Psyllid ID: psy1534

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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-------
Protein Sequence
MTSPVTETELVEQIAHQDFPMFQRIETGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKTDSTNAEKDKIGNLPNMNTNPTPTASVSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSGMAAYSQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHcccccccccccccccccEEEEccccccccHHHHHHccccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEccccccccccccccccccccHHHHHccccccccccccccccHHcccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEccHHHHHHHHHHHcccccccEEEEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHccHHHccccHHHHHHHHccccccccccccccccccccccccccccHHHHHHccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccEEEEEEEccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEcccccccccccccccccEEEEEEcccccHHHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEcccccHHHHHHHHHHcccccccccccccccccccccccccHHHHHHccccccccEEEEEEcccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccccccccEEEEEcccccHHHHHHHHHHHHHHHHHccccccEEEEcccccccHHHHHHHHHHccccccccccccccccEEcccccccccccccccccccccccccHHHHccccccccccccccccccHHHHHHccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEcccccEEEEEccHHHHHHHHHHHccccEccEEEEEEEc
Coil and Loop (DISEMBL)
MTSPVTETELVEQIahqdfpmfqrietgaplevpVVMDLIQGDASLYQISHLSTVGDVTYVEIlnddtgkprgsaivefqspdlVRKAVNKMHRFETKGRKLVIKEAVedkggrrnmgggggvdrDLSALLQnnsskfgntyglspqfleslgincplinKVFVANLDYKVDEKKLREVFRLAGKVENVEialdkdgksrgfgtvefdhpveAVQSISMLNNQNLFERRITVRMDRvadrldgpvrlpeglksigmglgangaplQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKlqydkssdendaasvntasktdstnaekdkignlpnmntnptptasvstPAALAAAVTALtqaqqppppqpslgnlglnlglggaandLTSNLTSTLTSLAAAnqntayplnqlssqsglgqsnILSGMAAYsqgmqsqtsslssgnnvysnqsapstdysrnasnmygnsrygsggnemdygggsgqasiqsggygnpragldsnrsmnqssnierdtvvvknlpptitWQELRDKFRncgdikfaeikgkgdiglvrfdseWTAKRAIDMMdrtridgkiidvtff
Flexible Loop (DISEMBL)
MTSPVTETELVEQIAHQDFPMFQRIETGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNddtgkprgsaivefqspdlvrkAVNKMhrfetkgrklvikeavedkggrrnmgggggvdRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFrlagkvenveialdkdgksrgFGTVEFDHPVEavqsismlnnqnlferRITVRMdrvadrldgpvrlPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLsliisnrntkevlERWDFKLQydkssdendaasvntasktdstnaekdkignlpnmntnPTPTASVSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSGMAAYSQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQssnierdtvvvknlpptitwqelrDKFRNCGDIKfaeikgkgdiglvrfdsewTAKRAidmmdrtridgkiidvtff
Low Complexity Region (SEG)
MTSPVTETELVEQIAHQDFPMFQRIETGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKggrrnmgggggVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKTDSTNAEKDKIGNLpnmntnptptasvstpaalaaavtaltqaqqppppqpslgnlglnlglggaandltsnltstltslaaanQNTAYPlnqlssqsglgqsnilsgMAAYSQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDygggsgqasiqsggygNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF
Disordered region (IsUnstruct)
**********VEQIAHQDFPMFQRIETGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTG****SAIVEFQSPDLVRKAVNK**********************************************FGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQY****************************************************************************LGL****************************************************************************************************************************************TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF*
Disordered Region (DISOPRED)
**********************************VVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK***************************************************PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR***************************************************************DF*********************************************************************************************************QNTAYPLNQLSSQSGLGQSNILSGMAAYSQGMQSQTSSLSSGNNVYSN***********************GGNEMDYG****************************SSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF
Disordered Region (DISEMBL)
*********LVEQIAHQDFPMFQRIETGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDK**********************KDKIGNLPNMNTNPTPTASVSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSGMAAY**************************DYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF
Disordered Region (DISPRO)
********ELVEQIA***FP*F*R**TGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED*G*RRN************************TYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYD******DAAS****SKTDSTNAEKDKIGNLPNMNTNPTPTASVSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSGMAAYSQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASN*************************************************ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTSPVTETELVEQIAHQDFPMFQRIETGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKTDSTNAEKDKIGNLPNMNTNPTPTASVSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSGMAAYSQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF
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	587	2.2.26 [Sep-21-2011]
Q9P2K5	600	Myelin expression factor	yes	N/A	0.306	0.3	0.446	7e-34
Q8C854	591	Myelin expression factor	yes	N/A	0.306	0.304	0.430	3e-32
Q62826	690	Heterogeneous nuclear rib	no	N/A	0.253	0.215	0.418	7e-29
P52272	730	Heterogeneous nuclear rib	no	N/A	0.301	0.242	0.415	2e-28
Q9D0E1	729	Heterogeneous nuclear rib	no	N/A	0.304	0.245	0.404	9e-28
Q9P3U1	464	Uncharacterized RNA-bindi	yes	N/A	0.284	0.359	0.290	5e-14
Q6BI95	627	Polyadenylate-binding pro	yes	N/A	0.270	0.253	0.255	6e-11
Q08937	291	29 kDa ribonucleoprotein	N/A	N/A	0.284	0.573	0.311	2e-10
A3LXL0	632	Polyadenylate-binding pro	yes	N/A	0.277	0.257	0.255	3e-10
P31209	653	Polyadenylate-binding pro	no	N/A	0.262	0.235	0.262	3e-10

>sp|Q9P2K5|MYEF2_HUMAN Myelin expression factor 2 OS=Homo sapiens GN=MYEF2 PE=1 SV=3

 Score =  145 bits (367), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 83/186 (44%), Positives = 116/186 (62%), Gaps = 6/186 (3%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +  R
Sbjct: 124 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 183

Query: 115 RNM---GGG--GGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
           R +   GG   GG   D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct: 184 RALQRTGGSFPGGHVPDMGSGLMNLPPSILNNPNIPPEVISNLQAGR-LGSTIFVANLDF 242

Query: 170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
           KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct: 243 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 302

Query: 230 ITVRMD 235
           + V+MD
Sbjct: 303 MHVKMD 308

Transcriptional repressor of the myelin basic protein gene (MBP). Binds to the proximal MB1 element 5'-TTGTCC-3' of the MBP promoter. Its binding to MB1 and function are inhibited by PURA.
Homo sapiens (taxid: 9606)

>sp|Q8C854|MYEF2_MOUSE Myelin expression factor 2 OS=Mus musculus GN=Myef2 PE=1 SV=1

 Score =  140 bits (353), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 80/186 (43%), Positives = 113/186 (60%), Gaps = 6/186 (3%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +  R
Sbjct: 115 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 174

Query: 115 RNM-----GGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
           R +        G    D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct: 175 RALQRTGTSFQGSHASDVGSGLVNLPPSILNNPNIPPEVISNLQAG-RLGSTIFVANLDF 233

Query: 170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
           KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct: 234 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 293

Query: 230 ITVRMD 235
           + V+MD
Sbjct: 294 MHVKMD 299

Transcriptional repressor of the myelin basic protein gene (MBP). Binds to the proximal MB1 element 5'-TTGTCC-3' of the MBP promoter. Its binding to MB1 and function are inhibited by PURA.

Mus musculus (taxid: 10090)

>sp|Q62826|HNRPM_RAT Heterogeneous nuclear ribonucleoprotein M OS=Rattus norvegicus GN=Hnrnpm PE=1 SV=4

 Score =  129 bits (324), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 77/184 (41%), Positives = 102/184 (55%), Gaps = 35/184 (19%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           VG+VTYVE+L D  GK RG A+VEF+  + ++KA   +++    GR L +KE  + +  R
Sbjct: 94  VGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAAEVLNKHSLSGRPLKVKEDPDGEHAR 153

Query: 115 RNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEK 174
           R M                 + + G+T                    VFVANLDYKV  K
Sbjct: 154 RAM---------------QKAGRLGST--------------------VFVANLDYKVGWK 178

Query: 175 KLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM 234
           KL+EVF +AG V   +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R + V+M
Sbjct: 179 KLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM 238

Query: 235 DRVA 238
           D  A
Sbjct: 239 DERA 242

Pre-mRNA binding protein, binds avidly to poly(G) and poly(U) RNA homopolymers. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.

Rattus norvegicus (taxid: 10116)

>sp|P52272|HNRPM_HUMAN Heterogeneous nuclear ribonucleoprotein M OS=Homo sapiens GN=HNRNPM PE=1 SV=3

 Score =  127 bits (319), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 81/195 (41%), Positives = 110/195 (56%), Gaps = 18/195 (9%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           VG+VTYVE+L D  GK RG A+VEF+  + ++KA   +++    GR L +KE  + +  R
Sbjct: 95  VGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAAEVLNKHSLSGRPLKVKEDPDGEHAR 154

Query: 115 RNMGGGGGVDRDLSALLQNNSSKFGNTYGLS--PQFLESLGINCPLINK---------VF 163
           R M       + + A         G    ++  P  L +  I   +I+          VF
Sbjct: 155 RAM-------QKVMATTGGMGMGPGGPGMITIPPSILNNPNIPNEIIHALQAGRLGSTVF 207

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ 223
           VANLDYKV  KKL+EVF +AG V   +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q
Sbjct: 208 VANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQ 267

Query: 224 NLFERRITVRMDRVA 238
            LF+R + V+MD  A
Sbjct: 268 LLFDRPMHVKMDERA 282

Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.

Homo sapiens (taxid: 9606)

>sp|Q9D0E1|HNRPM_MOUSE Heterogeneous nuclear ribonucleoprotein M OS=Mus musculus GN=Hnrnpm PE=1 SV=3

 Score =  125 bits (314), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 78/193 (40%), Positives = 105/193 (54%), Gaps = 14/193 (7%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           VG+VTYVE+L D  GK RG A+VEF+  + ++KA   +++    GR L +KE  + +  R
Sbjct: 94  VGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAAEVLNKHSLSGRPLKVKEDPDGEHAR 153

Query: 115 RNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK---------VFVA 165
           R M          +               + P  L +  I   +I+          VFVA
Sbjct: 154 RAM-----QKVMATTGGMGMGPGGPGMINIPPSILNNPNIPNEIIHALQAGRLGSTVFVA 208

Query: 166 NLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL 225
           NLDYKV  KKL+EVF +AG V   +I  DKDGKSRG G V F+  +EAVQ+ISM N Q L
Sbjct: 209 NLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGIVTFEQSIEAVQAISMFNGQLL 268

Query: 226 FERRITVRMDRVA 238
           F+R + V+MD  A
Sbjct: 269 FDRPMHVKMDERA 281

Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.

Mus musculus (taxid: 10090)

>sp|Q9P3U1|YKX5_SCHPO Uncharacterized RNA-binding protein C328.05 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC328.05 PE=4 SV=3

 Score = 80.1 bits (196), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 56/193 (29%), Positives = 92/193 (47%), Gaps = 26/193 (13%)

Query: 52  LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           +  VG+V   EILN   G  +G AI+E+ + +  R A+  +   +  GR + I+E     
Sbjct: 97  MGQVGNVLNCEILNLPNGLSKGCAIIEYSTAEEARTAIKTLSNQKFMGRLVYIRE----- 151

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
                       DR+ +A       +FG++           G +     ++FV NL Y V
Sbjct: 152 ------------DREQNA-------RFGSSSVSPSASSN--GKDSEPDRQLFVGNLPYNV 190

Query: 172 DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT 231
             + L+++FR AG V   +I ++++G+SRG G V      EA+ +I ML+N +   R + 
Sbjct: 191 RWQDLKDLFRQAGSVIRADIQMNQEGRSRGIGIVVMSSMKEAMHAIQMLHNTDFMGRTLE 250

Query: 232 VRMDRVADRLDGP 244
           VR+DR A     P
Sbjct: 251 VRLDRFAHHKSKP 263

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

>sp|Q6BI95|PABP_DEBHA Polyadenylate-binding protein, cytoplasmic and nuclear OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=PAB1 PE=3 SV=2

 Score = 69.7 bits (169), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 49/192 (25%), Positives = 91/192 (47%), Gaps = 33/192 (17%)

Query: 52  LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
               G +T + +  D  GK +G   V F++ +   KAV++++  E  G+K+ +  A + +
Sbjct: 252 FEAYGKITSIYLEKDHEGKSKGFGFVNFENHESAVKAVDELNDKEINGQKIYVGRAQKKR 311

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESL----GINCPLINKVFVANL 167
                              L+    ++ NT       LE L    G+N      +F+ NL
Sbjct: 312 -----------------ERLEELKKQYENTR------LEKLSKYQGVN------LFIKNL 342

Query: 168 DYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE 227
           D  +D +KL E F+  G + +  + +D+ GKS+GFG V F  P EA ++I+ +N + ++ 
Sbjct: 343 DDTIDSEKLEEEFKPFGSITSARVMVDETGKSKGFGFVCFSSPEEATKAITEMNQRMIYG 402

Query: 228 RRITVRMDRVAD 239
           + + V + +  D
Sbjct: 403 KPLYVALAQRKD 414

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

>sp|Q08937|ROC2_NICSY 29 kDa ribonucleoprotein B, chloroplastic OS=Nicotiana sylvestris PE=2 SV=1

 Score = 67.8 bits (164), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 56/180 (31%), Positives = 84/180 (46%), Gaps = 13/180 (7%)

Query: 56  GDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA-VEDKGG 113
           G+V  VE++ D  TG+ RG   V   + + V  A  + + +E  GR + +       K  
Sbjct: 111 GNVEMVEVIYDKLTGRSRGFGFVTMSTKEEVEAAEQQFNGYEIDGRAIRVNAGPAPAKRE 170

Query: 114 RRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDE 173
             + GGG G +         NSS FG   G         G +    N+V+V NL + VD+
Sbjct: 171 NSSFGGGRGGNSSYGGGRDGNSS-FGGARG---------GRSVDSSNRVYVGNLSWGVDD 220

Query: 174 KKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV 232
             L+E+F   G V + ++  D+D G+SRGFG V +    E   +I  LN  +L  R I V
Sbjct: 221 LALKELFSEQGNVVDAKVVYDRDSGRSRGFGFVTYSSSKEVNDAIDSLNGVDLDGRSIRV 280

Could be involved in splicing and/or processing of chloroplast RNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|A3LXL0|PABP_PICST Polyadenylate-binding protein, cytoplasmic and nuclear OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=PAB1 PE=3 SV=1

 Score = 67.4 bits (163), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 88/188 (46%), Gaps = 25/188 (13%)

Query: 52  LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
            +  G +T + +  D  GK +G   V ++  +   KAV +++  E  G+K+ +  A   +
Sbjct: 253 FTPYGAITSIYLEKDAEGKSKGFGFVNYEGHEAAVKAVEELNDKEINGQKIYVGRA---Q 309

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
             R  M        +L    +N   +  + Y          G+N      +F+ NLD  +
Sbjct: 310 KKRERM-------EELKKQYENTRLEKLSKYQ---------GVN------LFIKNLDDTI 347

Query: 172 DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT 231
           D +KL E F+  G + +  + +D+ GKS+GFG V F  P EA ++I+ +N +  F + + 
Sbjct: 348 DSEKLEEEFKPFGTITSARVMVDETGKSKGFGFVCFSSPEEATKAITEMNQRMFFGKPLY 407

Query: 232 VRMDRVAD 239
           V + +  D
Sbjct: 408 VALAQRKD 415

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (taxid: 322104)

>sp|P31209|PABP_SCHPO Polyadenylate-binding protein, cytoplasmic and nuclear OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pab1 PE=1 SV=2

 Score = 67.0 bits (162), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 90/179 (50%), Gaps = 25/179 (13%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           G++T + ++ D   KPRG   V + + +  +KAV++++  E KG+KL +  A + K  R 
Sbjct: 285 GEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA-QKKHER- 342

Query: 116 NMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKK 175
                   + +L    +    +  N Y          G+N      +F+ NL  +VD+++
Sbjct: 343 --------EEELRKRYEQMKLEKMNKYQ---------GVN------LFIKNLQDEVDDER 379

Query: 176 LREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM 234
           L+  F   G + + +I  D+ GKS+GFG V +  P EA ++++ +N + L  + + V +
Sbjct: 380 LKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	587
50880296	525	Hrp59 protein [Chironomus tentans]	0.761	0.851	0.391	2e-80
345494637	559	PREDICTED: myelin expression factor 2-li	0.778	0.817	0.401	1e-79
242016244	508	Nuclear and cytoplasmic polyadenylated R	0.359	0.415	0.589	1e-64
357619139	514	Hrp59 protein [Danaus plexippus]	0.364	0.416	0.536	2e-60
91076808	573	PREDICTED: similar to Hrp59 CG9373-PA [T	0.359	0.368	0.537	2e-59
193697751	490	PREDICTED: myelin expression factor 2-li	0.361	0.432	0.531	6e-58
383855600	542	PREDICTED: myelin expression factor 2-li	0.367	0.398	0.556	1e-57
328784140	544	PREDICTED: myelin expression factor 2 [A	0.367	0.397	0.56	2e-57
340714953	546	PREDICTED: myelin expression factor 2-li	0.367	0.395	0.553	3e-57
350402014	546	PREDICTED: myelin expression factor 2-li	0.367	0.395	0.553	4e-57

>gi|50880296|emb|CAH05070.1| Hrp59 protein [Chironomus tentans]

 Score =  306 bits (784), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 221/564 (39%), Positives = 299/564 (53%), Gaps = 117/564 (20%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           VG+V +VE+ ND++GKPRG  I+EF S D VR A++KM+R++  GR LVIKE   D G  
Sbjct: 48  VGEVAFVELFNDESGKPRGCGIIEFVSADSVRIALDKMNRYDLSGRNLVIKE---DSGNE 104

