 (94)
T d2cpha1          20 ANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   92 (94)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             CCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCCC
Confidence            6899999999999999999853       46899999999999999999999 99999999999999987653

>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=99.56  E-value=1.4e-15  Score=124.15  Aligned_cols=66  Identities=27%  Similarity=0.473  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEe-ee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERI-KS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sV-kt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|++||+|.++ ++      .++||||||+|.+.++|++|+++|||..|+|++|+|+||.++...
T Consensus        10 ~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~k   82 (83)
T d1x5ta1          10 IDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   82 (83)
T ss_dssp             CCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             CcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCcC
Confidence            6899999999999999765 33      256899999999999999999999999999999999999876544

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=3.6e-15  Score=125.14  Aligned_cols=66  Identities=21%  Similarity=0.370  Sum_probs=61.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|+.||.|..|++.   .+||||||+|++.++|.+|++.|||..|+|++|+|+||+..+..
T Consensus        26 ~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~r~~   94 (95)
T d1x4aa1          26 IRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT   94 (95)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCCC
T ss_pred             CCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCCCCC
Confidence            6899999999999999999864   47899999999999999999999999999999999999977654

>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=99.55  E-value=2.2e-15  Score=130.15  Aligned_cols=63  Identities=11%  Similarity=0.126  Sum_probs=59.5

Q ss_pred             HHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            3 EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +++|+++|+.||+|.+|++.++||||||+|.+.++|.+|+++|||+.|+|++|+|+||+....
T Consensus        24 k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~   86 (104)
T d1weya_          24 RAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI   86 (104)
T ss_dssp             HHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSC
T ss_pred             HHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCC
Confidence            478999999999999999999999999999999999999999999999999999999976544

>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=99.55  E-value=1.4e-15  Score=126.55  Aligned_cols=63  Identities=24%  Similarity=0.432  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||+|++|++.      .+||||||+|.+.++|.+|++.|||..|+|++|+|+||++.
T Consensus        20 ~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          20 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             CCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             CCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            6899999999999999999854      46899999999999999999999999999999999999865

>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=99.55  E-value=1.5e-15  Score=126.12  Aligned_cols=64  Identities=31%  Similarity=0.464  Sum_probs=59.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC----CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~----SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|+.||+|.+|++..    +||||||+|.+.++|++|++.|||..|+|++|+|++|+++.
T Consensus        20 ~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2          20 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            68999999999999999998653    68999999999999999999999999999999999998654

>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=99.55  E-value=3.7e-15  Score=125.09  Aligned_cols=65  Identities=20%  Similarity=0.227  Sum_probs=60.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|.+|++.      .+||||||+|.+.++|++|++.|||..|+|++|+|.||+++..
T Consensus        21 ~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~~   91 (93)
T d1x5ua1          21 VSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   91 (93)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             CCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            6899999999999999999853      5789999999999999999999999999999999999987653

>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=99.54  E-value=2.6e-15  Score=124.71  Aligned_cols=64  Identities=27%  Similarity=0.468  Sum_probs=59.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|+++|||..|+|++|+|+||++++
T Consensus        17 ~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1          17 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             CCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            6899999999999999999853      579999999999999999999999999999999999998654

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=3.4e-15  Score=123.49  Aligned_cols=64  Identities=19%  Similarity=0.423  Sum_probs=59.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+...
T Consensus        13 ~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          13 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             CCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            6899999999999999999864      568999999999999999999999999999999999998543

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=3.9e-15  Score=122.36  Aligned_cols=64  Identities=19%  Similarity=0.322  Sum_probs=61.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||.|..+++.++||||||+|.+.++|.+|++.|||..|+|++|+|.||++..
T Consensus        20 ~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          20 TSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            6899999999999999999998999999999999999999999999999999999999998654

>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=99.54  E-value=6.9e-15  Score=119.53  Aligned_cols=63  Identities=10%  Similarity=0.202  Sum_probs=59.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++|| |..+++.+.||||||+|.+.++|.+|++.|||+.++|++|+|+||+.+.
T Consensus        10 ~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1          10 VTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             CCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            68999999999999 7788888999999999999999999999999999999999999997653

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.3e-15  Score=125.75  Aligned_cols=75  Identities=21%  Similarity=0.271  Sum_probs=64.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCCCCCCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGSY   74 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~pgk~~p~y~   74 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.||+ .|+|++|+|.+|..+..+.+.-+.|.
T Consensus        22 ~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~~~pr~~~~g~~  100 (103)
T d2cqda1          22 TTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFA  100 (103)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTCCCCCCCCCCS
T ss_pred             CcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCCCCCCCCCCCCC
Confidence            6899999999999999999864      5789999999999999999999987 69999999999987766554545554


Q ss_pred             CC
Q 004908           75 SG   76 (724)
Q Consensus        75 sG   76 (724)
                      -|
T Consensus       101 ~G  102 (103)
T d2cqda1         101 IG  102 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            33