Query: 115 RNMGG------GGGVDRDLSALLQNNSSKFG-----------------NTYGLSPQFLES 151
           R+  G      G            N+SS+                   NTYGLS +FLE 
Sbjct: 105 RDKYGFVIKPQGSYRRDRDDDRSYNDSSRSHGGGGNNHGNNSSNLENFNTYGLSVKFLEG 164

Query: 152 LGIN-CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHP 210
           LGI   PL NKVFVANLDYKVD KKL++VF+LAGKV +V+++LDKDG SRGF  VE+DHP
Sbjct: 165 LGITQGPLHNKVFVANLDYKVDAKKLKQVFKLAGKVLSVDLSLDKDGNSRGFAVVEYDHP 224

Query: 211 VEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVAN 270
           VEAVQSISM + Q LF+RR+TVR+DR+ D+ +G V+LPEGLKS+G+GLG NG PL+DVA 
Sbjct: 225 VEAVQSISMFDRQTLFDRRMTVRLDRIPDKSEG-VKLPEGLKSVGIGLGPNGEPLRDVA- 282

Query: 271 WLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKTDSTNAEKDKI 330
                           RN   +                               N  ++ +
Sbjct: 283 ----------------RNLPNL-----------------------------QNNPSQNSM 297

Query: 331 GNLPNMNTNPTPTASVSTPAALAAAVTALTQAQQPPP---PQPSLGNLGLNLGLGGAAND 387
            NL   NTN  P +S+S          +L Q   P P   PQ        N  L G   +
Sbjct: 298 SNL---NTNINPLSSLS---------NSLNQLTTPTPVAAPQ--------NSSLLGVPTN 337

Query: 388 LTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSGMAAYSQGMQSQTSSLSSGNN 447
                 S L+ LAA  QN    L  L   S L  + +LS  AA    + S   +L++ N 
Sbjct: 338 ------SNLSGLAAL-QNVVGGLTSLGGVSALSANPLLSSAAA---SLNSLGLNLTASNQ 387

Query: 448 VYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMD---YGGGSGQ-ASIQSGGYGNPRAGLD 503
              NQ A     ++++ N Y  S + +G    D   +GG   +  +  +  Y N R    
Sbjct: 388 NDVNQ-AQQQSMNQSSFNAYNTSGFNTGNRNDDMPSFGGNQIRNYNTSNDDYNNSRNFGG 446

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
           S+ S  Q S    DT++V+NLP + TWQ LRDKFR+ G++KFAEI+G  D G+VRF  E 
Sbjct: 447 SSSSRKQQS----DTILVRNLPSSWTWQNLRDKFRDVGEVKFAEIRGL-DTGVVRFSKER 501

Query: 564 TAKRAIDMMDRTRIDGKIIDVTFF 587
            A  AI ++D +R DG+++++ +F
Sbjct: 502 EADVAIKLLDGSRFDGRVVEIDYF 525

Source: Chironomus tentans

Species: Chironomus tentans

Genus: Chironomus

Family: Chironomidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345494637|ref|XP_001603370.2| PREDICTED: myelin expression factor 2-like [Nasonia vitripennis]

 Score =  304 bits (778), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 229/571 (40%), Positives = 301/571 (52%), Gaps = 114/571 (19%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE--- 109
           + VG V +VE+  D+  KPRG  IVEF+  D V+ AV KMHRF+ KGRKLV+KE  +   
Sbjct: 67  TEVGKVAHVELFTDENDKPRGCGIVEFEDSDSVKVAVEKMHRFDIKGRKLVVKEDYDVER 126

Query: 110 DKGGRRNMGGGGGVDRDLSALLQN--------------------------NSSKFGNTYG 143
           DK GR   G      RD     Q+                          + +KFGNTYG
Sbjct: 127 DKYGRLTTGRNNDRSRDDRFRDQSRPNSGRQNIPVPTGATGAGGTGAATSSDNKFGNTYG 186

Query: 144 LSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFG 203
           LS QFLESLGI  PL+ +VFVANLDYKVDEKKL EVF+LAGKV +VE+  DKDGKSRGFG
Sbjct: 187 LSTQFLESLGIIGPLVTRVFVANLDYKVDEKKLLEVFKLAGKVLHVELGKDKDGKSRGFG 246

Query: 204 TVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGA 263
            VE+DHPVE+VQ+ISML+NQ L++RR+TVR+DR A+  D P +LPEGLK IGMGLGA G 
Sbjct: 247 VVEYDHPVESVQAISMLHNQQLYDRRMTVRLDR-ANEPDMPPKLPEGLKGIGMGLGAGGN 305

Query: 264 PLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASK-TDS 322
            L DVA                 RN   V                N++  VN  S    +
Sbjct: 306 RLTDVA-----------------RNIPNV--------------QPNNSPVVNPISAPVLT 334

Query: 323 TNAEKDKIGNLPNMNTNPTPTASVSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLG 382
           T A    + N+               PA LA   TALT +            LG NL   
Sbjct: 335 TGAFGAGLNNV--------------VPAQLA---TALTNSNAAALQASLASGLGANLA-- 375

Query: 383 GAANDLTSNLTSTLTSLAAANQNT----AYPLNQLSSQSGLGQSNILSGMAAYSQGMQSQ 438
                 TS L S+LT+  A+N N     A  L  L +     QSN     +   +G+   
Sbjct: 376 -----TTSLLNSSLTNELASNLNNFGQGAASLANLQASLANAQSN----NSFAPRGLSKL 426

Query: 439 TSSLS-SGNNVYSNQSAPSTDYSRNASNMYGNSR-YGSGGNEMDYGGGSGQASIQSGGYG 496
            + ++  GNN + N             N +G++R + SG N  D    S + S+    + 
Sbjct: 427 DNEVAFGGNNAFGN-------------NTFGSNRDFDSGFNRND----SERVSVGGAAFS 469

Query: 497 NPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGL 556
                +  NR  +  S    DT+V+ NLPP  TWQ LRDK ++ G++KFAE++G  D+G+
Sbjct: 470 TNAGQVGGNRQNSNGSRQMSDTIVIANLPPNTTWQMLRDKCQDIGEVKFAEMRG-ADVGM 528

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
           VRF +EW A+RA+ +M+R+RIDG+ +DV  +
Sbjct: 529 VRFATEWDAERAVSVMNRSRIDGRALDVRLY 559

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242016244|ref|XP_002428739.1| Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, putative [Pediculus humanus corporis] gi|212513424|gb|EEB16001.1| Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, putative [Pediculus humanus corporis]

 Score =  253 bits (647), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 132/224 (58%), Positives = 168/224 (75%), Gaps = 13/224 (5%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           +G+V +VE+ +D+  K +G  IVEF+ P+ V+KA+ K+HR++  GRK+++KE   D G  
Sbjct: 63  IGEVAFVELFSDENDKSKGCGIVEFELPESVKKAIEKLHRYDIDGRKIIVKE---DNGTA 119

Query: 115 RNMGGG--GGVDRDLSALLQNN----SSK---FGNTYGLSPQFLESLGINCPLINKVFVA 165
           R+  G   GG DR+     +      SSK   +G TYGLSP FLE LGI  PL+ +VFVA
Sbjct: 120 RDRYGSMRGGRDREREDRWEGGRDLPSSKPYTWGETYGLSPSFLEGLGIAPPLVCRVFVA 179

Query: 166 NLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL 225
           NLDYKV EKKLREVFRLAGKV +VE++LD DGKSRGF  VE+DHPVE+VQ+ISML+NQ L
Sbjct: 180 NLDYKVTEKKLREVFRLAGKVRDVELSLDSDGKSRGFAVVEYDHPVESVQAISMLHNQPL 239

Query: 226 FERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVA 269
           ++RR+TVRMDRV D LD   RLPEGL +IGMGLGANGAPL+D+A
Sbjct: 240 YDRRLTVRMDRV-DPLDTNSRLPEGLHNIGMGLGANGAPLRDIA 282

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357619139|gb|EHJ71829.1| Hrp59 protein [Danaus plexippus]

 Score =  240 bits (612), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 125/233 (53%), Positives = 163/233 (69%), Gaps = 19/233 (8%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           VGDV YVE+ ND+ GKPRG  +VEF + + ++KA+  MHR+E  GRKLV+KE   ++  R
Sbjct: 62  VGDVAYVELFNDENGKPRGCGVVEFSNSEAMKKALFVMHRYELNGRKLVLKEETGNERNR 121

Query: 115 ------------RNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
                       RNM      D+D   + +    +  NTYGLS QFLES+ +  PL+ KV
Sbjct: 122 LNSVRSGGGGGGRNMR----EDKDGWGVNKPREPENFNTYGLSLQFLESINVQPPLVKKV 177

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
           FVANLDYK D  K++EVF++AGKV N+++A+DKDG SRGF  +E+DHPVEAVQ+ISM + 
Sbjct: 178 FVANLDYKADRAKIKEVFKMAGKVRNIDLAIDKDGNSRGFAVIEYDHPVEAVQAISMFDK 237

Query: 223 QNLFERRITVRMDR-VADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQ 274
           Q L+ERR+TVRMDR V D+ +  +RLPEGLKSIG+GLG NG PL+DVA  L Q
Sbjct: 238 QMLYERRMTVRMDRGVTDKSE--LRLPEGLKSIGIGLGPNGEPLRDVARNLPQ 288

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91076808|ref|XP_974319.1| PREDICTED: similar to Hrp59 CG9373-PA [Tribolium castaneum] gi|270001929|gb|EEZ98376.1| hypothetical protein TcasGA2_TC000835 [Tribolium castaneum]

 Score =  236 bits (603), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 158/238 (66%), Gaps = 27/238 (11%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE---AVE 109
           S VGDV +VE+  DD  K RG  IVEF  P  V+K +  M RFE K RKL+IKE    + 
Sbjct: 70  SQVGDVQFVELFVDDNDKSRGCGIVEFSDPGSVKKCLEVMQRFEVKTRKLIIKEDAGNIR 129

Query: 110 DKGGRRNMGGGGGVDR------------DLSALLQNNS------SKFGNTYGLSPQFLES 151
           DK G  N+ GG G  R            D    L N S      +K+GNTYGLSP FLES
Sbjct: 130 DKHG--NIIGGSGSKRGRDENRYRDERYDSQQSLSNRSGPEVPENKWGNTYGLSPHFLES 187

Query: 152 LGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPV 211
           L I  PL N+VFVANL+Y VD+KKL+EVFRLAG++  V++  DKDG+SRGF  +E+DHPV
Sbjct: 188 LRIETPLCNRVFVANLEYNVDKKKLKEVFRLAGRIVRVDLHTDKDGRSRGFAIIEYDHPV 247

Query: 212 EAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVA 269
           EAVQ+ISM +NQ L++R ++VR+DR  + L    +LPEGLK IGMGLG NG PL+DVA
Sbjct: 248 EAVQAISMFHNQVLYDRPMSVRIDRANETL----KLPEGLKGIGMGLGTNGEPLRDVA 301

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193697751|ref|XP_001948840.1| PREDICTED: myelin expression factor 2-like [Acyrthosiphon pisum]

 Score =  231 bits (590), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 127/239 (53%), Positives = 157/239 (65%), Gaps = 27/239 (11%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE--AVEDKG 112
           VGDV++V + +D+  K RG   VEF   D  +KA++KMHRF+  GRKLV+KE     DK 
Sbjct: 47  VGDVSFVVVYSDEKDKSRGCGTVEFDRVDSAQKAIDKMHRFDINGRKLVVKEDDIDRDKT 106

Query: 113 GRRNMGGGGGVD-----------------------RDLSALLQNNSSKFGNTYGLSPQFL 149
           GR    G                            R  S +  ++  ++ NTYGLSPQFL
Sbjct: 107 GRPLPNGPRSSGGGGGGGGGGVGGGGGGGNIPTSIRSASRMPVSDDFQWDNTYGLSPQFL 166

Query: 150 ESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDH 209
           ESL I  PLIN++FVANLDYKVDEKKL+EVF+LAG+V  VEI  DK+GKS+G+G VE++H
Sbjct: 167 ESLHIRGPLINRIFVANLDYKVDEKKLKEVFKLAGRVLEVEIFSDKEGKSKGYGVVEYNH 226

Query: 210 PVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDV 268
           PVEAVQ+ISM NNQ LFER +++R+DR     D   RLPEGLKSIGMGLGA GAPL DV
Sbjct: 227 PVEAVQAISMFNNQFLFERPMSIRLDRTDK--DPLARLPEGLKSIGMGLGAGGAPLHDV 283

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383855600|ref|XP_003703298.1| PREDICTED: myelin expression factor 2-like [Megachile rotundata]

 Score =  230 bits (587), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 138/248 (55%), Positives = 166/248 (66%), Gaps = 32/248 (12%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE--- 109
           + VG V +VE+  D+  KPRG  IVEF+  D V+ AV KMHR++ KGRKLV+KE  +   
Sbjct: 77  TEVGKVAHVELFTDENDKPRGCGIVEFEDSDSVKIAVEKMHRYDIKGRKLVVKEDFDVER 136

Query: 110 DKGGRRNMG------------------GGGGVDRDLSALLQNNS----------SKFGNT 141
           DK GR   G                  GGG  + +  A                +KFGNT
Sbjct: 137 DKYGRLATGRNNDRVRDDRFRDPPRPQGGGRQNMNPPAGGGGGGGGGGGGGGGDNKFGNT 196

Query: 142 YGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRG 201
           YGLS QFLESLGIN PL+ +VFVANLDYKVDEKKL EVF+LAGKV +VE+  DKDGKSRG
Sbjct: 197 YGLSTQFLESLGINGPLVTRVFVANLDYKVDEKKLLEVFKLAGKVLHVELGKDKDGKSRG 256

Query: 202 FGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLGAN 261
           FG VE+DHPVE+VQ+ISML+NQ L++RR+TVR+DR A+  D P +LPEGLK IGMGLGA 
Sbjct: 257 FGVVEYDHPVESVQAISMLHNQQLYDRRMTVRLDR-ANEPDMPPKLPEGLKGIGMGLGAG 315

Query: 262 GAPLQDVA 269
           G  L DVA
Sbjct: 316 GNRLMDVA 323

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328784140|ref|XP_395436.3| PREDICTED: myelin expression factor 2 [Apis mellifera]

 Score =  230 bits (586), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 140/250 (56%), Positives = 165/250 (66%), Gaps = 34/250 (13%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE--- 109
           + VG V +VE+  D+  KPRG  IVEF+  D V+ AV KMHR++ KGRKLV+KE  +   
Sbjct: 77  TEVGKVAHVELFTDENDKPRGCGIVEFEDSDSVKIAVEKMHRYDIKGRKLVVKEDFDVER 136

Query: 110 DKGGR-------------------RNMGGG-----------GGVDRDLSALLQNNSSKFG 139
           DK GR                   R  GGG           GG             SKFG
Sbjct: 137 DKYGRLATARNNERVRDDRFRDPPRPQGGGRQNMNAPAGGGGGGGGGGGGGGGGGDSKFG 196

Query: 140 NTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKS 199
           NTYGLS QFLESLGIN PL+ +VFVANLDYKVDEKKL EVF+LAGKV +VE+  DKDGKS
Sbjct: 197 NTYGLSTQFLESLGINGPLVTRVFVANLDYKVDEKKLLEVFKLAGKVLHVELGKDKDGKS 256

Query: 200 RGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLG 259
           RGFG VE+DHPVE+VQ+ISML+NQ L++RR+TVR+DR A+  D P +LPEGLK IGMGLG
Sbjct: 257 RGFGVVEYDHPVESVQAISMLHNQQLYDRRMTVRLDR-ANEPDMPPKLPEGLKGIGMGLG 315

Query: 260 ANGAPLQDVA 269
           A G  L DVA
Sbjct: 316 AGGNRLMDVA 325

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714953|ref|XP_003395986.1| PREDICTED: myelin expression factor 2-like [Bombus terrestris]

 Score =  229 bits (584), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 140/253 (55%), Positives = 165/253 (65%), Gaps = 37/253 (14%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE--- 109
           + VG V +VE+  D+  KPRG  IVEF+  D V+ AV KMHR++ KGRKLV+KE  +   
Sbjct: 76  TEVGKVAHVELFTDENDKPRGCGIVEFEDSDSVKIAVEKMHRYDIKGRKLVVKEDFDVER 135

Query: 110 DKGGR-------------------RNMGGG--------------GGVDRDLSALLQNNSS 136
           DK GR                   R  GGG              GG             S
Sbjct: 136 DKYGRLATARNNERVRDDRFRDPPRPQGGGRQNMNAPAGGGGGGGGGGGGGGGGGGGGDS 195

Query: 137 KFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD 196
           KFGNTYGLS QFLESLGIN PL+ +VFVANLDYKVDEKKL EVF+LAGKV +VE+  DKD
Sbjct: 196 KFGNTYGLSTQFLESLGINGPLVTRVFVANLDYKVDEKKLLEVFKLAGKVLHVELGKDKD 255

Query: 197 GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGM 256
           GKSRGFG VE+DHPVE+VQ+ISML+NQ L++RR+TVR+DR A+  D P +LPEGLK IGM
Sbjct: 256 GKSRGFGVVEYDHPVESVQAISMLHNQQLYDRRMTVRLDR-ANEPDMPPKLPEGLKGIGM 314

Query: 257 GLGANGAPLQDVA 269
           GLGA G  L DVA
Sbjct: 315 GLGAGGNRLMDVA 327

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350402014|ref|XP_003486336.1| PREDICTED: myelin expression factor 2-like [Bombus impatiens]

 Score =  229 bits (583), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 140/253 (55%), Positives = 165/253 (65%), Gaps = 37/253 (14%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE--- 109
           + VG V +VE+  D+  KPRG  IVEF+  D V+ AV KMHR++ KGRKLV+KE  +   
Sbjct: 76  TEVGKVAHVELFTDENDKPRGCGIVEFEDSDSVKIAVEKMHRYDIKGRKLVVKEDFDVER 135