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.53  E-value=5.2e-15  Score=131.02  Aligned_cols=64  Identities=33%  Similarity=0.500  Sum_probs=59.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|+||+...
T Consensus        54 ~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~  123 (139)
T d1u6fa1          54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH  123 (139)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCC
T ss_pred             CCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            6899999999999999999864      368999999999999999999999999999999999997544

>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=99.53  E-value=5.6e-15  Score=126.61  Aligned_cols=63  Identities=14%  Similarity=0.323  Sum_probs=58.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||+|++|++.   ++||||||+|.+.++|.+|++.|||..|+|++|+|+||...
T Consensus        19 ~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1          19 ITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            6899999999999999999865   57999999999999999999999999999999999999653

>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=99.53  E-value=4.1e-15  Score=126.69  Aligned_cols=65  Identities=20%  Similarity=0.353  Sum_probs=60.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|+.||+|.+|++.      ++||||||+|.+.++|.+|+++|||..|+|++|+|+||+++..
T Consensus        30 ~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          30 FGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             CCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             CCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            6899999999999999999853      4689999999999999999999999999999999999987654

>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=99.53  E-value=7.9e-15  Score=121.17  Aligned_cols=65  Identities=23%  Similarity=0.444  Sum_probs=59.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|.+|++.      .+||||||+|.+.++|++|++.|||..|+|++|+|++|.+...
T Consensus        17 ~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          17 TNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             CCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             CCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            6899999999999999999743      4799999999999999999999999999999999999976544

>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=99.53  E-value=4.8e-15  Score=120.36  Aligned_cols=62  Identities=15%  Similarity=0.238  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|++||+|.++++      .++||||||+|.+.++|.+|++.|||..|+|++|+|.||++
T Consensus        13 ~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          13 YTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            689999999999999987764      35799999999999999999999999999999999999985

>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=99.53  E-value=6.1e-15  Score=123.78  Aligned_cols=63  Identities=21%  Similarity=0.281  Sum_probs=58.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|++||+|++|++.      .+||||||+|.+.++|.+|++.|||..|+|++|+|+||...
T Consensus        19 ~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~   87 (93)
T d1h2vz_          19 TTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF   87 (93)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCC
T ss_pred             CCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            6899999999999999999864      46799999999999999999999999999999999999643

>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=99.52  E-value=8.1e-15  Score=121.86  Aligned_cols=64  Identities=19%  Similarity=0.323  Sum_probs=59.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|+.||+|++|++.    ..||||||+|.+.++|.+|++.|||..|.|+.|+|.||++..
T Consensus        20 ~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~   87 (90)
T d2cqia1          20 VTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   87 (90)
T ss_dssp             CCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             CCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            6899999999999999999864    368999999999999999999999999999999999998653

>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=99.52  E-value=2.3e-14  Score=122.22  Aligned_cols=66  Identities=21%  Similarity=0.242  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHh--cCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGL--QGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaL--NGk~f~GRrIrVefAk~~~~p   66 (724)
                      |||++|+++|++||+|++|++.+.||||||+|++.++|++|++.|  ++..++|++|+|.||+.+...
T Consensus        27 ~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~~   94 (104)
T d1wexa_          27 VVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             CCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCccC
Confidence            689999999999999999999999999999999999999999988  556789999999999876543

>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=99.51  E-value=1.6e-14  Score=118.53  Aligned_cols=62  Identities=27%  Similarity=0.409  Sum_probs=57.5

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-CCCeEEEEeCCHHHHHHHHHHhcCCcc-CCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-SRNYSFVEFRSVDEARRAKEGLQGRLF-NDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-SRGFAFVeF~s~EdA~kAIEaLNGk~f-~GRrIrVefAk~   62 (724)
                      +||++|+++|+.||+|++|++.+ .||||||+|.+.++|.+|++.|||..| +|++|+|+|||+
T Consensus        20 ~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~akk   83 (83)
T d2b0ga1          20 TNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK   83 (83)
T ss_dssp             CCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECCC
T ss_pred             CCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEecC
Confidence            68999999999999999999765 579999999999999999999999998 568999999984

>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=99.51  E-value=1.6e-14  Score=119.18  Aligned_cols=63  Identities=21%  Similarity=0.293  Sum_probs=57.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCcc-CCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLF-NDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f-~GRrIrVefAk~~   63 (724)
                      ++|++|+++|++||+|.++...  +.||||||+|++.++|.+|+++|||..+ +|+.|+|+|||..
T Consensus        22 ~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          22 VSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            6899999999999999888754  5789999999999999999999999988 6899999999864