Query: 110 DKGGR-------------------RNMGGG--------------GGVDRDLSALLQNNSS 136
           DK GR                   R  GGG              GG             S
Sbjct: 136 DKYGRLATARNNERVRDDRFRDPPRPQGGGRQNMNAPAGGGGGGGGGGGGGGGGGGGGDS 195

Query: 137 KFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD 196
           KFGNTYGLS QFLESLGIN PL+ +VFVANLDYKVDEKKL EVF+LAGKV +VE+  DKD
Sbjct: 196 KFGNTYGLSTQFLESLGINGPLVTRVFVANLDYKVDEKKLLEVFKLAGKVLHVELGKDKD 255

Query: 197 GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGM 256
           GKSRGFG VE+DHPVE+VQ+ISML+NQ L++RR+TVR+DR A+  D P +LPEGLK IGM
Sbjct: 256 GKSRGFGVVEYDHPVESVQAISMLHNQQLYDRRMTVRLDR-ANEPDMPPKLPEGLKGIGM 314

Query: 257 GLGANGAPLQDVA 269
           GLGA G  L DVA
Sbjct: 315 GLGAGGNRLMDVA 327

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	587
FB|FBgn0260010	632	rump "rumpelstiltskin" [Drosop	0.231	0.215	0.659	1.4e-84
UNIPROTKB|F1NIP6	541	MYEF2 "Uncharacterized protein	0.354	0.384	0.413	1.3e-49
UNIPROTKB|Q5ZHY2	616	MYEF2 "Uncharacterized protein	0.354	0.337	0.413	1.2e-48
UNIPROTKB|F1PIL7	492	MYEF2 "Uncharacterized protein	0.357	0.426	0.408	1.4e-48
UNIPROTKB|F1SN63	533	MYEF2 "Uncharacterized protein	0.357	0.393	0.408	1.4e-48
UNIPROTKB|A6QQP0	543	MYEF2 "MYEF2 protein" [Bos tau	0.356	0.384	0.406	1.4e-48
UNIPROTKB|Q9P2K5	600	MYEF2 "Myelin expression facto	0.357	0.35	0.408	2.4e-48
ZFIN|ZDB-GENE-051120-114	557	myef2 "myelin expression facto	0.362	0.382	0.410	5.1e-48
UNIPROTKB|D4AB08	567	Myef2 "Protein Myef2" [Rattus	0.357	0.370	0.408	7.6e-48
UNIPROTKB|D4A1T2	574	Myef2 "Protein Myef2" [Rattus	0.357	0.365	0.408	9.4e-48

FB|FBgn0260010 rump "rumpelstiltskin" [Drosophila melanogaster (taxid:7227)]

 Score = 478 (173.3 bits), Expect = 1.4e-84, Sum P(3) = 1.4e-84
 Identities = 91/138 (65%), Positives = 118/138 (85%)

Query:   133 NNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIA 192
             NNSS + N YGLS  FLESLGI+ PL NKVFVANLDYKVD KKL++VF+LAGKV++V+++
Sbjct:   206 NNSSNY-NLYGLSASFLESLGISGPLHNKVFVANLDYKVDNKKLKQVFKLAGKVQSVDLS 264

Query:   193 LDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLK 252
             LDK+G SRGF  +E+DHPVEAVQ+ISML+ Q LF+RR+TVR+DR+ D+ +G ++LPEGL 
Sbjct:   265 LDKEGNSRGFAVIEYDHPVEAVQAISMLDRQMLFDRRMTVRLDRIPDKNEG-IKLPEGLG 323

Query:   253 SIGMGLGANGAPLQDVAN 270
              +G+GLG NG PL+DVA+
Sbjct:   324 GVGIGLGPNGEPLRDVAH 341

GO:0003729 "mRNA binding" evidence=ISS;IDA

GO:0003730 "mRNA 3'-UTR binding" evidence=IDA;TAS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008298 "intracellular mRNA localization" evidence=IMP

GO:0008595 "anterior/posterior axis specification, embryo" evidence=IMP

GO:0007067 "mitosis" evidence=IMP

GO:0035282 "segmentation" evidence=IGI

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0007277 "pole cell development" evidence=IGI

GO:0009952 "anterior/posterior pattern specification" evidence=IGI

GO:0045451 "pole plasm oskar mRNA localization" evidence=IGI

UNIPROTKB|F1NIP6 MYEF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 379 (138.5 bits), Expect = 1.3e-49, Sum P(2) = 1.3e-49
 Identities = 93/225 (41%), Positives = 126/225 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  E +   
Sbjct:    74 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPEGEHAR 133

Query:   115 XXXXXXXXV-----DRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                             D++  L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   134 RALQRGGGQFAGGHGPDVAPGLMNLPPSIVNNPNIPPEVISNLQAG-RLGSTIFVANLDF 192

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   193 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 252

Query:   230 ITVRMD---------RVADRLDGPVRLPEGLKSIGMGLGANGAPL 265
             + V+MD         RV D      +LP GL  IGMGLG  G P+
Sbjct:   253 MHVKMDDKSVPHEDFRVVDSKAS--QLPRGLGGIGMGLGPGGQPI 295

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q5ZHY2 MYEF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 379 (138.5 bits), Expect = 1.2e-48, Sum P(2) = 1.2e-48
 Identities = 93/225 (41%), Positives = 126/225 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  E +   
Sbjct:   142 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPEGEHAR 201

Query:   115 XXXXXXXXV-----DRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                             D++  L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   202 RALQRGGGQFAGGHGPDVAPGLMNLPPSIVNNPNIPPEVISNLQAG-RLGSTIFVANLDF 260

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   261 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 320

Query:   230 ITVRMD---------RVADRLDGPVRLPEGLKSIGMGLGANGAPL 265
             + V+MD         RV D      +LP GL  IGMGLG  G P+
Sbjct:   321 MHVKMDDKSVPHEDFRVVDSKAS--QLPRGLGGIGMGLGPGGQPI 363

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0014902 "myotube differentiation" evidence=IEA

GO:0030182 "neuron differentiation" evidence=IEA

UNIPROTKB|F1PIL7 MYEF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 371 (135.7 bits), Expect = 1.4e-48, Sum P(2) = 1.4e-48
 Identities = 91/223 (40%), Positives = 126/223 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +   
Sbjct:    73 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 132

Query:   115 XXXXXXXXVDR-----DLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                             D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   133 RALQRTGGSFPGGHVPDMGSGLMNLPPSILNNPNIPPEVISNLQAG-RLGSTIFVANLDF 191

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   192 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 251

Query:   230 ITVRMDRVA----DRL--DGPV-RLPEGLKSIGMGLGANGAPL 265
             + V+MD  +    D    D    +LP GL  IGMGLG  G P+
Sbjct:   252 MHVKMDDKSVPHEDYRSHDSKTPQLPRGLGGIGMGLGPGGQPI 294

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1SN63 MYEF2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 370 (135.3 bits), Expect = 1.4e-48, Sum P(2) = 1.4e-48
 Identities = 91/223 (40%), Positives = 126/223 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +   
Sbjct:    71 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 130

Query:   115 XXXXXXXXVDR-----DLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                             D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   131 RALQRTGGSFPGGHVPDMGSGLMNLPPSILNNPNIPPEVITNLQAG-RLGSTIFVANLDF 189

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   190 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 249

Query:   230 ITVRMDRVA----DRL--DGPV-RLPEGLKSIGMGLGANGAPL 265
             + V+MD  +    D    D    +LP GL  IGMGLG  G P+
Sbjct:   250 MHVKMDDKSVPHEDYRSHDSKTPQLPRGLGGIGMGLGPGGQPI 292

GO:0030182 "neuron differentiation" evidence=IEA

GO:0014902 "myotube differentiation" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|A6QQP0 MYEF2 "MYEF2 protein" [Bos taurus (taxid:9913)]

 Score = 372 (136.0 bits), Expect = 1.4e-48, Sum P(2) = 1.4e-48
 Identities = 91/224 (40%), Positives = 126/224 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +   
Sbjct:   124 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 183

Query:   115 XXXXXXXXVDR-----DLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                             D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   184 RALQRTGGSFPGGHVPDMGSGLMNLPPSILNNPNIPPEVISNLQAG-RLGSTIFVANLDF 242

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   243 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 302

Query:   230 ITVRMD-RVADRLD-------GPVRLPEGLKSIGMGLGANGAPL 265
             + V+MD +     D        P +LP GL  IGMGLG  G P+
Sbjct:   303 MHVKMDDKSVPHEDYRSHDSKAP-QLPRGLGGIGMGLGPGGQPI 345

GO:0030182 "neuron differentiation" evidence=IEA

GO:0014902 "myotube differentiation" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9P2K5 MYEF2 "Myelin expression factor 2" [Homo sapiens (taxid:9606)]

 Score = 376 (137.4 bits), Expect = 2.4e-48, Sum P(2) = 2.4e-48
 Identities = 91/223 (40%), Positives = 127/223 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +   
Sbjct:   124 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 183

Query:   115 XXXXXXXXVDR-----DLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                             D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   184 RALQRTGGSFPGGHVPDMGSGLMNLPPSILNNPNIPPEVISNLQAG-RLGSTIFVANLDF 242

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   243 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 302

Query:   230 ITVRMDRVA---DRL---DGPV-RLPEGLKSIGMGLGANGAPL 265
             + V+MD  +   +     DG   +LP GL  IGMGLG  G P+
Sbjct:   303 MHVKMDDKSVPHEEYRSHDGKTPQLPRGLGGIGMGLGPGGQPI 345

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0014902 "myotube differentiation" evidence=IEP

GO:0030182 "neuron differentiation" evidence=IEP

GO:0005730 "nucleolus" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

ZFIN|ZDB-GENE-051120-114 myef2 "myelin expression factor 2" [Danio rerio (taxid:7955)]

 Score = 374 (136.7 bits), Expect = 5.1e-48, Sum P(2) = 5.1e-48
 Identities = 94/229 (41%), Positives = 128/229 (55%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M + +  GR L IKE  + +   
Sbjct:   105 VGEVTYVELFKDGEGKSRGCGVVEFKDEEFVKKAIEVMSKHDLNGRPLNIKEDPDGEHAR 164

Query:   115 XXXXXXXXV-----DRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                     +      +D S +  N      N   +  + + +L     L   +FVANLD+
Sbjct:   165 RVLQRSGRMYGGGRGQDSSGI--NIPPSIANNPNIPHEIISALQAG-RLGATIFVANLDF 221

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V   ++  DKDGKSRG GTV F+ P+EAVQ+ISM N Q LF+R+
Sbjct:   222 KVGWKKLKEVFGMAGTVRRADVKEDKDGKSRGMGTVTFEQPLEAVQAISMFNGQMLFDRQ 281

Query:   230 ITVRMDRVADRLDG--PV----RLPEGLKSIGMGLGANGAPLQDVANWL 272
             + V+MD  +   D   PV    +LP GL  IGMGLG  G P+   AN L
Sbjct:   282 MHVKMDDKSLPPDDFRPVEKSPQLPRGLGGIGMGLGPGGQPIN--ANCL 328

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|D4AB08 Myef2 "Protein Myef2" [Rattus norvegicus (taxid:10116)]

 Score = 373 (136.4 bits), Expect = 7.6e-48, Sum P(2) = 7.6e-48
 Identities = 91/223 (40%), Positives = 127/223 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +   
Sbjct:   115 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 174

Query:   115 XXXXXXXXVDR-----DLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                       +     D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   175 RALQRTGTSFQGSHASDVGSGLVNLPPSIVNNPNIPPEVINNLQAG-RLGSTIFVANLDF 233

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   234 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 293

Query:   230 ITVRMDRVA----DRL--DGPV-RLPEGLKSIGMGLGANGAPL 265
             + V+MD  +    D    D    +LP GL  IGMGLG  G P+
Sbjct:   294 MHVKMDDKSVPHEDYRSHDSKTSQLPRGLGGIGMGLGPGGQPI 336

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|D4A1T2 Myef2 "Protein Myef2" [Rattus norvegicus (taxid:10116)]

 Score = 373 (136.4 bits), Expect = 9.4e-48, Sum P(2) = 9.4e-48
 Identities = 91/223 (40%), Positives = 127/223 (56%)

Query:    55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKXXX 114
             VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE  + +   
Sbjct:   115 VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALETMNKYDLSGRPLNIKEDPDGENAR 174

Query:   115 XXXXXXXXVDR-----DLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
                       +     D+ + L N      N   + P+ + +L     L + +FVANLD+
Sbjct:   175 RALQRTGTSFQGSHASDVGSGLVNLPPSIVNNPNIPPEVINNLQAG-RLGSTIFVANLDF 233

Query:   170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
             KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+  +EAVQ+ISM N Q LF+R 
Sbjct:   234 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRP 293

Query:   230 ITVRMDRVA----DRL--DGPV-RLPEGLKSIGMGLGANGAPL 265
             + V+MD  +    D    D    +LP GL  IGMGLG  G P+
Sbjct:   294 MHVKMDDKSVPHEDYRSHDSKTSQLPRGLGGIGMGLGPGGQPI 336

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0014902 "myotube differentiation" evidence=IEA

GO:0030182 "neuron differentiation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	587
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-39
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	3e-25
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	4e-25
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	1e-19
smart00360	73	smart00360, RRM, RNA recognition motif	2e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-18
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-17
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-17
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	8e-16
smart00360	73	smart00360, RRM, RNA recognition motif	1e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-14
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-14
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	6e-14
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	8e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-13
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-13
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	1e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-12
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-11
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-11
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-11
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-11
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	3e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-11
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	6e-11
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-10
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-10
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	2e-10
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-10
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	6e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
smart00360	73	smart00360, RRM, RNA recognition motif	2e-09
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	2e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-09
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-09
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-09
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-09
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	4e-09
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-09
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	5e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	5e-09
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	4e-08
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	5e-08
cd12601	74	cd12601, RRM2_SRSF1_like, RNA recognition motif 2	6e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	6e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	6e-08
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-08
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-07
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-07
cd12764	72	cd12764, RRM2_SRSF4, RNA recognition motif 2 in ve	2e-07
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-07
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	3e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	5e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	6e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	6e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-07
cd12766	73	cd12766, RRM2_SRSF6, RNA recognition motif 2 found	6e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	7e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-07
cd12602	76	cd12602, RRM2_SF2_plant_like, RNA recognition moti	8e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-07
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	1e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-06
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-06
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-06
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-06
cd12768	76	cd12768, RRM2_SRSF9, RNA recognition motif 2 in ve	2e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-06
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-06
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	3e-06
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-06
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	4e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-06
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	8e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	8e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	8e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	8e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	9e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-05
cd12767	76	cd12767, RRM2_SRSF1, RNA recognition motif 2 in se	1e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-05
pfam02301	186	pfam02301, HORMA, HORMA domain	1e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	2e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-05
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-05
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	3e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-05
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	3e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	4e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	7e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	8e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	8e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-05
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	9e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	9e-05
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	1e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	1e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-04
cd12765	75	cd12765, RRM2_SRSF5, RNA recognition motif 2 in ve	1e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-04
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	2e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	4e-04
cd12542	78	cd12542, RRM2_LARP7, RNA recognition motif 2 in La	4e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	4e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	4e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	4e-04
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	5e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	6e-04
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	6e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	7e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	8e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	8e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	8e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	9e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	9e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	9e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	9e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.001
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.001
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.001
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.001
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.001
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.001
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.001
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.001
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.002
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.002
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.002
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.002
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.002
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.002
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	0.002
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.002
cd12541	76	cd12541, RRM2_La, RNA recognition motif 2 in La au	0.002
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.002
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.002
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.002
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.002
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.002
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.002
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.002
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.003
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.003
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.003
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.003
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.003
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.003
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.003
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.003
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	0.003
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.004
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.004
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.004
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.004
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.004
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	0.004
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.004
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.004
cd12256	89	cd12256, RRM2_LKAP, RNA recognition motif 2 in Lim	0.004

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score =  138 bits (350), Expect = 1e-39
 Identities = 48/74 (64%), Positives = 60/74 (81%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FVANLDYKV  KKL+EVF+LAGKV   +I  DK+GKSRG G V+F+HP+EAVQ+ISM N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 222 NQNLFERRITVRMD 235
            Q LF+R + V+MD
Sbjct: 61  GQMLFDRPMRVKMD 74

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 98.9 bits (246), Expect = 3e-25
 Identities = 48/74 (64%), Positives = 57/74 (77%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           VFVANLDYKV  KKL+EVF +AG V   +I  DKDGKSRG GTV F+ P+EAVQ+ISM N
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62

Query: 222 NQNLFERRITVRMD 235
            Q LF+R + V+MD
Sbjct: 63  GQLLFDRPMHVKMD 76

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 98.6 bits (245), Expect = 4e-25
 Identities = 46/74 (62%), Positives = 58/74 (78%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FVANLD+KV  KKL+EVF +AG V+  +I  DKDGKSRG GTV F+ P+EAVQ+ISM N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 222 NQNLFERRITVRMD 235
            Q LF+R + V+MD
Sbjct: 63  GQFLFDRPMHVKMD 76

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 82.9 bits (205), Expect = 1e-19
 Identities = 29/54 (53%), Positives = 40/54 (74%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE 106
             VG+VTYVE+  D+ GK RG  +VEF+  + V+KA+  M+R+E KGRKLV+KE
Sbjct: 22  EKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVVKE 75

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 79.2 bits (196), Expect = 2e-18
 Identities = 30/73 (41%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            +FV NL     E++LRE+F   GKVE+V +  DK+ GKS+GF  VEF+   +A +++  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 220 LNNQNLFERRITV 232
           LN + L  R + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 77.7 bits (192), Expect = 7e-18
 Identities = 31/72 (43%), Positives = 46/72 (63%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NL     E+ LRE+F   G++E+V I  DKDGKS+GF  VEF+ P +A +++  LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 222 NQNLFERRITVR 233
            + L  R++ V 
Sbjct: 61  GKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 76.2 bits (188), Expect = 3e-17
 Identities = 27/72 (37%), Positives = 46/72 (63%), Gaps = 5/72 (6%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-----IGLVRFDSEWTAKRAIDMMD 573
           + V+NLP ++TWQ+L+D FR CG++  A++K   D      G V F+S   A+RAI+M +
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 574 RTRIDGKIIDVT 585
              ++G+ ++V 
Sbjct: 61  GYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 75.8 bits (187), Expect = 4e-17
 Identities = 29/72 (40%), Positives = 42/72 (58%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NLD +V E+ L E+F  AG +E V+I  D +GK + F  V F H V    +I +LN
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 222 NQNLFERRITVR 233
              LF R + ++
Sbjct: 64  GIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 71.9 bits (177), Expect = 8e-16
 Identities = 29/72 (40%), Positives = 45/72 (62%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NL + V  + L+++FR  G V   ++  D DG+S+GFGTV F+ P +A ++I M N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 222 NQNLFERRITVR 233
             +L  R + VR
Sbjct: 61  GYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

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

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
           T+ V NLPP  T +ELR+ F   G ++   +       K KG    V F+SE  A++A++
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKG-FAFVEFESEEDAEKALE 59

Query: 571 MMDRTRIDGKIIDV 584
            ++   +DG+ + V
Sbjct: 60  ALNGKELDGRPLKV 73

Length = 73

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

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 23/70 (32%), Positives = 41/70 (58%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NL     E+ L+++F   G +E++ I  D+ G+S+GF  VEF+   +A +++  LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 222 NQNLFERRIT 231
            + L  R + 
Sbjct: 61  GKELGGRELR 70

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

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NL +  ++  L E F+  G+V +V IA D DG+S+GFG VEF    E  Q     +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFAT-EEGAQKALEKS 60

Query: 222 NQNLFERRITVRM 234
            + L  R I V +
Sbjct: 61  GEELLGREIRVDL 73

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 67.0 bits (163), Expect = 6e-14
 Identities = 33/70 (47%), Positives = 48/70 (68%), Gaps = 4/70 (5%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIK---GKGD-IGLVRFDSEWTAKRAIDMMDR 574
           + V+NLP  +TWQ+L++KF  CG + FAEIK   GK    G VRFDS  +A++A  +M+ 
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMNG 61

Query: 575 TRIDGKIIDV 584
            +I+G+ IDV
Sbjct: 62  IKINGREIDV 71

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 66.1 bits (162), Expect = 8e-14
 Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
           VVV  LP   +WQ+L+D  R  GD+ +A++ + +   G+V F S+   +RA+  +D T  
Sbjct: 3   VVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGTEF 62

Query: 578 DGKIIDV 584
            G+ + V
Sbjct: 63  RGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It 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 with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 64.9 bits (159), Expect = 3e-13
 Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            ++V NL Y V E+ L+++F   G+V +  +  D++ G+SRGFG VE +   EA  +I  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 220 LNNQNLFERRITVR 233
           LN  +   R +TV 
Sbjct: 61  LNGTDFGGRTLTVN 74

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

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

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 21/58 (36%), Positives = 38/58 (65%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           VFV+NLDY V E +LR++F   G++ +V +  +  GKS+G+  VEF++     +++ +
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 59

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

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

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 7/70 (10%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMM 572
           + V NLPP  T ++L+D F   G I+   I      + KG    V F+ E  A++A++ +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKG-FAFVEFEDEEDAEKALEAL 59

Query: 573 DRTRIDGKII 582
           +   + G+ +
Sbjct: 60  NGKELGGREL 69

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

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

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 7/72 (9%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMM 572
           + V NLPP  T ++LR+ F   G+I+   I      K KG    V F+S   A++A++ +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKG-FAFVEFESPEDAEKALEAL 59

Query: 573 DRTRIDGKIIDV 584
           +   +DG+ + V
Sbjct: 60  NGKELDGRKLKV 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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 63.4 bits (154), Expect = 1e-12
 Identities = 31/70 (44%), Positives = 46/70 (65%), Gaps = 4/70 (5%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIK---GKGD-IGLVRFDSEWTAKRAIDMMDR 574
           + V+NLP   TW+ L+DKF  CG + +A+IK   GK    G+VRF+S   A+RA  MM+ 
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACRMMNG 61

Query: 575 TRIDGKIIDV 584
            +++G+ IDV
Sbjct: 62  YKLNGREIDV 71

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           VFV N+ Y   E++L E+F   G V +  +  D+D GK +G+G  EF+    A  +I  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 221 NNQNLFERRITV 232
           N      R + V
Sbjct: 61  NGYEFNGRALRV 72

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

>gnl|CDD|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 = 63.0 bits (154), Expect = 2e-12
 Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           NK+FV+ L  +  EK+L  +F   G+VE V +  D + G+SRGFG V F+   +A  +I 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 219 MLNNQNLFERRITV 232
            LN + L  R I V
Sbjct: 62  DLNGKELEGRVIKV 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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 62.7 bits (152), Expect = 2e-12
 Identities = 29/72 (40%), Positives = 41/72 (56%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NL+ +V E+ L E+F  AG +  V I  DK+GK + FG V F H      +I++LN
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 222 NQNLFERRITVR 233
              L+ R I V 
Sbjct: 64  GIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 28/69 (40%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           ++V NL   V E+ LRE F   GKVE V +  +KD + RGF  VEF  P +A  ++  LN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 222 NQNLFERRI 230
              L  R +
Sbjct: 60  GLVLDGRTL 68

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

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

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 23/72 (31%), Positives = 38/72 (52%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           ++ V NL +K  E  L+++F   G V  V I    DGK +GF  V+F    +A ++I  +
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 221 NNQNLFERRITV 232
           N + +  R + V
Sbjct: 61  NGKKIKGRPVAV 72

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 59.3 bits (143), Expect = 2e-11
 Identities = 31/78 (39%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           ++FV NL + +  +KL+E F   G V   EI ++ +GKS+G GTV FD P  A ++  ++
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLM 59

Query: 221 NNQNLFERRITVRMDRVA 238
           N   +  R I VR+DR A
Sbjct: 60  NGIKINGREIDVRLDRNA 77

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 59.1 bits (144), Expect = 3e-11
 Identities = 24/73 (32%), Positives = 46/73 (63%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             V+V NL   +D++KL+E+F   GK+ + ++  D +GKS+GFG V F++   A +++  
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 220 LNNQNLFERRITV 232
           LN + +  +++ V
Sbjct: 62  LNGKEVNGKKLYV 74

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 58.9 bits (142), Expect = 3e-11
 Identities = 25/52 (48%), Positives = 36/52 (69%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE 106
           VG+VTYVE+L D  GK RG A+VEF+  + ++KAV  +++    GR L +KE
Sbjct: 24  VGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEVLNKHVLNGRPLKVKE 75

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK 105
              S  G++  V I+ D  GK +G A VEF+SP+   KA+  ++  E  GRKL + 
Sbjct: 17  ELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

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

 Score = 65.2 bits (159), Expect = 4e-11
 Identities = 46/172 (26%), Positives = 88/172 (51%), Gaps = 29/172 (16%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE----TKGRKLVIKEAVEDK 111
           G++T   ++ D +G+ RG A V F+  +   KAV +M+  +     +G+KL +  A   K
Sbjct: 203 GEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRA--QK 260

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
              R        + +L    +    +         + +++ G+N      ++V NLD  V
Sbjct: 261 RAER--------EAELRRKFEELQQE---------RKMKAQGVN------LYVKNLDDTV 297

Query: 172 DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ 223
            ++KLRE+F   G++ + ++ LD+ G SRGFG V F +P EA ++++ ++ +
Sbjct: 298 TDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGR 349

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

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 58.0 bits (140), Expect = 6e-11
 Identities = 29/72 (40%), Positives = 43/72 (59%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NLD KV E+ + E+F  AG V  V+I  DKDGK + F  V F H V    ++++LN
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 222 NQNLFERRITVR 233
              L+ R + ++
Sbjct: 64  GIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 23/65 (35%), Positives = 37/65 (56%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           ++ V+NL Y V E+ L E+F   G+V+ V+I  D+ G+S G   V F+   +A ++I   
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 221 NNQNL 225
           N   L
Sbjct: 62  NGVLL 66

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 62.3 bits (150), Expect = 1e-10
 Identities = 33/82 (40%), Positives = 49/82 (59%), Gaps = 1/82 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           N +FV NL Y V E+ LRE+F+  G V+ V +  D++ GKSRGF  VEF+    A ++I 
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 219 MLNNQNLFERRITVRMDRVADR 240
            LN + L  R + V+  + A +
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQ 197

Length = 306

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           V+V NLD KV E+ L E+F  AG V NV I  D+     +G+G VEF    +A  +I ++
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 221 NNQNLFERRITVR 233
           N   L+ + I V 
Sbjct: 61  NMIKLYGKPIRVN 73

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 56.4 bits (137), Expect = 2e-10
 Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           VFV NL + ++E++LR+ F   G VE V I  D+  G  +GFG V F    ++V     L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTK-DSVALALKL 60

Query: 221 NNQNLFERRITV 232
           N   L  R+I V
Sbjct: 61  NGIKLKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 56.6 bits (136), Expect = 2e-10
 Identities = 25/52 (48%), Positives = 36/52 (69%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE 106
           VG+VTYVE+  D  GK RG  +VEF+  + V+KA+  M++++  GR L IKE
Sbjct: 24  VGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVMNKYDLNGRPLNIKE 75

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 30/74 (40%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L   V E+ LRE F   G VE+VEI  DK+ GK RGF  V FD   + V  I +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDY-DPVDKIVL 59

Query: 220 LNNQNLFERRITVR 233
                +   R+ V+
Sbjct: 60  QKYHTINGHRVEVK 73

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           ++V  L  +VDEK L   F   G +++++I LD +  K RGF  VEF+ P +A  +I  +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 221 NNQNLFERRITV 232
           N   LF R I V
Sbjct: 61  NESELFGRTIRV 72

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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 55.5 bits (134), Expect = 6e-10
 Identities = 26/76 (34%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFR-LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +VF++N+ Y +  + L+++FR   G+V  VE+  D++GKSRG G VEF       +++  
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 220 LNNQNLFERRITVRMD 235
           +N   L  R++ V+ D
Sbjct: 61  MNRYELKGRKLVVKED 76

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD----IGLVRFDSEWTAKRAIDMMDR 574
           + V+NLPP++T ++LR+ F   G ++   +    D       V F S   A+ A+  ++ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 575 TRIDGK 580
             +DG+
Sbjct: 61  LVLDGR 66

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

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 51  HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
             S  G V  V ++ D +TGK +G A VEF+S +   KA+  ++  E  GR L +
Sbjct: 19  LFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 54.2 bits (130), Expect = 2e-09
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           ++FV NL +    K L++ F   G V   +I ++ +GKS+G G V F+ P  A ++  M+
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMM 59

Query: 221 NNQNLFERRITVRMDRVA 238
           N   L  R I VR+DR A
Sbjct: 60  NGYKLNGREIDVRIDRNA 77

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 60.2 bits (146), Expect = 2e-09
 Identities = 50/191 (26%), Positives = 76/191 (39%), Gaps = 44/191 (23%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           +A LY        G V  V +  D  T +  G   V FQ+P    +A+  M+     G+ 
Sbjct: 14  EAKLYD--LFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKP 71

Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
           + I  +  D   RR+     GV               GN                     
Sbjct: 72  IRIMWSQRDPSLRRS-----GV---------------GN--------------------- 90

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +FV NLD  VD K L + F   G + + ++A D++GKSRG+G V F+    A  +I  +N
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 222 NQNLFERRITV 232
              L ++ + V
Sbjct: 151 GMLLNDKEVYV 161

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

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

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N++FV  +     E++LR+ F   G V++V+I  D+ G S+G+G V F+   E  + I  
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFET-QEDAEKILA 61

Query: 220 LNNQNLFERRITVR 233
           + N N   +++ + 
Sbjct: 62  MGNLNFRGKKLNIG 75

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 59.5 bits (144), Expect = 2e-09
 Identities = 51/213 (23%), Positives = 92/213 (43%), Gaps = 35/213 (16%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           S VG V  V+ + D ++ + +G A VEF   + V KA+  +      GR ++++ +  +K
Sbjct: 111 SKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQSSQAEK 169

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
                                N ++K                 + P   K++V NL + +
Sbjct: 170 ---------------------NRAAKAATH----------QPGDIPNFLKLYVGNLHFNI 198

Query: 172 DEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRI 230
            E++LR++F   G +E+V++  D + G+S+GFG ++F    EA +++ ++N   L  R I
Sbjct: 199 TEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPI 258

Query: 231 TV-RMDRVADRLDGPVRLPEGLKSIGMGLGANG 262
            V         LD      +  K   MG   N 
Sbjct: 259 KVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNT 291

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

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 26/74 (35%), Positives = 41/74 (55%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           ++ V NL   V E +LRE F   G+V +V++   +DGKSR FG V F    +A Q++   
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 221 NNQNLFERRITVRM 234
           N   +   +I+V +
Sbjct: 62  NKTFIDTSKISVEL 75

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 29/73 (39%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           VFV  L  KV E+ L E F  AGKV +V I  D++  +S+G   VEF    E+V     L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYD-EESVPLALGL 60

Query: 221 NNQNLFERRITVR 233
             Q L  + I V+
Sbjct: 61  TGQRLLGQPIMVQ 73

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is 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 = 53.3 bits (129), Expect = 3e-09
 Identities = 23/71 (32%), Positives = 43/71 (60%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +F+ NLD  +D K L + F   G + + ++A D++G S+G+G V F+    AV++I  +N
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 222 NQNLFERRITV 232
              L ++++ V
Sbjct: 65  GMLLNDKKVFV 75

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

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISM 219
           ++FV NL +   E++LRE+F   G++  V + LDK   +S+GF  V F  P  AV++ S 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 220 LNNQNLFERRI 230
           L+   +F+ R+
Sbjct: 61  LDGS-IFQGRL 70

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

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

 Score = 53.6 bits (129), Expect = 3e-09
 Identities = 20/73 (27%), Positives = 46/73 (63%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +K+FV+ L + V +++L ++F+  G V++V +  ++ GK +G   VE+++   A Q++  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 220 LNNQNLFERRITV 232
           ++   + E+ I+V
Sbjct: 63  MDGTEIKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISMLNN 222
           V  L     E+ LREVF   G +E V++  D K G+SRGFG V F+   +A ++   LN 
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 223 QNLFERRITV 232
             +  RRI V
Sbjct: 64  MEIDGRRIRV 73

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

 Score = 52.9 bits (127), Expect = 4e-09
 Identities = 24/71 (33%), Positives = 42/71 (59%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           ++V NLD +V E  L+++F++ G V+NV+I  DK+ K   +G VE+    +A  ++  LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 222 NQNLFERRITV 232
            + +    I V
Sbjct: 61  GRQIENNEIRV 71

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

>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 52.8 bits (127), Expect = 5e-09
 Identities = 22/70 (31%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
            ++V+NL   ++WQ+L+D  R  G++ +A+  K + + G+V F +    KRAI+ +D T 
Sbjct: 2   RLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQRPNEGVVEFATYSDMKRAIEKLDGTE 61

Query: 577 IDGKIIDVTF 586
           ++G+ I +  
Sbjct: 62  LNGRKIKLIE 71

This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 52.8 bits (127), Expect = 5e-09
 Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           ++FV NL Y   E  L ++F   G++  V +A+DK  GKS+GF  V F  P +AV++   
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 220 LNNQNLFERRI 230
           L+ + +F+ R+
Sbjct: 64  LDGK-VFQGRL 73

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

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 52.5 bits (126), Expect = 6e-09
 Identities = 22/73 (30%), Positives = 42/73 (57%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N++FV  +D+K +E  LR+ F   G V+ V+I  D+ G S+G+G V F+   +A + +  
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQE 62

Query: 220 LNNQNLFERRITV 232
            N     ++++ +
Sbjct: 63  ANRLCFRDKKLNI 75

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 53.0 bits (128), Expect = 6e-09
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLN 221
           FVA L+Y   E KLR  F   G ++ + +  DK  GK RG+  +EF+H  +   +    +
Sbjct: 5   FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 222 NQNLFERRITVRMDR 236
            + +  RR+ V ++R
Sbjct: 65  GKKIDGRRVLVDVER 79

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

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

 Score = 51.8 bits (125), Expect = 8e-09
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +  L  +   S  G +  + I+ D+TG+ +G A VEF+  +   KA+  ++  E  GR+L
Sbjct: 12  EEDLKDL--FSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69

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

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

 Score = 52.3 bits (126), Expect = 8e-09
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKS----RGFGTVEFDHPVEAVQS 216
           +++V NLD+K+DE  LR +F   G+VE++ I   +D K      GF  V F     A  +
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 217 ISMLNNQNLFERRITV 232
           + + N   L  R+I+V
Sbjct: 62  LQL-NGTELGGRKISV 76

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

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

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 26/59 (44%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLN 221
           V NL    DE  LRE+FR  G +  V +A DK+ G+SRGF  V F    +A ++I  LN
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN 62

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

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSR-GFGTVEFDHPVEAVQSISML 220
           ++V NL +   E+++ E+F   G ++ + + LD+  K+  GF  VE+    +A  ++  L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 221 NNQNLFERRITVRMD 235
           N   L +R I V  D
Sbjct: 61  NGTKLDDRIIRVDWD 75

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            +FV NL + VD++ L+  F   G V    +  D++ G+SRGFG V+F+ P +A ++I  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 220 LNNQNLFERRITVRM 234
           ++ + L  R I V  
Sbjct: 61  MDGKELDGRPINVDF 75

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           +FV N+DY    ++L+E F+  G +  + I  DK  G+ +GF  +EF     +V++  +L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDK-SSVENALLL 60

Query: 221 NNQNLFERRITV 232
           N      R+I V
Sbjct: 61  NESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 55.7 bits (133), Expect = 2e-08
 Identities = 44/180 (24%), Positives = 75/180 (41%), Gaps = 21/180 (11%)

Query: 51  HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
                G V  V ++ D +TGK RG A VEF+S +   KA+ +++  E +GR L +++A  
Sbjct: 135 LFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP 194