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.1e-14  Score=124.78  Aligned_cols=65  Identities=20%  Similarity=0.294  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCcc--CCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLF--NDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f--~GRrIrVefAk~~~~   65 (724)
                      |||++|+++|++||+|++|+++  +.||||||+|.+.++|.+|++.|||+.|  .|++|+|.|++....
T Consensus        19 vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          19 VTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             CCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            6899999999999999999875  5789999999999999999999999998  578999999986543

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.50  E-value=9.6e-15  Score=120.77  Aligned_cols=61  Identities=26%  Similarity=0.456  Sum_probs=55.5

Q ss_pred             CHHHHHHHhhhcCceeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            2 DEQMLHNAMILFGEIERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +|++|+++|++||+|++|++.       ++||||||+|.+.++|.+|++ |||..|+|++|+|.||+++
T Consensus        18 ~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          18 DENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             CHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             cHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            466799999999999999853       468999999999999999996 9999999999999999865

>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=99.50  E-value=7.2e-15  Score=124.60  Aligned_cols=64  Identities=22%  Similarity=0.372  Sum_probs=59.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..|+|++|+|+||..+.
T Consensus        20 ~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~~   89 (104)
T d1p1ta_          20 ATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             SCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             CCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            6899999999999999999854      368999999999999999999999999999999999997653

>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=99.50  E-value=1.3e-14  Score=119.73  Aligned_cols=60  Identities=28%  Similarity=0.412  Sum_probs=55.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefA   60 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++.|||..++|  ++|+|.||
T Consensus        18 ~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          18 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            6899999999999999999864      468999999999999999999999999998  56999997

>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=6.7e-15  Score=122.63  Aligned_cols=63  Identities=11%  Similarity=0.193  Sum_probs=57.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++|| |..+++.+.||||||+|.+.++|++|+++|||..|+|++|+|+||+.+.
T Consensus        17 ~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_          17 SNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             cChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            68999999999999 5556677789999999999999999999999999999999999997654

>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=99.50  E-value=1e-14  Score=120.88  Aligned_cols=64  Identities=17%  Similarity=0.156  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|++||+|.+|++. .+|||||+|.+.++|++|++.|||+.|+|+.|+|.|++.+..
T Consensus        12 ~~~~~l~~~F~~~G~v~~~~i~-~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~   75 (87)
T d3begb1          12 GSWQDLKDHMREAGDVCYADVY-RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   75 (87)
T ss_dssp             CCTTHHHHHHGGGSCEEEEEEC-TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             CCHHHHHHHHhhhccccccccc-ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcC
Confidence            6899999999999999999975 579999999999999999999999999999999999875543

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.50  E-value=1.3e-14  Score=119.15  Aligned_cols=60  Identities=17%  Similarity=0.323  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCC--CcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFND--PRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~G--RrIrVefA   60 (724)
                      ++|++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..+.|  ++|+|.||
T Consensus        18 ~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          18 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             CCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            6899999999999999999854      468999999999999999999999999987  88999997

>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=99.49  E-value=7.1e-15  Score=126.94  Aligned_cols=60  Identities=25%  Similarity=0.381  Sum_probs=56.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|++||+|++|++.     ++||||||+|.+.++|.+|++.|||+.|+||+|+|+|+
T Consensus        39 ~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          39 FFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3588999999999999999964     57899999999999999999999999999999999986

>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=99.47  E-value=2.2e-14  Score=121.98  Aligned_cols=64  Identities=11%  Similarity=0.167  Sum_probs=60.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHH--HhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKE--GLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIE--aLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|.+|++.+.||||||+|.+.++|.+|++  ++++..|+|++|+|.||++..
T Consensus        31 ~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          31 YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             CCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             cCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            5899999999999999999999999999999999999999998  688999999999999997653

>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=99.47  E-value=2.2e-14  Score=120.15  Aligned_cols=64  Identities=17%  Similarity=0.132  Sum_probs=59.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHh--cCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGL--QGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaL--NGk~f~GRrIrVefAk~~~   64 (724)
                      +||+||+++|++||+|.+|++.+.|+||||+|++.++|.+|++.|  ++..++|++|+|+||++..
T Consensus        21 ~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1          21 NLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             SHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             CCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            478999999999999999999999999999999999999999966  7888999999999998543

>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=99.46  E-value=2.5e-14  Score=119.62  Aligned_cols=64  Identities=14%  Similarity=0.202  Sum_probs=56.8

Q ss_pred             CCHHHHHHHhhhcCceeEee--------------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK--------------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk--------------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|+.||+|..+.              +.+++|||||+|.+.++|.+|++.|||..|+|++|+|.+|+.+.
T Consensus        20 ~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          20 VTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             CCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             CCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            68999999999999996442              12467999999999999999999999999999999999998653

>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=99.46  E-value=2.5e-14  Score=116.78  Aligned_cols=57  Identities=32%  Similarity=0.525  Sum_probs=53.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEE
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI   57 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrV   57 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.|||..|+|++|+|
T Consensus        21 ~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          21 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            6899999999999999999853      46899999999999999999999999999999997