Query: 110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
               R  +        +L A      S+           L             +V NL  
Sbjct: 195 ASQPRSEL------SNNLDASFAKKLSRGKALLLEKSDNL-------------YVGNLPL 235

Query: 170 KVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSISMLNNQNLFER 228
           K  E++L ++F+  G +    +   KDGK  +    V  +   +A++S S  N + +  R
Sbjct: 236 KTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGR 295

Length = 306

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 22/61 (36%), Positives = 40/61 (65%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
           +V NLD  +D+++LRE F   G + + ++  D+ G+S+GFG V F  P EA ++++ +N 
Sbjct: 5   YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNG 64

Query: 223 Q 223
           +
Sbjct: 65  R 65

This subfamily corresponds to the RRM4 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 theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. 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. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L Y   +  LR+ F   G++E   +  D+  GKSRG+G V F     A ++   
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 220 LN 221
            N
Sbjct: 62  PN 63

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK----SRGFGTVEFDHPVEAVQS 216
           ++++ NLD ++ E  L ++F   GK++  +    K G      RG+  V F+   EA ++
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 217 ISMLNNQNLFERRITVR 233
           +  LN +    +++ VR
Sbjct: 61  LKSLNGKTALGKKLVVR 77

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

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           VF+ NL +   E++L+E+F   G+V+   I  DK  G S+G   V+F     A + +   
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 221 NNQN-----LFERRITVRM 234
           +N       L  RR+ V +
Sbjct: 63  DNAEDSGLSLDGRRLIVTL 81

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

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

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           KV+V NL  +  +++L + F   G + +V +A        GF  VEF+ P +A  ++  L
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR----NPPGFAFVEFEDPRDAEDAVRAL 56

Query: 221 NNQNLFERRITVRMDR 236
           + + +   R+ V + R
Sbjct: 57  DGRRICGNRVRVELSR 72

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

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 4/75 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV NL + V  K+L+E F   GKV++  +  DK+ G S+G+G V F    + +++   
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR-DGLENAL- 58

Query: 220 LNNQNLFE-RRITVR 233
              +++ E  ++ V+
Sbjct: 59  QKQKHILEGNKLQVQ 73

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALD--KDGKSRGFGTVEFDHPVEAVQSISML 220
           ++ NL Y V E+ ++E FR    V +V +  +    G+ RGFG  EF+     +Q++S+ 
Sbjct: 5   YLGNLPYDVTEEDIKEFFR-GLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSL- 62

Query: 221 NNQNLFERRITV 232
           N+++L  RRI V
Sbjct: 63  NDESLKNRRIRV 74

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|241045 cd12601, RRM2_SRSF1_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins

 Score = 49.8 bits (119), Expect = 6e-08
 Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           V+V  LPPT +WQ+L+D  R  GD+ +A++   G  G+V F      K A+  +D ++
Sbjct: 3   VIVSGLPPTGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFLRYEDMKYAVKKLDDSK 59

This subfamily corresponds to the RRM2 of serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins. SRSF1, also termed ASF-1, is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9, also termed SRp30C, has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 49.9 bits (120), Expect = 6e-08
 Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQS 216
           N + +  LD    E+ + +       V   ++ L +D   G SRGF  VEF    +A Q 
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62

Query: 217 ISMLNNQNLFE---RRITV 232
           +  LNN + F    R + V
Sbjct: 63  MDALNNLDPFVIDGRVVRV 81

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

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

 Score = 49.6 bits (119), Expect = 6e-08
 Identities = 25/69 (36%), Positives = 38/69 (55%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ 223
           V NL   + E KLR++F   G + +V++   KDGK R FG V +    EA +++   NN 
Sbjct: 5   VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNS 64

Query: 224 NLFERRITV 232
            +   +ITV
Sbjct: 65  FIDTSKITV 73

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

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 49.8 bits (119), Expect = 7e-08
 Identities = 24/58 (41%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
           N VFV  +D ++DE ++R  F   G V+ V+I  D+ G S+G+G V F   V+ VQ I
Sbjct: 6   NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVD-VQKI 62

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 49.5 bits (119), Expect = 8e-08
 Identities = 24/71 (33%), Positives = 41/71 (57%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+ V N+ ++  +K+LRE+F   G+V++V +    DG  RGF  VEF    EA  ++  
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 220 LNNQNLFERRI 230
           L + +L+ R +
Sbjct: 61  LKSTHLYGRHL 71

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

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 13/48 (27%), Positives = 29/48 (60%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
            G+V   ++  D+ G+ +G   V F+SP+  ++A+   + ++ +GR+L
Sbjct: 22  CGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGREL 69

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSISM 219
           K+F+  L +  +E+ L +VF   G++  V +  D++ + SRGFG V F++P +A  ++  
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 220 LNNQNLFERRITV 232
           +N +++  R+I V
Sbjct: 62  MNGKSVDGRQIRV 74

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

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

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 20/73 (27%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           + V  L   V++  L+E+F   G V++V++ +D++    RG+  VEF+ P +A ++I  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 221 NNQNLFERRITVR 233
           +   +  + +TV 
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 8/69 (11%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
           TV V NL  ++   ELR  F  CG+I    +      K KG    V F++E + + A+  
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKG-YAYVEFENEESVQEAL-K 58

Query: 572 MDRTRIDGK 580
           +DR  I G+
Sbjct: 59  LDRELIKGR 67

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

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 3/72 (4%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           V++ NL + + E  +RE F+   ++ +V +A DK+ G+ +GFG V+F    E++ +   L
Sbjct: 2   VYIGNLAWDITEDDVREFFK-GCEITSVRLATDKETGEFKGFGHVDFADE-ESLDAALKL 59

Query: 221 NNQNLFERRITV 232
           +   L  R I +
Sbjct: 60  DGTVLCGRPIRI 71

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLN 221
           +V NL + + E  LR +F   G++E V++  D + G+S+G+G ++F    +A +++  LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 222 NQNLFERRITV 232
              L  R I V
Sbjct: 62  GFELAGRPIKV 72

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

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

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 6/67 (8%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK------SRGFGTVEFDHPVEAVQ 215
           +FV NL++K  E+ L++ F   G V +V IA  KD K      S G+G VEF     A +
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 216 SISMLNN 222
           ++  L  
Sbjct: 63  ALKRLQG 69

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

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +++ +L +   EK+L++ F   G V+NV +A   K G S+ +G ++F +P  A  +   +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 221 NNQNLFERRITVR 233
           NN  L  + + V 
Sbjct: 62  NNYLLMGKVLQVH 74

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           V++ +L +   E +LR+ F   G V  + ++  K  GKS+G+  VEF+ P  A      +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 221 NNQNLFERRITVR 233
           NN  LFER +  +
Sbjct: 62  NNYLLFERLLKCK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +V++  L Y+  E+ +   F+  G++  + +         GFG VEF+ P +A  ++  L
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINL-------KNGFGFVEFEDPRDADDAVYEL 53

Query: 221 NNQNLFERRITVRMDR 236
           N + L   R+ V   R
Sbjct: 54  NGKELCGERVIVEHAR 69

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

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISM 219
            + V  L +K  E+ L++ F   G++  V++  D K G+S+GFG V F       Q   +
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADY--EDQVKVL 58

Query: 220 LNNQNLFERRITVRMDR 236
                +  R   V++  
Sbjct: 59  SQRHMIDGRWCDVKIPN 75

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 22/65 (33%), Positives = 42/65 (64%), Gaps = 1/65 (1%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
           ++V+NL    +WQ+L+D  R  G++ +A+  KG+ + G++ F S    KRA++ +D T +
Sbjct: 3   LIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGVIEFRSYSDMKRALEKLDGTEV 62

Query: 578 DGKII 582
           +G+ I
Sbjct: 63  NGRKI 67

This subgroup corresponds to the RRM2 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4), a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFRS4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, SRSF4 activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 47.9 bits (114), Expect = 3e-07
 Identities = 22/73 (30%), Positives = 43/73 (58%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+ V NL ++  +K +R +F   G++++V +    D  +RGF  VEF    EA+ +++ L
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNAL 61

Query: 221 NNQNLFERRITVR 233
            + +L  RR+ ++
Sbjct: 62  KDTHLLGRRLVLQ 74

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

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 47.7 bits (113), Expect = 3e-07
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +VFV  +   V E +L  VF   G++  + + +D DGK+RG+  V +    EA +++  L
Sbjct: 3   EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVREL 62

Query: 221 NN 222
           NN
Sbjct: 63  NN 64

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 47.3 bits (113), Expect = 5e-07
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISML 220
           V+V+NL + +    L ++F   GKV  V I  DK+  KS+G   + F    +A + +  L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 221 NNQNLFERRITVRM 234
           NN+ LF R +   +
Sbjct: 64  NNKELFGRTLKCSI 77

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

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 28/63 (44%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP--VEAVQSI 217
           K+FV  L   V E++ +E F   GKV + ++  D D G+SRGFG V FD    VE V S 
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 218 SML 220
            ML
Sbjct: 61  GML 63

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 48.9 bits (116), Expect = 6e-07
 Identities = 43/137 (31%), Positives = 65/137 (47%), Gaps = 8/137 (5%)

Query: 127 LSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKV 186
           L  LL+ N S  GN        L SL +   +  K+F+  L +  D+  LR+ F   G V
Sbjct: 7   LGGLLRQNISSNGN--VPVTSMLGSLRL---MSTKLFIGGLSWGTDDASLRDAFAHFGDV 61

Query: 187 ENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPV 245
            + ++ +D++ G+SRGFG V F+    A  +IS ++ + L  R I  R++   DR   P 
Sbjct: 62  VDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHI--RVNPANDRPSAPR 119

Query: 246 RLPEGLKSIGMGLGANG 262
               G    G G G  G
Sbjct: 120 AYGGGGGYSGGGGGYGG 136

Length = 144

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 47.3 bits (113), Expect = 6e-07
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGK-VENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           +F+ NLD +VDEK L + F   G  ++  +I  D D G S+GF  + +D    +  +I  
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 220 LNNQNLFERRITV 232
           +N Q L  R ITV
Sbjct: 64  MNGQYLCNRPITV 76

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

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

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL Y   +++L E F   G ++   +  DK   K RGFG V F    +A +++   
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 221 NNQNLFERRITV 232
                  R+I V
Sbjct: 62  KKTKFGGRKIHV 73

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

>gnl|CDD|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 46.9 bits (111), Expect = 6e-07
 Identities = 22/65 (33%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
           ++V+NL    +WQ+L+D  R  G++ +A+  K + + G++ F S    KRA++ +D T I
Sbjct: 3   LIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERANEGVIEFRSYSDMKRALEKLDGTEI 62

Query: 578 DGKII 582
           +G+ I
Sbjct: 63  NGRKI 67

This subgroup corresponds to the RRM2 of SRSF6, also termed pre-mRNA-splicing factor SRp55, an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVF-RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           +++ V NL   + E +L+E F +  G++ +V++   +DGKSR    + +    EA ++  
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 219 MLNNQNLFERRITVRM 234
             NN  +   +I+V  
Sbjct: 61  YFNNTYINTSKISVEF 76

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 46.5 bits (111), Expect = 8e-07
 Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           G+VT   ++ D +TG+ RG   VE ++ +    A+ K++  +  GR L + EA
Sbjct: 24  GEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEA 76

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

>gnl|CDD|241046 cd12602, RRM2_SF2_plant_like, RNA recognition motif 2 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 46.7 bits (111), Expect = 8e-07
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI--KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
           V+V  LP + +WQ+L+D  R  GD+ F+++   G+G  G+V F +    K AI  +D T
Sbjct: 3   VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTTGIVDFTNYDDMKYAIRKLDDT 61

This subfamily corresponds to the RRM2 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 76

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

 Score = 51.3 bits (123), Expect = 9e-07
 Identities = 41/178 (23%), Positives = 69/178 (38%), Gaps = 40/178 (22%)

Query: 44  ASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV 103
            +L+     S  G++   ++  D+ GK RG   V F+  +  + A+ K++      ++ V
Sbjct: 103 KALFDT--FSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKE-V 159

Query: 104 IKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVF 163
                  K  R                      KF N Y                     
Sbjct: 160 YVGRFIKKHEREA----------------APLKKFTNLY--------------------- 182

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V NLD  V+E KLRE+F   G++ +  +  D  G+SRGF  V F+   +A +++  +N
Sbjct: 183 VKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

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

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFR-LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +VF++N+ Y +  + ++++ R   G+V  VE+  D +GKSRG G VEF       +++ +
Sbjct: 1   RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEV 60

Query: 220 LNNQNLFERRITVRMD 235
           +N  +L  R + ++ D
Sbjct: 61  MNKYDLNGRPLNIKED 76

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-----IGLVRFDSEWTAKRAIDMMD 573
           ++VKNLP  +T   LR+ F + G++   ++    D      G V F SE  A++A+   +
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 574 RTRIDGKIIDVTF 586
           +T ID   I V  
Sbjct: 63  KTFIDTSKISVEL 75

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 20/67 (29%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSIS 218
           N+++VA++   + E  ++ VF   GK+++  +A D + GK +G+G +E+++P  A  +I+
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 219 MLNNQNL 225
            +N  +L
Sbjct: 61  SMNLFDL 67

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

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 23/49 (46%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFD 208
           K+FV  L   V E  L E F   G VE  E+  DK  GK RGFG V F 
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQ 49

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 8/73 (10%)

Query: 519 VVVKNLPPTITWQELRDKFRN-CGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
           V + N+P  + WQ+L+D FR   G++ + E+      K +G  G+V F  + + ++A++ 
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRG-CGVVEFKDKESVQKALET 60

Query: 572 MDRTRIDGKIIDV 584
           M+R  + G+ + V
Sbjct: 61  MNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 11/77 (14%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIK--------GKGDIGLVRFDSEWTAKRAI 569
            + V NL   +T ++L + F   G++K  +I         G  D+   + +    A+RAI
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKRED---AERAI 58

Query: 570 DMMDRTRIDGKIIDVTF 586
              +   +DG+ + V  
Sbjct: 59  KQFNGVLLDGQPMQVEL 75

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 49.6 bits (117), Expect = 2e-06
 Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 6/87 (6%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLV 557
            +    Q S  E +T+ V NLP  +T ++LR+ F+  G +K   +    +         V
Sbjct: 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFV 162

Query: 558 RFDSEWTAKRAIDMMDRTRIDGKIIDV 584
            F+SE +A++AI+ ++   ++G+ + V
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPLRV 189

Length = 306

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 17/62 (27%), Positives = 35/62 (56%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+ V+NLD+ V +  ++E+F   G ++   +  D+ G+S G   V F+   +A++++   
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQY 61

Query: 221 NN 222
           N 
Sbjct: 62  NG 63

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFD--HPVEAV--Q 215
           K+FV  +    +E  LR+ F   GK++ +EI  D+  GK RGFG V FD   PV+ +  Q
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61

Query: 216 SISMLNNQNLFERR 229
               +N  N   R+
Sbjct: 62  KYHTINGHNAEVRK 75

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241212 cd12768, RRM2_SRSF9, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 20/58 (34%), Positives = 37/58 (63%), Gaps = 1/58 (1%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           V+V  LPP+ +WQ+L+D  R  GD+ +A+++  G +G+V F  +   + A+  +D T+
Sbjct: 3   VIVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-MGVVEFLRKEDMEYALRKLDDTK 59

This subgroup corresponds to the RRM2 of SRSF9, also termed pre-mRNA-splicing factor SRp30C, an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 76

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQSIS 218
           ++V NL +   ++ L      AG V+   I   +    GKS+GF  VEF     A     
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 219 MLNNQNLFERRITVR 233
            L  +    ++  V 
Sbjct: 61  KLEGREFNGKKCVVT 75

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 49  ISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           I   S VG V    ++ D DTGKP+G    EF+  +    A+  ++ +E  GR L
Sbjct: 16  IEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRAL 70

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

>gnl|CDD|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 = 44.9 bits (107), Expect = 3e-06
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 5/64 (7%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V+V NL + + E++L+  F   G +E V +  DK     G+  V FD    A  +I  +N
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK-----GYAFVRFDTHEAAATAIVAVN 57

Query: 222 NQNL 225
             ++
Sbjct: 58  GTSI 61

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

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

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 7/77 (9%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +VF+  L+    EK +   F+  G++ ++++        RGFG VEFD P +A  ++  L
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDL-------KRGFGFVEFDDPRDADDAVYEL 53

Query: 221 NNQNLFERRITVRMDRV 237
           + + L   R+T+   R 
Sbjct: 54  DGKELCNERVTIEHARA 70

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL +  DE  + E F   G++ +V +  D D G+ +GFG VEF     A  ++  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 221 NNQNLFERRITVRMD 235
              +L  R   VR+D
Sbjct: 61  GGTDLLGR--PVRLD 73

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

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

 Score = 49.1 bits (117), Expect = 4e-06
 Identities = 28/73 (38%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           VFV  L  K  E+ L E F   GKV +V+   D++  +S+G   VEF + VE+V     L
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEF-YDVESVIKALAL 150

Query: 221 NNQNLFERRITVR 233
             Q L  R I V+
Sbjct: 151 TGQMLLGRPIIVQ 163

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

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL Y    + L   F+ AG   +V +  DK  GKS+G   VEFD   EA+     L
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTA-EAMTKALKL 61

Query: 221 NNQNLFERRITV 232
           ++  L  R+I V
Sbjct: 62  HHTLLKGRKINV 73

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 44.5 bits (106), Expect = 4e-06
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 7/72 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIG----LVRFDSEWTAKRAIDMMD 573
           TV VKNLP   T  ++R  F++CG+I+  E+K     G    ++ F++E  A  A+   D
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIR--EVKIVESEGGLVAVIEFETEDEALAAL-TKD 58

Query: 574 RTRIDGKIIDVT 585
             R+ G  I V+
Sbjct: 59  HKRLGGNEISVS 70

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 44.3 bits (105), Expect = 5e-06
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 10/72 (13%)