>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=3.3e-14  Score=120.96  Aligned_cols=64  Identities=14%  Similarity=0.070  Sum_probs=59.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      ++|++|+++|+.||+|++|++. .+|||||+|.+.++|++|++.|||.+|+|+.|+|.|++.+..
T Consensus        27 ~~~~~L~~~F~~~G~v~~~~i~-~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          27 GSWQDLKDHMREAGDVCYADVQ-KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             CCHHHHHHHHTTSSCEEEEEEE-TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             CCHHHHHHHHHhhccccccccc-ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            6899999999999999999976 689999999999999999999999999999999999976544

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=4.8e-14  Score=116.48  Aligned_cols=64  Identities=17%  Similarity=0.223  Sum_probs=59.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHh--cCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGL--QGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaL--NGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|++||.|.+|++.+.+|||||+|.+.++|++|++.|  ++..++|++|+|.||+.+.
T Consensus        20 ~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          20 VTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             CCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             CCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            689999999999999999999999999999999999999999976  5778999999999998653

>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=99.45  E-value=1.3e-14  Score=121.93  Aligned_cols=65  Identities=18%  Similarity=0.293  Sum_probs=60.0

Q ss_pred             CCHHHHHHHhhhcCceeEeee-cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS-YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt-~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|+.||+|..++. .++||||||+|.+.++|.+|++.|||..|+|++|+|+||+++..
T Consensus        28 ~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          28 ITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             CCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            689999999999999998864 46799999999999999999999999999999999999987654

>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=99.45  E-value=8.3e-14  Score=115.57  Aligned_cols=64  Identities=14%  Similarity=0.352  Sum_probs=57.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhc------CCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQ------GRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLN------Gk~f~GRrIrVefAk~~~   64 (724)
                      +||++|+++|++||+|.+|++.      .+||||||+|.+.++|.+|++.||      |..|+|++|+|+||+++.
T Consensus        20 ~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          20 SEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             CCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCC
Confidence            6899999999999999999853      478999999999999999999997      678999999999998653

>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=99.44  E-value=3.2e-14  Score=119.41  Aligned_cols=64  Identities=19%  Similarity=0.179  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+++|+.||.|.++++      .++||||||+|.+.++|.+|++.|||..|.|++|+|+||+++.
T Consensus        30 ~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~   99 (102)
T d2cpxa1          30 VTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK   99 (102)
T ss_dssp             CCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCS
T ss_pred             CCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCcc
Confidence            689999999999999998864      3589999999999999999999999999999999999998654

>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=99.44  E-value=1.8e-14  Score=120.86  Aligned_cols=62  Identities=18%  Similarity=0.218  Sum_probs=57.2

Q ss_pred             CCHHHHHHHhhhcCceeEeee-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKS-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||.|.+|++     .++||||||+|.+.++|.+|++ |||..|+|++|+|++|+.+
T Consensus        25 ~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          25 KSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             SCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             chHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCCC
Confidence            689999999999999988764     4789999999999999999996 9999999999999999853

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=1e-13  Score=110.25  Aligned_cols=59  Identities=17%  Similarity=0.250  Sum_probs=54.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +||++|+++|+.||.|+++.+.      +.+|||||+|.+.++|++|++ |||..|+|++|+|.+|
T Consensus        11 ~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          11 TTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            6899999999999999999743      578999999999999999996 9999999999999987

>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=99.42  E-value=3.9e-14  Score=121.24  Aligned_cols=62  Identities=21%  Similarity=0.346  Sum_probs=57.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||+|.+|++.      ++||||||+|.+.++|.+|+ +|||..|+|++|+|.+|+++
T Consensus        30 ~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          30 IRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHH
T ss_pred             CCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEECCCC
Confidence            6899999999999999999854      57999999999999999999 49999999999999998654

>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=99.42  E-value=8.8e-14  Score=115.76  Aligned_cols=64  Identities=27%  Similarity=0.399  Sum_probs=57.3

Q ss_pred             CCHHHHH----HHhhhcCceeEeeec---CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCC
Q 004908            1 MDEQMLH----NAMILFGEIERIKSY---PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSEL   64 (724)
Q Consensus         1 VdEedLr----elFS~FGeI~sVkt~---~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~   64 (724)
                      ++|++|+    ++|++||+|++|++.   ++||||||+|++.++|.+|++.|||..|+|++|+|.||+.+.
T Consensus        15 ~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~   85 (91)
T d1nu4a_          15 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   85 (91)
T ss_dssp             SCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             CCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCc
Confidence            5777775    568999999999864   469999999999999999999999999999999999998654

>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=99.41  E-value=5.3e-14  Score=119.36  Aligned_cols=62  Identities=23%  Similarity=0.363  Sum_probs=56.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|+.||+|.++++.     ++||||||+|.+.++|.+|++.|||+.|.||+++|.++++
T Consensus        30 ~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          30 MDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            6899999999999999988743     4689999999999999999999999999999999987764

>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=99.41  E-value=1.1e-13  Score=118.92  Aligned_cols=65  Identities=18%  Similarity=0.226  Sum_probs=58.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      ++|++|+++|++||+|++|++.      .+||||||+|.+.++|.+|++ |||..|+|++|+|.+|+++...
T Consensus        32 ~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke~~  102 (103)
T d1x4ba1          32 TTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES  102 (103)
T ss_dssp             CCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCCCC
T ss_pred             CCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccCCC
Confidence            6899999999999999999863      579999999999999999995 8999999999999999876543

>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=99.40  E-value=6.5e-14  Score=114.42  Aligned_cols=59  Identities=17%  Similarity=0.228  Sum_probs=54.8

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +||++|+++|++||+|++|++      .++||||||+|.+.++|++|++ |||..|+||+|+|..|
T Consensus        12 ~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          12 TTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            589999999999999999985      3589999999999999999997 7999999999999987

>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=99.40  E-value=1.8e-13  Score=110.60  Aligned_cols=59  Identities=19%  Similarity=0.274  Sum_probs=54.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++ +++..|+|++|+|..|
T Consensus        11 ~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          11 TTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            6899999999999999999853      478999999999999999997 8999999999999765

>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=99.40  E-value=6.3e-14  Score=116.25  Aligned_cols=63  Identities=17%  Similarity=0.264  Sum_probs=57.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|++||+|.+|++. .+||||||+|++.++|++|++  +|..|+|++|+|++|+++..
T Consensus        17 ~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_          17 MTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            6899999999999999999854 579999999999999999995  88999999999999976544

>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=99.39  E-value=2.6e-13  Score=113.65  Aligned_cols=66  Identities=18%  Similarity=0.294  Sum_probs=57.6

Q ss_pred             CCHHHHHHHhhhcCc-eeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhcCCc--cCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGE-IERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQGRL--FNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGe-I~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLNGk~--f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|+.||+ |++|++.       ++||||||+|.+.++|.+|++.|++..  ++|++|+|+||++...+
T Consensus        13 ~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~   88 (96)
T d2disa1          13 KKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   88 (96)
T ss_dssp             SCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             CCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCC
Confidence            689999999999996 8999853       478999999999999999999997654  47999999999876554

>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=99.39  E-value=1.3e-13  Score=115.74  Aligned_cols=63  Identities=17%  Similarity=0.289  Sum_probs=56.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|+.||+|.+|++.      ++||||||+|.+.++|++|+++++  .|+|+.|+|.+|.++..
T Consensus        20 ~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~--~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          20 TTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE--EETTEEEEEECCCTTCC
T ss_pred             CCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC--ccCCEEeEEEeCCCCCC
Confidence            6899999999999999999853      578999999999999999999655  89999999999987543

>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=99.37  E-value=2.6e-13  Score=112.01  Aligned_cols=60  Identities=15%  Similarity=0.249  Sum_probs=55.3

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      +||++|+++|+.||+|.+|++.      ++||||||+|.+.++|++|++ ++|..|+|++|+|..|.
T Consensus        18 ~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          18 TTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            6899999999999999999853      578999999999999999997 69999999999999885

>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=99.37  E-value=3.8e-13  Score=113.62  Aligned_cols=63  Identities=14%  Similarity=0.265  Sum_probs=54.1

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|+.|| |.+|++.       ++||||||+|.+.|+|++|+ +|||..|+|++|+|+||+++..
T Consensus        27 ~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~~   96 (104)
T d1wi8a_          27 VTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             CCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             CCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCCC
Confidence            68999999999999 6666532       46899999999999997665 6999999999999999987654

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=9.7e-14  Score=110.30  Aligned_cols=56  Identities=23%  Similarity=0.326  Sum_probs=52.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEE
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT   56 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIr   56 (724)
                      +||++|+++|++||.|.++++.      .+||||||+|.+.++|.+|++.|||+.|+|+.||
T Consensus        10 ~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          10 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             CCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            6899999999999999999853      4789999999999999999999999999999875

>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=99.36  E-value=3.1e-13  Score=108.79  Aligned_cols=59  Identities=20%  Similarity=0.297  Sum_probs=53.6

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +||++|+++|+.||.|.++++.      .+||||||+|.+.|+|.+|+ +|||..|+||+|+|..|
T Consensus        14 ~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          14 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            6899999999999999999853      46899999999999888888 59999999999999876

>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=99.35  E-value=2e-13  Score=113.81  Aligned_cols=58  Identities=12%  Similarity=0.235  Sum_probs=52.0