Query: 520 VVKNLPPTITWQELRDKFRNCGDIKFAEIK-------GKGDIGLVRFDSEWTAKRAIDMM 572
           +V  LP   T Q+L+D F   G++   ++K        KG  G VRF       +   + 
Sbjct: 3   IVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKG-FGFVRFADYEDQVKV--LS 59

Query: 573 DRTRIDGKIIDV 584
            R  IDG+  DV
Sbjct: 60  QRHMIDGRWCDV 71

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 44.4 bits (105), Expect = 5e-06
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           VFV N+ Y+  E++L+++F   G V +  +  D++ GK +G+G  E+     A+ ++  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 221 NNQNLFERRITV 232
           N   L  R++ V
Sbjct: 61  NGYELNGRQLRV 72

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

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 43.9 bits (103), Expect = 8e-06
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFR-LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + F++N+ + V  + L+++ +   G+V  VE+ +D +GKSRG   VEF       +++ +
Sbjct: 1   RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEV 60

Query: 220 LNNQNLFERRITVRMD 235
           LN   L  R + V+ D
Sbjct: 61  LNKHVLNGRPLKVKED 76

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGD-----IGLVRFDSEWTAKRAIDM 571
           T+ V+NLP   T ++L + F   G IK   + K KG       G V F  E  AKRA++ 
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 572 MDRTRIDGKIIDVTF 586
             +T+  G+ I V F
Sbjct: 61  KKKTKFGGRKIHVEF 75

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

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 44.1 bits (104), Expect = 8e-06
 Identities = 21/61 (34%), Positives = 35/61 (57%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+FV  L+ +  EK++ EVF   G+VE++ +  D+  +SRG   V++     A  +I  L
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 221 N 221
           N
Sbjct: 61  N 61

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 43.8 bits (103), Expect = 8e-06
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFD 208
           K+FV  +    +E  LR+ F   GK+E +EI  D   GK RGF  V FD
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 50

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQ 215
           P  N +FV  L+    ++ L  +F   GK+++ E+  D K G S  +  +EF+   +  +
Sbjct: 1   PPENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

Query: 216 SISMLNNQNLFERRITV 232
           +   ++N  + +RRI V
Sbjct: 61  AYFKMDNVLIDDRRIHV 77

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 19/40 (47%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 51 HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAV 89
          + S  G+V  VEI+ D +TGK RG A V F   D V K V
Sbjct: 19 YFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRA 568
           E+  + V  LP ++T +EL   F+  G +K   +      K KG +  V +++E +A +A
Sbjct: 1   EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKG-LAYVEYENESSASQA 59

Query: 569 IDMMDRTRIDGKIIDV 584
           +  MD T I  K I V
Sbjct: 60  VLKMDGTEIKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|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 = 43.0 bits (102), Expect = 1e-05
 Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI---KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           TV V NLP  +T +EL+  F   G I+  E+   K KG    VRFD+   A  AI  ++ 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIE--EVRVFKDKG-YAFVRFDTHEAAATAIVAVNG 58

Query: 575 TRIDGKII 582
           T I+G+ +
Sbjct: 59  TSINGQTV 66

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSISMLNN 222
           V NL Y+     LR VF   G+V +V I  D+  + SRGF  V F    +A  ++  ++ 
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 223 QNLFERRITV 232
           + L  R + V
Sbjct: 63  KELDGRELRV 72

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

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+FV NL      ++LR +F   G V   E  + K+     +G V  +   +A  +I  L
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTV--TECDVVKN-----YGFVHMEEEEDAEDAIKAL 53

Query: 221 NNQNLFERRITV 232
           N      +RI V
Sbjct: 54  NGYEFMGKRINV 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|241211 cd12767, RRM2_SRSF1, RNA recognition motif 2 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
             VVV  LPP+ +WQ+L+D  R  GD+ +A++   G  G+V F  +     A+  +D T+
Sbjct: 1   YRVVVSGLPPSGSWQDLKDHMREAGDVCYADVFRDG-TGVVEFVRKEDMTYAVRKLDNTK 59

This subgroup corresponds to the RRM2 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit, a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 76

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISM 219
           ++F+ NL Y   E+ L ++F   G +  V + +DK   K +GF  V +  P  AV++ + 
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 220 LNNQNLFERRI 230
           L+   +F+ R+
Sbjct: 64  LDGT-VFQGRL 73

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++ V+N+ ++  +  LR++F   G + +VEI  ++ G S+GFG V F +  +A ++   
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREK 59

Query: 220 LNNQNLFERRITVR 233
           L+   +  R+I V 
Sbjct: 60  LHGTVVEGRKIEVN 73

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           +++  L Y++ E  +  VF   G++ ++ +  DK  GKS+GF  + ++     + ++  L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 221 NNQNLFERRITVRMDRVAD 239
           N   L  R  T+R+D V +
Sbjct: 72  NGIKLLGR--TIRVDHVRN 88

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|216966 pfam02301, HORMA, HORMA domain

 Score = 45.8 bits (109), Expect = 1e-05
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 268 VANWLLQEKVQKLSLII---SNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKT 320
           V + L +  ++KL L+I    +    EVLER+ F   Y   S  N + S  T  +T
Sbjct: 58  VFDALEKGYLKKLVLVIYDDKDPEKNEVLERYQFDFSYF-PSGGNSSDSEKTEDET 112

The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity. Length = 186

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 162 VFVANLDYKVDEKKLREVFR-LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           V +  L +   E+ +R+ F  L    + + I  D DG+  G   VEF  P +A +++   
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK- 60

Query: 221 NNQNLFERRITVR 233
           +N  +  R I V 
Sbjct: 61  HNNKMGGRYIEVF 73

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           NK+F+  L   + E +++E+    GK++   +  D   G S+G+   E+  P    Q+I+
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 219 MLNNQNLFERRITVR 233
            LN   L ++++TV+
Sbjct: 61  GLNGMQLGDKKLTVQ 75

This subfamily corresponds to the RRM2 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 = 77

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 11/78 (14%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDI-----GLVRFDSEWTAK 566
           T+ VKNL    T + L+  F  CG ++   I      KG G +     G V F S+  A+
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 567 RAIDMMDRTRIDGKIIDV 584
           +A+  +  T +DG  +++
Sbjct: 62  KALKRLQGTVLDGHALEL 79

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

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 43.1 bits (101), Expect = 2e-05
 Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFD 208
           K+FV  +    +E  LR+ F   GK+E +E+  D+  GK RGF  V FD
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFD 50

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD----IGLVRFDSEWTAKRAIDM 571
           R T+ V NL PT T  +L + F   G++K+  + G          V F  + +   A+ +
Sbjct: 4   RRTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALKL 63

Query: 572 MDRTRIDGKIIDVT 585
                  G+ + V 
Sbjct: 64  NGAM-FGGRPLKVN 76

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

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 516 RD--TVVVKNLPPTITWQELRDKFRNCGDIKFA---EIKGKGDIGLVRFDSEWTAKRAID 570
           RD  T+ VKNLP  IT  EL++ F +  DI+     +   KG I  + F +E  A++A++
Sbjct: 1   RDARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGSSKG-IAYIEFKTEAEAEKALE 59

Query: 571 MMDRTRIDGKIIDVTF 586
                 +DG+ I V +
Sbjct: 60  EKQGAEVDGRSIVVDY 75

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 20/67 (29%), Positives = 34/67 (50%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+FV  L  K +E  +R +F   G +E   +  D++G+SRG   V F     A+ +I  +
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAM 62

Query: 221 NNQNLFE 227
           ++    E
Sbjct: 63  HHSQTME 69

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIAL-DKDGKSRGFGTVEFDHPVEAVQSISMLN 221
            V NL  +  +++ RE+    G VE   +   +  G+S+G+G VE+     A+++ + L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 222 NQNLFERRITV-RMD 235
            + +  R++ V   D
Sbjct: 63  GKQIGGRKLQVDWAD 77

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 18/63 (28%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 171 VDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR 229
           + +++LR +F   G +E+ +I  D+  G+S G+G V++    +A ++I+ LN   +  +R
Sbjct: 12  MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKR 71

Query: 230 ITV 232
           + V
Sbjct: 72  LKV 74

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

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV +L  ++D + LR  F   G++ +  +  D + GKS+G+G V F    +A  +I  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 221 NNQNLFERRI 230
           N Q L  R I
Sbjct: 62  NGQWLGGRAI 71

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 11/80 (13%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-----------IGLVRFDSEWTAK 566
           T+ VKNL  + T Q L D F++     FA +K K D            G V F ++  A+
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 567 RAIDMMDRTRIDGKIIDVTF 586
            A+  MD   +DG  + V F
Sbjct: 62  AALKAMDGFVLDGHTLVVKF 81

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLN 221
           +V +L   V E  L E+F  AG V ++ +  D    +S G+  V F +P +A +++  LN
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 222 NQNLFERRITV 232
              +  + I +
Sbjct: 63  FDVIKGKPIRI 73

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

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 6/64 (9%)

Query: 50  SHLSTVGDVTYVEI-LNDDTGKPRGSAIVEFQSPDLVRKAV-----NKMHRFETKGRKLV 103
              S  G+V Y  I  +  TG  +G+A V+F++ +  +K +      +       GR+L+
Sbjct: 19  ELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLI 78

Query: 104 IKEA 107
           +  A
Sbjct: 79  VTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 13/48 (27%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 56  GDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           G++ +V++  D  TG+ +G   ++F   +  +KA+ +++ FE  GR +
Sbjct: 23  GEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPI 70

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVE--------NVEIALDKDGKSRGFGTVEFDHPVEA 213
           ++++ L   V E  L E+F   G ++         ++I  DK+ + +G  TV +D P  A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 214 VQSISMLNNQNLFERRITVRM 234
             +I   N       +I V +
Sbjct: 61  QAAIEWFNGYEFRGNKIKVSL 81

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           +F+ +L  +  ++ L ++F   G V + ++ +DK+ G+S+ FG V +D+P  A  +I  +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 221 NNQNLFERRITV 232
           N   +  +R+ V
Sbjct: 61  NGFQVGGKRLKV 72

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 16/75 (21%)

Query: 164 VANLDYKVDEKKLREVFRLA---------GKVENVEIALDKD-------GKSRGFGTVEF 207
           + NL   VDEKKL+E+F  A          K++ V+I  D         GKS+G+G VEF
Sbjct: 5   IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 208 DHPVEAVQSISMLNN 222
            +   A++++  LNN
Sbjct: 65  TNHEHALKALRALNN 79

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +H    G    V +L D  TGK +G A VEF + + + KA+   H    KGRK+
Sbjct: 19  AHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHT-LLKGRKI 71

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 15/35 (42%), Positives = 22/35 (62%)

Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRF 95
          + I+ DD G+P G A VEF SP+  R+A+ K +  
Sbjct: 30 IHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNK 64

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L     E+ +R +F   G +E V I  DKD G+S+G   V+F    EA ++I  
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 220 LNNQNLFE 227
           L+ +    
Sbjct: 61  LHGKVTMP 68

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

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 10/72 (13%)

Query: 160 NKVFVANLDYKVDE---KKLREVFR------LAGKVENVEIALDKDGKSRGFGTVEFDHP 210
           N V V  L   V E   +KL++V R        GK+  + + +D+ GK++G+  VEF  P
Sbjct: 2   NVVVVDGLP-VVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATP 60

Query: 211 VEAVQSISMLNN 222
            EA +++  LN 
Sbjct: 61  EEAKEAVKALNG 72

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 41.7 bits (98), Expect = 4e-05
 Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEF 207
           +FV NL ++  E +LR  F   G++  V +   +D GK +GF  V+F
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF 47

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           ++V+ L   + +K+L ++F   G++    I  D+  G SRG G + FD  +EA ++I  L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 221 NNQ 223
           N Q
Sbjct: 63  NGQ 65

This subfamily corresponds to the RRM2 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 the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is 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 also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV +L  +V +  L   F       +  +  D K G+SRG+G V F    +A  +I+ +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 221 NNQNLFERRI 230
           N + L  R I
Sbjct: 62  NGKWLGSRPI 71

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

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

 Score = 40.6 bits (96), Expect = 5e-05
 Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 176 LREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM 234
           L ++F   G VE +++      K  GF  VEF     A +++  LN      R + V  
Sbjct: 1   LYKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

(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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 41.0 bits (97), Expect = 6e-05
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
              S  G V  V ++ +   +PRG A VEF SP+    A+ K++     GR L
Sbjct: 17  EFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68

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

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 41.2 bits (96), Expect = 7e-05
 Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL  + DE  L ++F   G V NV++  D    K +GFG V   +  EA  +I+ L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 221 NNQNLFERRITV 232
           N   L +R + V
Sbjct: 64  NGYRLGDRVLQV 75

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 40.6 bits (96), Expect = 7e-05
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHP--VEAV 214
           F+  L +   E+ LRE F   G+V +  I  D   G+SRGFG V F  P  V+ V
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKV 56

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

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

 Score = 41.0 bits (97), Expect = 8e-05
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 7/72 (9%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMM 572
           V VKNL   +  ++L++ F   G I  A++      K KG  G V F++   A++A++ +
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKG-FGFVNFENHEAAQKAVEEL 62

Query: 573 DRTRIDGKIIDV 584
           +   ++GK + V
Sbjct: 63  NGKEVNGKKLYV 74

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 40.9 bits (96), Expect = 8e-05
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDH--PVEAVQSI 217
           K+FV  L     E  +++ F   GKVE+  +  DK   + RGFG V F+    V+ V  I
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 218 SM--LNNQ 223
               +NN+
Sbjct: 61  HFHEINNK 68

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSIS 218
            K+FV  L   V E  LR+ F   G V  V +  D + K  RGFG + F+   ++V  + 
Sbjct: 3   KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESE-DSVDQVV 61

Query: 219 MLNNQNLFERRITVR 233
             +  ++  +++ V+
Sbjct: 62  NEHFHDINGKKVEVK 76

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 40.6 bits (95), Expect = 9e-05
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           V V N+ P  T +++ D F  CG I        G+     + F+    AK A+ ++D   
Sbjct: 1   VYVSNISPKTTEKQISDFFSFCGKISNLDLTNDGESQTATITFEKPSAAKTAL-LLDNAL 59

Query: 577 IDGKIIDVT 585
           + GK+I VT
Sbjct: 60  LGGKVIQVT 68

This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 68

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 41.1 bits (96), Expect = 9e-05
 Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 5/72 (6%)

Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
           P  +++FV NL + VD+ +L+E F+  G V  VE+ ++  GK   FG V FD   E VQ 
Sbjct: 1   PDSHQLFVGNLPHDVDKSELKEFFQQYGNV--VELRINSGGKLPNFGFVVFDDS-EPVQK 57

Query: 217 ISMLNNQNLFER 228
           I  L+N+ +  R
Sbjct: 58  I--LSNRPIMFR 67

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 3/59 (5%)

Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEF--DHPVEAV 214
           + K+FV  L+ +  E+K+RE F   G++E +E+ +D K  K RGF  + F  + PV+ V
Sbjct: 4   VKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKV 62

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 19/62 (30%), Positives = 34/62 (54%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +VFV  +   + E +L  +F  AGK+    + ++  G++RG+  V +    EA  +I +L
Sbjct: 3   EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRIL 62

Query: 221 NN 222
           NN
Sbjct: 63  NN 64

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFD 208
           K+FV  L  +  E+K+RE F   G +  +E+ +DK   K RGF  + FD
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFD 49

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 3/57 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEF--DHPVEAV 214
           K+FV  L     E+K+RE F   G+VE++E+ +D K  K RGF  + F  + PV+ +
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISM 219
           +V+V ++ +++ E  +R+ F   G +++++++ D    K +GF  VE++ P  A  ++  
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 220 LNNQNLFERRITV 232
           +N   L  R I V
Sbjct: 62  MNGVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

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

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 173 EKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT 231
           +++ R +F   G V+N +I  DK  G S GFG V++    +A ++I  LN   L  +RI 
Sbjct: 14  DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIK 73

Query: 232 VRMDR 236
           V   R
Sbjct: 74  VAYAR 78

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 22/67 (32%), Positives = 40/67 (59%), Gaps = 1/67 (1%)

Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
           + ++V+NL   ++WQ+L+D  R  G++ FA+  + K + G+V F S    K AI+ +   
Sbjct: 4   NRLIVENLSSRVSWQDLKDFMRQAGEVTFADAHRPKLNEGVVEFASYSDLKNAIEKLSGK 63

Query: 576 RIDGKII 582
            I+G+ I
Sbjct: 64  EINGRKI 70

This subgroup corresponds to the RRM2 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5), is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 75

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 516 RDTVVVKNLPPTITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMD 573
           R  + V NLP  IT +E ++ F   G++   F   K KG  G +R D+   A++A   +D
Sbjct: 1   RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFLN-KEKG-FGFIRLDTRTNAEKAKAELD 58

Query: 574 RTRIDGKIIDVTF 586
                G+ + V F
Sbjct: 59  GIMRKGRQLRVRF 71

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

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

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           ++V +LD  V E KL ++F+  G V +V +  D    +S G+G V F +P +A +++  +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 221 NNQNLFERRITV 232
           N + L  + I +
Sbjct: 63  NFKRLGGKPIRI 74

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

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 7/72 (9%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMM 572
           + +KNL  +I  + L D F   G+I   ++        KG  G V F++E  A RAI+ +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKG-YGFVHFETEEAAVRAIEKV 63

Query: 573 DRTRIDGKIIDV 584
           +   ++ K + V
Sbjct: 64  NGMLLNDKKVFV 75

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 50  SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
            H  + G +  + IL D  TG+P+G A +EF     V  A+  ++  E +GR++ +
Sbjct: 18  EHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLNESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 13/81 (16%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
           TV ++NLP   T +EL++ F   G++K+A I         KG    V+F ++ +A++ ++
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKG-TAFVKFKTKESAQKCLE 60

Query: 571 MMDRT-----RIDGKIIDVTF 586
             D        +DG+ + VT 
Sbjct: 61  AADNAEDSGLSLDGRRLIVTL 81

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 519 VVVKNLPPTITWQELRDKFRNCG----DIKFAEIKGKGD---IGLVRFDSEWTAKRAIDM 571
           ++VKNLP ++T  EL++ F   G    D+K       G    I  + + +E  A++A D 
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLR-TEDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 572 MDRTRIDGKIIDVTF 586
            + T I+   I V F
Sbjct: 62  FNNTYINTSKISVEF 76

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           V+V N+DY    ++L   F   G V  V I  DK  G  +GF  +EF    E+V++ ++ 
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRT-ALA 59

Query: 221 NNQNLFE-RRITVRMDR 236
            +++LF  R+I V   R
Sbjct: 60  LDESLFRGRQIKVMPKR 76

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 22/63 (34%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEA-VQSISM 219
           +FV  L   V E  L E F   G V +VEI   KD G  RGF  ++         +  S 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 220 LNN 222
           LN 
Sbjct: 62  LNG 64

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

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           ++V N+        LR +F   G + +V I LD    + RGF  V+F+   +A  ++  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 221 NNQNLFERRITV 232
           +      R I +
Sbjct: 63  DRTRFLGREIEI 74

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

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 8/66 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V  LP T+T QEL   F   G I  + I         +G +G +RFD    A+RAI  ++
Sbjct: 5   VSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRG-VGFIRFDKRIEAERAIKALN 63

Query: 574 RTRIDG 579
            T   G
Sbjct: 64  GTIPPG 69

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           ++V+ L   + +++L  +F   G++    I  D   G SRG G + FD  +EA ++I  L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 221 NNQNL--FERRITVR 233
           N          ITV+
Sbjct: 63  NGTIPPGATEPITVK 77

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           +FV  +  +  E+ + + F   G+++N+ + LD+  G  +G+  +E++   EA  +I  L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 221 NNQNLFERRITV 232
           N + L  + I+V
Sbjct: 69  NGKELLGQTISV 80

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEF--DHPVE 212
           KVFV  L     E++++E F   G++EN+E+ +D K  + RGF  V +  + PV+
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQ 55

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>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 = 39.9 bits (94), Expect = 2e-04
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 6/90 (6%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV  L  +  E+ LREVF   G +  + +  D   G S+G+  VE++H  +A+++    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 221 NNQNLFERRITVRMDRVADR-LDG--PVRL 247
           +   +    I V  D   +R L G  P RL
Sbjct: 66  HKLVIDGSEIFV--DFERERTLPGWIPRRL 93

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

>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 11/66 (16%), Positives = 30/66 (45%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
           + ++ P +T ++++  F   G++K+ +     D G +RF +   A++A +          
Sbjct: 6   ITSIGPGVTREDIKAVFAQFGEVKYVDFTEGADTGYIRFKTPEAAQKAREAFVEKGEGLL 65

Query: 581 IIDVTF 586
             ++  
Sbjct: 66  GKEIKL 71

This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           G +T  +++ DD GK +G   V F++ +  +KAV +++  E  G+KL +  A
Sbjct: 26  GKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRA 77

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 8/76 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
           T+ V NL  ++  + L+ +F   G +  A +       + +G  G V F+S   AK+AI+
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRG-FGYVDFESPEDAKKAIE 59

Query: 571 MMDRTRIDGKIIDVTF 586
            MD   +DG+ I+V F
Sbjct: 60  AMDGKELDGRPINVDF 75

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
           +FV NL Y +   +L+EVF  A    ++ +   KDG S+G   +EF    EA
Sbjct: 6   LFVKNLPYNITVDELKEVFEDA---VDIRLPSGKDGSSKGIAYIEFKTEAEA 54

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL    DE  L ++F   G V NV++  D    K +G+G V   +  EA  +I+ L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 221 NNQNLFERRITV 232
           N   L  R + V
Sbjct: 64  NGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 516 RDTVVVKNLPPTITWQELRDKFRNCGDI---KFAEIKGKGD---IGLVRFDSEWTAKRAI 569
           +  ++V  LP  +T  E+R  F + G+I   K    K  G     G V +     A++AI
Sbjct: 1   KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 570 DMMDRTRIDGKIIDVTF 586
           + ++  R+  K I V++
Sbjct: 61  NTLNGLRLQNKTIKVSY 77

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 43.5 bits (102), Expect = 3e-04
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +VFV  +   + E +L  +F  AG +  + + +D  G++RG+  V F    EA +++ +L
Sbjct: 60  EVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLL 119

Query: 221 NN 222
           NN
Sbjct: 120 NN 121

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 4/67 (5%)

Query: 521 VKNLPPTITWQELRDKFRNCGDI-KFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDG 579
           V+NLP + T ++LR+ F   G++ +  +IK   D   V F+    A +A++ M+   ++G
Sbjct: 6   VRNLPLSTTEEQLRELFSEYGEVERVKKIK---DYAFVHFEERDDAVKAMEEMNGKELEG 62

Query: 580 KIIDVTF 586
             I+V+ 
Sbjct: 63  SPIEVSL 69

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 162 VFVANL--DYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           VFV  +  D   DE  L  +F  AG +  + + +D  G +RG+  V + +   A +++  
Sbjct: 4   VFVGKIPRDLFEDE--LVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQ 61

Query: 220 LNNQNLFERR 229
           L+N   +E R
Sbjct: 62  LHN---YEIR 68

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           VKNL  +I  + LR++F   G I  A++      + KG  G V F S   A +A+  M+ 
Sbjct: 6   VKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKG-FGFVCFSSPEEATKAVTEMNG 64

Query: 575 TRIDGKIIDVTF 586
             I GK + V  
Sbjct: 65  RIIGGKPLYVAL 76

This subfamily corresponds to the RRM4 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 theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. 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. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 24/62 (38%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 49  ISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKA-VNKMHRFETKGRKLVIKE 106
             H S  G V   E++ D  TGK RG   V FQ+ D   KA V K H     G ++ +K+
Sbjct: 17  TEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFH--PINGHRVEVKK 74

Query: 107 AV 108
           AV
Sbjct: 75  AV 76

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++FV NL   + E++ +E+F   G+V   E+ L+K+   +GFG +  D    A ++ + 
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYGEV--SEVFLNKE---KGFGFIRLDTRTNAEKAKAE 56

Query: 220 LNNQNLFERRITVR 233
           L+      R++ VR
Sbjct: 57  LDGIMRKGRQLRVR 70

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

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLA-GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           KV V+NL   V E ++RE F    G ++ V ++ ++ GKS G   + F    +A ++   
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 220 LNNQNLFERR 229
            N +     R
Sbjct: 61  FNGRIDDGNR 70

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|240986 cd12542, RRM2_LARP7, RNA recognition motif 2 in La-related protein 7 (LARP7) and similar proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 11/51 (21%), Positives = 25/51 (49%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAI 569
           V +K   P    +E +D+ ++  D+ + ++K       VRF +   A++ +
Sbjct: 4   VKIKLDEPLPDRKEFKDELKDHADVAYVDVKEGDTEAYVRFKTPEAAQKVV 54

This subgroup corresponds to the RRM2 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 78

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +V++  L Y+  E+ +   F+  GK+  V++         G+G VEFD   +A  ++  L
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEVDL-------KNGYGFVEFDDLRDADDAVYEL 53

Query: 221 NNQNLFERRITV 232
           N ++L   R+ V
Sbjct: 54  NGKDLCGERVIV 65

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 163 FVANL--DYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           FV  L   ++ D   LR++F   GK    ++A+  +G+ RGF  VE+    +A ++   L
Sbjct: 6   FVDRLPKTFR-DVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 221 NNQNLFERRITV 232
           N  +L    I V
Sbjct: 65  NGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

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

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEF 207
           + +L+  +DE  +   F   G+V +V+I  +K  GKS G+G VEF
Sbjct: 4   MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEF 48

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 6/57 (10%)

Query: 525 PPTITWQELRDKFRNCGDIKFAEI---KGKGD---IGLVRFDSEWTAKRAIDMMDRT 575
           P + T ++LR+KF+  GDI++  I   K  G+    G V+F     A  A++  D++
Sbjct: 9   PKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKS 65

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 17/52 (32%), Positives = 25/52 (48%)

Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRA 568
             ++VKNLP   T +ELR+ F   G +    +     I LV F     A++A
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKA 52

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           ++V NL  ++ E +LR++F   G +    +  DK  G  RG   V +D   EA  +IS L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 221 NN 222
           N 
Sbjct: 63  NG 64

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEF-DHPVEAVQSISML 220
           ++V NLD  V E  L E+F   G +++ ++  +       F  VE+ DH   A  ++  +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAF--VEYYDHR-SAAAALQTM 57

Query: 221 NNQNLFERRITV 232
           N + +  + I V
Sbjct: 58  NGRLILGQEIKV 69

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

>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 24/82 (29%), Positives = 32/82 (39%), Gaps = 16/82 (19%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKG--------------KGDIGLVRFDSEWT 564
           V V  LP  IT +E  + F  CG IK     G              KGD  L  +  E +
Sbjct: 4   VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGD-ALCCYLKEES 62

Query: 565 AKRAIDMMDRT-RIDGKIIDVT 585
            + AI ++D T    G  + V 
Sbjct: 63  VELAIQLLDGTEIGRGYKMKVE 84

This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 92

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISM 219
            VFV N+   V +  +R++    GKV + +   D   GK + FG  EF+ P  A++++ +
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 220 LNNQNLFERRITVRMDR 236
           LN   L  +++ V++D 
Sbjct: 62  LNGLELGGKKLLVKVDA 78

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V  L   +  + L   F   GDIK  +I       K +G    V F+    A  AID M+
Sbjct: 3   VGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRG-FAFVEFEEPEDAAAAIDNMN 61

Query: 574 RTRIDGKIIDVT 585
            + + G+ I V 
Sbjct: 62  ESELFGRTIRVN 73

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

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-----IGLVRFDSEWTAKRAIDMMD 573
           ++VKNLP  I   +LR  F   G I   ++K   D      G V + +E  A++A+   +
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 574 RTRIDGKIIDVTF 586
            + ID   I V  
Sbjct: 63  NSFIDTSKITVEI 75

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

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 15/82 (18%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKF--------------AEIKGKGDIGLVRFDSEWT 564
           + +  LP  +T   L + F   G IK                E + KG+   V +D    
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGE-ATVTYDDPSA 59

Query: 565 AKRAIDMMDRTRIDGKIIDVTF 586
           A+ AI+  +     G  I V+ 
Sbjct: 60  AQAAIEWFNGYEFRGNKIKVSL 81

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEI-ALDKDGKSRGFGTVEFDHPVEAVQSI 217
           ++FV NL + + E +L+E F+  G V  V I +    G+   FG V FD P EAVQ I
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP-EAVQKI 61

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           ++V NL     E++LRE+F   G+VE V+       K + +  V F+   +AV+++  +N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVK-------KIKDYAFVHFEERDDAVKAMEEMN 56

Query: 222 NQNLFERRITV 232
            + L    I V
Sbjct: 57  GKELEGSPIEV 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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 38.1 bits (88), Expect = 9e-04
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL    DE  L ++F   G V NV++  D    K +GFG V   +  EA  +I+ L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 221 NNQNLFERRITV 232
           N   L +R + V
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 38.2 bits (88), Expect = 9e-04
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL    DE  L ++F   G V NV++  D    K +GFG V   +  EA  +I+ L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 221 NNQNLFERRITV 232
           N   L +R + V
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 10/41 (24%), Positives = 24/41 (58%)

Query: 67  DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
             GK + +A   F +     +A++++H+ +  G++LV++ A
Sbjct: 33  RRGKLKNTAFATFDNEQAASQALSRLHQLKILGKRLVVEYA 73

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

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
           G+V  V I  DD G+ +G   VEF + +  +KA+ K    E  GR++ +  A E
Sbjct: 24  GEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK-SGEELLGREIRVDLATE 76

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 41  QGDASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG 99
             +  L +  H    GDV  V I+ D  TG  +G   V F++ D V  A+ K++  + KG
Sbjct: 11  IEEEELRK--HFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLNGIKLKG 67

Query: 100 RKLVIK 105
           RK+ +K
Sbjct: 68  RKIRVK 73

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>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 = 37.2 bits (87), Expect = 0.001
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 12/69 (17%)

Query: 521 VKNLPPTITWQELRDKFRNCG-----DIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT 575
           V NLP   T +ELR  F   G     D+    +K   + G V  + E  A+ AI  ++  
Sbjct: 4   VGNLPDATTSEELRALFEKYGTVTECDV----VK---NYGFVHMEEEEDAEDAIKALNGY 56

Query: 576 RIDGKIIDV 584
              GK I+V
Sbjct: 57  EFMGKRINV 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 36.7 bits (86), Expect = 0.001
 Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 51  HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK 105
             S  G+V  +++L    G     A VEF + +   KAV  ++     GR L + 
Sbjct: 4   LFSPFGNVEKIKLLKKKPGF----AFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54

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

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 38.2 bits (88), Expect = 0.001
 Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           ++V+ L   + +K+L ++F   G++    I +D+  G SRG G + FD  +EA ++I  L
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 221 NNQ 223
           N Q
Sbjct: 65  NGQ 67

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ 223
           V NL   V  + L + F   G+VE   + +D  G+S G G VEF     A  +I    ++
Sbjct: 4   VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRC-SE 62

Query: 224 NLF 226
             F
Sbjct: 63  GCF 65

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 514 IERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI----KGKGDIGLVRFDSEWTAKRAI 569
           I++ ++ V  L P +T +EL ++F   G I    +            ++F+ E  A RA+
Sbjct: 1   IDKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAV 60

Query: 570 DMMDRTRIDGKIIDVTF 586
           +  + + +  K + V +
Sbjct: 61  ESENHSMLKNKTMHVQY 77

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

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP 210
           K+FV  L +   +K L++ F   G+V +  I +D + G+SRGFG + F   
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDA 51

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISMLNN 222
           V  L     E+ LREVF   G +  V +  D + G+SRGF  V F+   ++ +++   N 
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 223 QNLFERRITV 232
             L  RRI V
Sbjct: 64  MELDGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) 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-alpha 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 = 79

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           V+V  L      + L+ VF   G V  V +   K  G  +GF  +EF+ P EA ++   L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 221 NNQ 223
           NN 
Sbjct: 62  NNP 64

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

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 7/65 (10%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMM 572
           + V NL   + W++L++ F+  G +  A+I      K +G +G+V+F+    A +AI M 
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRG-MGVVQFEHPIEAVQAISMF 59

Query: 573 DRTRI 577
           +   +
Sbjct: 60  NGQML 64

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 42  GDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           G   L ++  L+  G V   +I  D  GK RG  +V+F+ P    +A++  +      R 
Sbjct: 11  GWKKLKEVFKLA--GKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRP 68

Query: 102 LVIK 105
           + +K
Sbjct: 69  MRVK 72

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 18/48 (37%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
           S  G++T V ++ +  GK +G A VEF++ + V++A+ K+ R   KGR
Sbjct: 21  SKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-KLDRELIKGR 67

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

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 50  SHLSTVGDVTYVEI-LNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +     GD+  ++I L+ +T K RG A VEF+ P+    A++ M+  E  GR +
Sbjct: 17  AAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTI 70

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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 52  LSTVGDVTYVEIL-NDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK 105
            S  G VT + +  +  TGK +G A VEF+SP++ +     M+ +    R L  K
Sbjct: 20  FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKCK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 22/79 (27%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI--------------GLVRFDSEWTAK 566
           V NL    T  +LR  F   G++        GD+                VRF  +  A+
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEV--------GDVYIPRDRYTRESRGFAFVRFYDKRDAE 54

Query: 567 RAIDMMDRTRIDGKIIDVT 585
            A+D MD   +DG+ + V 
Sbjct: 55  DAMDAMDGKELDGRELRVQ 73

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

>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V+V+N+  K  EK++ + F   GK+ N  + L  DG+S+   T+ F+ P  A ++  +L+
Sbjct: 1   VYVSNISPKTTEKQISDFFSFCGKISN--LDLTNDGESQT-ATITFEKP-SAAKTALLLD 56

Query: 222 NQNLFERRITV 232
           N  L  + I V
Sbjct: 57  NALLGGKVIQV 67

This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 68

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKG---DIGLVRFDSEWTAKRAIDMMDR 574
           T++V++LPP ++  +  D  ++ G      +  +G   +     FD+E  A +A+  + +
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60

Query: 575 TRIDGKIIDVTFF 587
            +I GK + V + 
Sbjct: 61  LKILGKRLVVEYA 73

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

>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-GLVRFDSEWTAKRAID 570
           +    +    + ++L++ F   G++ + +   +G   G VRF  E  AK A++
Sbjct: 4   LHFSGVGEQTSREDLKEAFEEFGEVAWVDFA-RGQTEGYVRFKEENAAKEALE 55

This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 76

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 50  SHLSTVGDVTYVEI-LNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
            H S+ G++T V I  + +TG  +G A +EF+S D V KA+ ++   +  G  LV+ EA
Sbjct: 22  EHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKAL-ELDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           ++V+ L   + +K++ ++F   G++    I +D+  G SRG G + FD  +EA ++I  L
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 221 NNQ 223
           N Q
Sbjct: 64  NGQ 66

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFA------EIKGKGDIGLVRFDSEWTAKRAIDM 571
           T+ V+NL  ++T ++L D F +   IK A      E       G V F     A+ A+  
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 572 MDRTRIDGKIIDVTF 586
           +   ++ G+I+ +  
Sbjct: 61  LKNKKLHGRILRLDI 75

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV NL + V ++ L + F     +++  +  D + G+SRG+G V F    +A ++++ L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 221 NNQNLFERRITV 232
            N+ L  R + +
Sbjct: 62  KNKKLHGRILRL 73

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSIS 218
            +V  +NL+  +DE  L+++ +  G+VE V+I    K  K  G   V FD    A + + 
Sbjct: 3   REVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVE 62