Q ss_pred             CCHHHH---HHHhhhcCceeEeeecC---------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEE
Q 004908            1 MDEQML---HNAMILFGEIERIKSYP---------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIM   58 (724)
Q Consensus         1 VdEedL---relFS~FGeI~sVkt~~---------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVe   58 (724)
                      ++|++|   +++|++||+|++|++.+         .+|||||+|++.++|.+|+++|||..|+|++|+|.
T Consensus        20 ~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          20 LADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             TCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            578898   77899999999998642         34899999999999999999999999999999984

>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=99.35  E-value=5.1e-13  Score=114.42  Aligned_cols=50  Identities=24%  Similarity=0.457  Sum_probs=48.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCcc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLF   50 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f   50 (724)
                      +||++|+++|++||+|++|++.+.||||||+|.+.++|.+|+++|||+.+
T Consensus        32 vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          32 VSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            68999999999999999999999999999999999999999999999987

>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=99.34  E-value=7e-13  Score=113.02  Aligned_cols=61  Identities=25%  Similarity=0.343  Sum_probs=56.1

Q ss_pred             HHHHHHHhhhcCceeEeeec--CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            3 EQMLHNAMILFGEIERIKSY--PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~--~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +++|++.|++||+|++|++.  ..+|||||+|++.++|.+|++.|||+.|+||+|+|+|+...
T Consensus        33 ~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          33 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             HHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSC
T ss_pred             HHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCc
Confidence            47899999999999999865  46899999999999999999999999999999999998643

>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=99.32  E-value=4.5e-13  Score=109.27  Aligned_cols=59  Identities=19%  Similarity=0.306  Sum_probs=53.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|++|++. ++..|+|+.|+|..|
T Consensus        11 ~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          11 TPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            6899999999999999999853      5799999999999999999974 778999999999876

>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=99.30  E-value=1.4e-12  Score=105.69  Aligned_cols=59  Identities=14%  Similarity=0.149  Sum_probs=53.8

Q ss_pred             CCHHHHHHHhhhcCceeEeeec----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERIKSY----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|+.||+|++|++.    ..+|||||+|++.++|.+|+ .|||+.|+|++|+|+.+
T Consensus        12 ~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          12 YNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            6899999999999999999865    34679999999999999998 59999999999999875

>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=99.30  E-value=1e-12  Score=108.65  Aligned_cols=60  Identities=18%  Similarity=0.310  Sum_probs=55.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      +||++|+++|+.||.|.+|++.     ++||||||+|.+.++|.+|++ ++|..|+|++|+|.|++
T Consensus        18 ~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          18 ATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             CCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            5899999999999999999864     468999999999999999995 79999999999999875

>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=99.30  E-value=6.3e-13  Score=108.78  Aligned_cols=60  Identities=17%  Similarity=0.156  Sum_probs=54.2

Q ss_pred             CCHHHHHHHhhhcCceeEe-ee-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            1 MDEQMLHNAMILFGEIERI-KS-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sV-kt-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      ++|++|+++|+.||.|.+. .+     .++||||||+|.+.++|++|++.|||+.++||+|+|.+|
T Consensus        21 ~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          21 VSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            6899999999999999753 32     356899999999999999999999999999999999986

>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=99.25  E-value=1.6e-12  Score=110.32  Aligned_cols=64  Identities=14%  Similarity=0.130  Sum_probs=55.0

Q ss_pred             CCHHHHHHHhhhcCceeEeeec-----CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY-----PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP   66 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~-----~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~p   66 (724)
                      +||++|+++|+.||.| +|.+.     ..||||||+|.+.++|++|++ |||+.|+||.|+|.+++.....
T Consensus        27 ~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          27 ATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             CCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCC
T ss_pred             CCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCC
Confidence            6899999999999854 55532     468999999999999999986 9999999999999999866543

>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=99.25  E-value=5.6e-12  Score=107.81  Aligned_cols=60  Identities=23%  Similarity=0.383  Sum_probs=54.8

Q ss_pred             HHHHHHHhhhcCceeEeeecC--------CCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            3 EQMLHNAMILFGEIERIKSYP--------SRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         3 EedLrelFS~FGeI~sVkt~~--------SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      .++|++.|++||+|++|++.+        .+||+||+|++.++|.+|+++|||+.|+||.|+|.|+..
T Consensus        28 ~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          28 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECH
T ss_pred             HHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCH
Confidence            468999999999999998642        468999999999999999999999999999999999864

>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=99.24  E-value=4.7e-12  Score=109.73  Aligned_cols=62  Identities=15%  Similarity=0.100  Sum_probs=57.2

Q ss_pred             CCHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCH-HHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSV-DEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~-EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|++||+|.+|++.+.||||||+|.+. ++|.+|+.+|||..+.++.++|.++..
T Consensus        23 ~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          23 TCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            68999999999999999999999999999999985 789999999999999988888877643

>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=99.22  E-value=8.3e-12  Score=105.94  Aligned_cols=64  Identities=17%  Similarity=0.073  Sum_probs=56.4

Q ss_pred             CCHHHHHHHhhhcCceeEee-e-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCCCC
Q 004908            1 MDEQMLHNAMILFGEIERIK-S-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELA   65 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk-t-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~~~   65 (724)
                      +||++|+++|+.||.|.++. +     .+.+|||||+|++.++|++|++ |||..|+||.|+|.+++....
T Consensus        27 ~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~   96 (104)
T d1wg5a_          27 CSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEV   96 (104)
T ss_dssp             CCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTTS
T ss_pred             CCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHHh
Confidence            68999999999999998753 2     2578999999999999999996 999999999999999986643

>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=99.20  E-value=5.8e-13  Score=110.08  Aligned_cols=61  Identities=23%  Similarity=0.411  Sum_probs=53.7

Q ss_pred             CCHHHHHHHhhhcCceeEee-----------ecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIK-----------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVk-----------t~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|+.||.|.++.           +.++||||||+|.+.|+|++|++ |||..|+|++|+|..++.
T Consensus        13 ~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r~k~   84 (90)
T d1u2fa_          13 ITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHD   84 (90)
T ss_dssp             CCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBCTTC
T ss_pred             cchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECCCCC
Confidence            68999999999999987654           33689999999999999999985 999999999999975543

>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=99.18  E-value=5.4e-12  Score=106.48  Aligned_cols=62  Identities=15%  Similarity=0.167  Sum_probs=54.9

Q ss_pred             CCHHHHHHHhhhcCceeEe-ee-----cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccCC
Q 004908            1 MDEQMLHNAMILFGEIERI-KS-----YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE   63 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sV-kt-----~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~~   63 (724)
                      +||++|+++|+.||.|..+ .+     .++||||||+|.+.++|.+|++ |||..|+||+|+|.++..+
T Consensus        20 ~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~~   87 (103)
T d2cpya1          20 ITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLE   87 (103)
T ss_dssp             SCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECHH
T ss_pred             CCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCHH
Confidence            6899999999999999764 32     2579999999999999999996 9999999999999998643

>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=99.13  E-value=1.6e-11  Score=110.04  Aligned_cols=61  Identities=21%  Similarity=0.298  Sum_probs=55.9

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|+.||+|..|++.      ++||||||+|.+.++|.+|++ ++|..|+|++|+|.+|.+
T Consensus       109 ~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         109 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             CCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            6899999999999999999754      468999999999999999997 799999999999999864

>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=99.11  E-value=3.8e-11  Score=99.77  Aligned_cols=59  Identities=20%  Similarity=0.313  Sum_probs=51.4

Q ss_pred             CHHHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCc-EEEEeccC
Q 004908            2 DEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR-ITIMFSSS   62 (724)
Q Consensus         2 dEedLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRr-IrVefAk~   62 (724)
                      +++.| ++|++||+|.++++.+.||||||+|++.++|++|++ |||+.|+|+. |.|..++.
T Consensus        17 ~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          17 ASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             HHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             HHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            44555 579999999999999999999999999999999996 9999999985 67877653

>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=98.99  E-value=4.3e-11  Score=103.06  Aligned_cols=61  Identities=13%  Similarity=0.111  Sum_probs=53.5

Q ss_pred             CCHHHHHHHhhhcCceeEeee------cCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            1 MDEQMLHNAMILFGEIERIKS------YPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt------~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +||++|+++|+.||.|.++.+      ..++|||||+|.+.++|.+|++ |||..|+||.|.|..+.+
T Consensus        30 ~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          30 AENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             CCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             CcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcCh
Confidence            689999999999999976432      3568999999999999999996 999999999999998854

>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=98.54  E-value=4.7e-08  Score=87.14  Aligned_cols=60  Identities=15%  Similarity=0.238  Sum_probs=50.7

Q ss_pred             CCHHHHHHHhhhcCceeEeeec------CCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSY------PSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~------~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk   61 (724)
                      +||++|+++|++||+|++|++.      ++||||||+|.+.++|.+|++.+ +..++++.+.+....
T Consensus        18 ~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~-~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_          18 TTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR-PHKVDGRVVEPKRAV   83 (183)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTC-SCEETTEECEEEECC
T ss_pred             CCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhc-CCcccccchhhhhhh
Confidence            6899999999999999999853      56899999999999999998865 555677777776654

>d1ow1a_ b.131.1.3 (A:) SMART/HDAC1 associated repressor protein, SHARP {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SPOC domain-like
superfamily: SPOC domain-like
family: SPOC domain
domain: SMART/HDAC1 associated repressor protein, SHARP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=0.00012  Score=68.85  Aligned_cols=78  Identities=22%  Similarity=0.376  Sum_probs=62.0

Q ss_pred             eeecccccchh-----HHHHHhhhccCceEEEEeCCCchhhh-------hHHHHHHhhccccccceEeecCC------cE
Q 004908          309 VVNCSARTGLD-----MLAKHYAEAIGFDIVFFLPDSEDDFA-------SYTEFLRYLGSKNRAGVAKFDDG------TT  370 (724)
Q Consensus       309 ~ldctaRT~ld-----~l~khy~~a~~~~vvff~P~s~~D~~-------~y~eFl~YL~~K~rAgV~K~~~~------tt  370 (724)
                      .|-.|-|--||     -|.+.-..+.++-+++-|||+.+.-.       --+-|++||++|+-||||-+..+      -.
T Consensus        52 ~LrI~QRlRLd~~kLe~V~rRi~~~~~~c~lLAlp~~~~~~d~~~q~~~l~~~lV~YLkqKqAAGVI~l~~~~~~~~~~V  131 (170)
T d1ow1a_          52 PLRIAQRMRLEATQLEGVARRMTVETDYCLLLALPCGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYV  131 (170)
T ss_dssp             CEEECEEEECSHHHHHHHHHHTSSTTTEEEEEEEECCSSHHHHHHHHHHHHHHTHHHHHHHTEEEEEEECCTTCCSCCEE
T ss_pred             cEEeeeecccChHHHHHHHHHHhcCCCceEEEEeeCCCCccccchhhhHHHHHHHHHHHHhccCceEecCCCCCCCceEE
Confidence            57777776554     67777777888999999998864332       12369999999999999999854      38


Q ss_pred             EEEeCCChhhhcceee
Q 004908          371 LFLVPPSDFLSKVLKV  386 (724)
Q Consensus       371 LFLVPPSdf~~~vLkV  386 (724)
                      |++.||.+|+.+.|+=
T Consensus       132 Lh~FPPCeFs~~~L~~  147 (170)
T d1ow1a_         132 LQIFPPCEFSESHLSR  147 (170)
T ss_dssp             EEEECSSHHHHHHHHH
T ss_pred             EEecCCcHHHHHHHHH
Confidence            9999999999988874

>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=97.17  E-value=0.00043  Score=57.32  Aligned_cols=59  Identities=17%  Similarity=0.336  Sum_probs=53.0

Q ss_pred             HHHHHHhhhcCceeEeeecC-CCC--eEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEeccC
Q 004908            4 QMLHNAMILFGEIERIKSYP-SRN--YSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS   62 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~-SRG--FAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefAk~   62 (724)
                      +.|.++|+++|.|.+|.+.+ .+|  .|-|...+..||.-|+..|+-+.|+++||.|.|+..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            46778999999999999864 344  899999999999999999999999999999999863

>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=95.88  E-value=0.0044  Score=53.31  Aligned_cols=54  Identities=15%  Similarity=0.169  Sum_probs=46.9

Q ss_pred             HHHHHHhhhcCceeEeeecCCCCeEEEEeCCHHHHHHHHHHhcCCccCCCcEEEEec
Q 004908            4 QMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS   60 (724)
Q Consensus         4 edLrelFS~FGeI~sVkt~~SRGFAFVeF~s~EdA~kAIEaLNGk~f~GRrIrVefA   60 (724)
                      .+|-+.|..||+|.=|+.+  .+-..|+|.+-+.|.+|+ .|+|..+.|+.|+|.--
T Consensus        39 ~~Llq~l~~~GeViLvRFv--~d~mwVTF~dG~SAL~al-~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN--QGQMLVTFADSHSALSVL-DVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE--TTEEEEECSCSHHHHHHH-HGGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEe--CCeEEEEECCcHHHHHHh-ccCCeEEcceEEEEecC
Confidence            4688999999999999976  456799999999998887 59999999999999753

>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=81.23  E-value=1.3  Score=37.11  Aligned_cols=61  Identities=11%  Similarity=0.337  Sum_probs=48.4

Q ss_pred             CCHHHHHHHhhhcCceeEeeecC-------CC-CeEEEEeCCHHHHHHHHHHhcCCccCCCc-----EEEEecc
Q 004908            1 MDEQMLHNAMILFGEIERIKSYP-------SR-NYSFVEFRSVDEARRAKEGLQGRLFNDPR-----ITIMFSS   61 (724)
Q Consensus         1 VdEedLrelFS~FGeI~sVkt~~-------SR-GFAFVeF~s~EdA~kAIEaLNGk~f~GRr-----IrVefAk   61 (724)
                      +||+++.+.++..|++....-.+       ++ .-|+|.|.+.++...-.+..+|..|.+.+     -.|+||-
T Consensus        13 Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~VE~AP   86 (91)
T d1uw4a_          13 LTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAP   86 (91)
T ss_dssp             CCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECEEEECS
T ss_pred             CCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeEEEEcC
Confidence            58999999999999998765321       11 47999999999999999999999995532     3567763