Query: 219 MLNNQNLFERRITVRMD 235
            LN  ++  + I V +D
Sbjct: 63  KLNQTSVMGKIIKVFLD 79

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

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 37.5 bits (86), Expect = 0.002
 Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           ++V+ L   + +K+L ++F   G++    I +D+  G SRG G + FD  +EA ++I  L
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 221 NNQ 223
           N Q
Sbjct: 68  NGQ 70

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 19/70 (27%), Positives = 36/70 (51%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           ++F+  L   + E +L  +    GK+  + + +D +G +RG+  V F +  EA  +I  L
Sbjct: 3   EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQL 62

Query: 221 NNQNLFERRI 230
           NN  +   R+
Sbjct: 63  NNYEIRNGRL 72

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, 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. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +V++  L Y V EK ++  F   GK+  +++         G+G VEF+   +A  ++  L
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL-------KNGYGFVEFEDSRDADDAVYEL 53

Query: 221 NNQNLFERRITVRMDR 236
           N ++L   R+ V   R
Sbjct: 54  NGKDLCGERVIVEHAR 69

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

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 12/83 (14%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK---------DGKSRGFGTVEFDHPV 211
           +V+++NL Y   E+ L E        E V + +             +  G    EF  P 
Sbjct: 1   RVYISNLSYSSSEEDLEEFL---KDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPE 57

Query: 212 EAVQSISMLNNQNLFERRITVRM 234
           +A + +  LN +    R++ V++
Sbjct: 58  QAEKVVKDLNGKVFKNRKLFVKL 80

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 7/71 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRF----DSEWTAKRAIDMMD 573
           T++V NL   I+ QELR  F   G++K  +I+        +F    D    A+ A+D ++
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVK--DIRETPLRPSQKFVEFYDIR-AAEAALDALN 59

Query: 574 RTRIDGKIIDV 584
                G  + V
Sbjct: 60  GRPFLGGRLKV 70

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

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEI--ALDKDGKSRGFGTVEFDHPVEAVQSI 217
           +K+ V N+ ++   K+LRE+F   G+++ V +   +   G  RGFG V+F    +A ++ 
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 218 SML-NNQNLFERRI 230
             L ++ +L+ RR+
Sbjct: 61  KALCHSTHLYGRRL 74

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 4/64 (6%)

Query: 49  ISHLSTVGDVTYVEILNDDTGK----PRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
           +   S  G +   + L   +G     PRG   V F++ +   KA+  ++     G+KLV+
Sbjct: 17  LKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVV 76

Query: 105 KEAV 108
           + A 
Sbjct: 77  RWAH 80

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

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI----KGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           V N+P      +LR  F   G I   EI    +G    G V F +   A RA + +  T 
Sbjct: 5   VSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHGTV 64

Query: 577 IDGKIIDV 584
           ++G+ I+V
Sbjct: 65  VEGRKIEV 72

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI---KGKG---DIGLVRFDSEWTAKRAIDM 571
            +++  LP T+T +E R  F   G +K  +I   K  G     G V + S   A+RAI  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 572 MDRTRIDGKIIDVTF 586
           ++  ++  K I V +
Sbjct: 62  LNGLQLQNKRIKVAY 76

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 37.0 bits (85), Expect = 0.003
 Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSISML 220
           +F+ +L  +  ++ L ++F   G V + ++ +DK    S+ FG V +D+PV A  +I  +
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 221 NNQNLFERRITVRMDRVAD 239
           N   +  +R+ V++ R  +
Sbjct: 70  NGFQIGMKRLKVQLKRSKN 88

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           VFV +L  ++  + ++  F   GK+ +  +  D   GKS+G+G V F + ++A  +I  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 221 NNQNLFERRI 230
             Q L  R+I
Sbjct: 64  GGQWLGGRQI 73

This subgroup corresponds to the RRM2 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 = 80

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISML 220
           +F+ NL    DE  L ++F   G V NV++  D    K +GFG V   +  EA  +I+ L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 221 NNQNLFERRITV 232
           N   L ++ + V
Sbjct: 64  NGYRLGDKILQV 75

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 7/75 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRG-FGTVEFDHPVEAVQSIS 218
             VFV+       E++L + F   G V NV +  DKD   +G +  VEFD   E V  + 
Sbjct: 3   RSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIM--DKD---KGVYAIVEFDS-KEGVDKVL 56

Query: 219 MLNNQNLFERRITVR 233
                 L   R+ VR
Sbjct: 57  SEPQHTLNGHRLRVR 71

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

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

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIK-FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           T+VV NL P+++  +L   F   G+IK   E   K     + F    +A+ A+  ++R+ 
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSE 62

Query: 577 IDGKIIDV 584
           I GK I +
Sbjct: 63  IAGKRIKL 70

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

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISMLNN 222
           V  L     E+ LREVF   G + +V I  D+   +SRGF  V F++  +A ++    N 
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 223 QNLFERRITV 232
             L  RRI V
Sbjct: 74  MELDGRRIRV 83

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). 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. It 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. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 19/73 (26%), Positives = 42/73 (57%), Gaps = 8/73 (10%)

Query: 519 VVVKNLPPTITWQELRDKFRN-CGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
           V + N+P  + WQ ++D  R   G++ + E+      K +G  G+V F  E   K+A+++
Sbjct: 2   VFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGC-GVVEFKDEEFVKKALEV 60

Query: 572 MDRTRIDGKIIDV 584
           M++  ++G+ +++
Sbjct: 61  MNKYDLNGRPLNI 73

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 10/76 (13%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDI-------KFAEIKGKGDIGL--VRFDSEWTAKRAI 569
           + V+NL   +   +LR  F   G++       K  E +G+ + G   V F    +A+ A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 570 DMMDRTRIDGKIIDVT 585
             ++ T + G+ I V+
Sbjct: 63  Q-LNGTELGGRKISVS 77

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

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGL------VRFDSEWTAKRAIDMM 572
           + V  L   +    L++ F N G +K  ++    ++ L      V F+S   A++AI  M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 573 DRTRIDGKIIDVT 585
           D  +IDG+ + V 
Sbjct: 61  DGGQIDGQEVTVE 73

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 23/81 (28%), Positives = 31/81 (38%), Gaps = 18/81 (22%)

Query: 519 VVVKNLPPTITW----QELRDKFRNCG-----DIKFAEI----KGKGDIGLVRFDSEWTA 565
           + V NL    TW    ++L       G      IKF E     K KG    V F SE  A
Sbjct: 1   LYVGNL----TWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKG-FAYVEFASEAAA 55

Query: 566 KRAIDMMDRTRIDGKIIDVTF 586
               + ++    +GK   VT+
Sbjct: 56  AAVKEKLEGREFNGKKCVVTY 76

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 5/50 (10%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
           V NL +   E++LRE+F   G +  + +       SR    VEF  P +A
Sbjct: 5   VKNLPFGTTEEELRELFEKFGSLGRLLLP-----PSRTIALVEFLEPSDA 49

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIK-FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           T+V+ NL PT++ + LR  F+  GD+K   E   K +   V F     A +A+  M+   
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKE 62

Query: 577 IDGK 580
           I GK
Sbjct: 63  ISGK 66

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

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           V+V N+DY    ++L   F   G +  V I  DK  G  +G+  +EF        ++++ 
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL- 60

Query: 221 NNQNLFERRI 230
            +++ F  R+
Sbjct: 61  -DESSFRGRV 69

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-KDGKSRGFGTVEF 207
           K+F+  L Y+  +  L+  F   G++ +  +  D    +SRGFG V F
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTF 48

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP) and similar proteins

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 164 VANLDYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           V+NLDY++  K+L++     F+  GKV +V +    DG       V  +   +A  +IS 
Sbjct: 9   VSNLDYRLSRKELQQTLTNQFKRHGKVLSVSLRPQTDGSLVASVRVP-NLQ-DAQYAISQ 66

Query: 220 LNNQNLFERRITV 232
           L+ + +  +RI V
Sbjct: 67  LHRRKIGSKRILV 79

This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. Length = 89

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	587
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG4212|consensus	608		100.0
KOG0144|consensus	510		100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0117|consensus	506		100.0
KOG0145|consensus	360		100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0127|consensus	678		100.0
KOG0123|consensus	369		100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0148|consensus	321		100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0148|consensus	321		99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.96
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
KOG0124|consensus	544		99.95
KOG0147|consensus	549		99.94
KOG0131|consensus	203		99.94
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.94
KOG0123|consensus	369		99.94
KOG0105|consensus	241		99.94
KOG0117|consensus	506		99.93
KOG0146|consensus	371		99.93
KOG0110|consensus	725		99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.93
KOG4211|consensus	510		99.93
KOG0109|consensus	346		99.92
KOG0145|consensus	360		99.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.92
KOG0127|consensus	678		99.91
KOG0146|consensus	371		99.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.89
KOG0144|consensus	510		99.88
KOG0110|consensus	725		99.87
KOG4205|consensus	311		99.86
KOG0109|consensus	346		99.85
KOG0105|consensus	241		99.83
KOG1190|consensus	492		99.82
KOG0131|consensus	203		99.81
KOG4211|consensus	510		99.79
KOG1190|consensus	492		99.77
KOG0124|consensus	544		99.77
KOG0147|consensus	549		99.77
KOG4206|consensus	221		99.74
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.73
KOG4307|consensus	944		99.7
KOG1456|consensus	494		99.7
KOG1548|consensus	382		99.7
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.69
KOG4212|consensus	608		99.68
KOG0106|consensus	216		99.68
KOG0106|consensus	216		99.65
KOG1456|consensus	494		99.62
KOG4205|consensus	311		99.6
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.59
KOG1457|consensus	284		99.59
KOG1365|consensus	508		99.59
KOG0120|consensus	500		99.56
KOG0120|consensus	500		99.55
KOG0125|consensus	376		99.55
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.51
KOG0107|consensus	195		99.51
KOG4206|consensus	221		99.51
KOG0149|consensus	247		99.51
KOG1457|consensus	284		99.5
KOG0126|consensus	219		99.49
KOG0122|consensus	270		99.47
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.47
KOG0107|consensus	195		99.47
KOG0125|consensus	376		99.46
KOG0122|consensus	270		99.46
KOG0121|consensus	153		99.45
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.45
KOG0149|consensus	247		99.44
PLN03120	260	nucleic acid binding protein; Provisional	99.43
KOG0121|consensus	153		99.43
KOG1548|consensus	382		99.43
PLN03120	260	nucleic acid binding protein; Provisional	99.42
KOG4207|consensus	256		99.41
PLN03213	759	repressor of silencing 3; Provisional	99.37
KOG0113|consensus	335		99.37
PLN03121	243	nucleic acid binding protein; Provisional	99.36
KOG0130|consensus	170		99.36
smart00362	72	RRM_2 RNA recognition motif.	99.35
KOG0114|consensus	124		99.35
KOG4207|consensus	256		99.35
KOG0113|consensus	335		99.35
KOG0114|consensus	124		99.32
PLN03121	243	nucleic acid binding protein; Provisional	99.31
smart00362	72	RRM_2 RNA recognition motif.	99.31
PLN03213	759	repressor of silencing 3; Provisional	99.31
KOG4454|consensus	267		99.31
KOG1365|consensus	508		99.29
KOG0108|consensus	435		99.29
smart00360	71	RRM RNA recognition motif.	99.28
KOG0111|consensus	298		99.28
KOG0111|consensus	298		99.27
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.25
KOG0126|consensus	219		99.24
smart00360	71	RRM RNA recognition motif.	99.22
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.22
KOG0130|consensus	170		99.22
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.2
smart00361	70	RRM_1 RNA recognition motif.	99.18
KOG0108|consensus	435		99.18
KOG0129|consensus	520		99.16
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.11
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.1
smart00361	70	RRM_1 RNA recognition motif.	99.06
KOG4208|consensus	214		99.03
KOG0128|consensus	881		98.95
KOG0415|consensus	479		98.92
KOG0415|consensus	479		98.9
KOG0226|consensus	290		98.89
KOG4210|consensus	285		98.83
KOG0132|consensus	894		98.76
KOG4307|consensus	944		98.73
KOG4661|consensus	940		98.72
KOG0153|consensus	377		98.71
KOG0132|consensus	894		98.7
KOG0533|consensus	243		98.69
KOG0153|consensus	377		98.69
KOG4208|consensus	214		98.68
KOG0128|consensus	881		98.65
KOG0533|consensus	243		98.65
KOG0112|consensus	975		98.59
KOG4661|consensus	940		98.56
KOG0129|consensus	520		98.47
KOG0151|consensus	877		98.45
KOG4454|consensus	267		98.45
KOG0226|consensus	290		98.43
KOG4209|consensus	231		98.39
KOG0116|consensus	419		98.37
KOG0116|consensus	419		98.36
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.33
KOG4660|consensus	549		98.25
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.25
KOG0151|consensus	877		98.24
KOG4660|consensus	549		98.24
KOG4209|consensus	231		98.23
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.22
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.2
KOG2193|consensus	584		98.09
KOG1995|consensus	351		98.02
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.99
KOG0112|consensus	975		97.79
KOG1995|consensus	351		97.72
KOG4676|consensus	479		97.72
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.71
KOG2314|consensus	698		97.61
KOG0115|consensus	275		97.59
KOG4676|consensus	479		97.58
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.55
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.53
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.49
KOG2193|consensus	584		97.49
KOG2314|consensus	698		97.26
KOG4210|consensus	285		97.21
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.13
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.09
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.0
KOG2202|consensus	260		96.91
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.86
KOG4849|consensus	498		96.85
KOG1855|consensus	484		96.81
KOG1855|consensus	484		96.73
KOG2202|consensus	260		96.73
KOG0115|consensus	275		96.62
KOG4849|consensus	498		96.62
KOG1996|consensus	378		96.61
KOG3152|consensus	278		96.59
KOG1996|consensus	378		96.51
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.35
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.92
KOG0921|consensus	1282		95.85
KOG3152|consensus	278		95.81
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.59
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.46
KOG2591|consensus	684		95.32
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.3
KOG2416|consensus	718		94.99
KOG4285|consensus	350		94.22
KOG2068|consensus	327		93.83
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.82
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	93.77
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.74
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.59
KOG2591|consensus	684		93.27
KOG2416|consensus	718		93.25
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.02
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	92.64
KOG2135|consensus	526		92.62
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.33
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.27
KOG3285|consensus	203		89.99
KOG4574|consensus	1007		89.79
KOG4574|consensus	1007		89.26
KOG2068|consensus	327		88.74
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	88.55
KOG4285|consensus	350		88.49
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.29
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	88.25
KOG0804|consensus	493		87.16
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	86.88
KOG2135|consensus	526		85.98
KOG2253|consensus	668		85.92
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	84.45
KOG2253|consensus	668		83.62
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	80.19

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

Probab=100.00  E-value=9.4e-45  Score=399.70  Aligned_cols=346  Identities=23%  Similarity=0.316  Sum_probs=275.6

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccccc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK  111 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~  111 (587)
                      .|||+|||.++||++| ++|++||+|.+|+|++|. +++++|||||+|.+.++|++|++.|++..|.|++|+|.|+.++.
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            6999999999999999 899999999999999997 89999999999999999999999999999999999999987443


Q ss_pred             CCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEE
Q psy1534         112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEI  191 (587)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i  191 (587)
                      ..+.                                         ....+|||+|||.++++++|+++|+.||.|.+|+|
T Consensus        82 ~~~~-----------------------------------------~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i  120 (562)
T TIGR01628        82 SLRR-----------------------------------------SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKV  120 (562)
T ss_pred             cccc-----------------------------------------cCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEe
Confidence            2111                                         11357999999999999999999999999999999


Q ss_pred             eeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCC-CCCCCCCCcccccCCCCCCCchHHHHHH
Q psy1534         192 ALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLD-GPVRLPEGLKSIGMGLGANGAPLQDVAN  270 (587)
Q Consensus       192 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~~-~~~~~~~~~~~~g~~~~~~~~~l~~~~~  270 (587)
                      .++.+|+++|||||+|.+.++|.+|++.||+..+.++.|.|.....+.... ........+...+++...+++.|+++|.
T Consensus       121 ~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~  200 (562)
T TIGR01628       121 ATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFA  200 (562)
T ss_pred             eecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHH
Confidence            999889999999999999999999999999999999999997655443321 1222345677889999999999999999


Q ss_pred             hhhccccceeEEEEeccCccceeeeeceeeeeecCCCCCCc-eeEecCCCCCCHHHHHHHHhcCCCCCCC----CCCCCC
Q psy1534         271 WLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA-ASVNTASKTDSTNAEKDKIGNLPNMNTN----PTPTAS  345 (587)
Q Consensus       271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~fv~~~~~~~~~~~~~~ai~~l~g~~~~----g~~~~~  345 (587)
                      .++.+..                 .   .+..+ .++.+++ +||.    |.+.+++.+|+..|+|..+.    ++.+. 
T Consensus       201 ~fG~i~~-----------------~---~i~~~-~~g~~~G~afV~----F~~~e~A~~Av~~l~g~~i~~~~~g~~l~-  254 (562)
T TIGR01628       201 KFGEITS-----------------A---AVMKD-GSGRSRGFAFVN----FEKHEDAAKAVEEMNGKKIGLAKEGKKLY-  254 (562)
T ss_pred             hcCCEEE-----------------E---EEEEC-CCCCcccEEEEE----ECCHHHHHHHHHHhCCcEecccccceeeE-
Confidence            9876411                 0   22223 3556666 6999    88999999999999998887    66554 


Q ss_pred             CchhhhhcccccccccCCCCCCCCCCcccccccCCCCCCcccccccccccccccccccCCCCCCCCCCCCCCCCCCCccc
Q psy1534         346 VSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNIL  425 (587)
Q Consensus       346 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~  425 (587)
                      +..+...         ......    +.                    ..+...                          
T Consensus       255 v~~a~~k---------~er~~~----~~--------------------~~~~~~--------------------------  275 (562)
T TIGR01628       255 VGRAQKR---------AEREAE----LR--------------------RKFEEL--------------------------  275 (562)
T ss_pred             eecccCh---------hhhHHH----HH--------------------hhHHhh--------------------------
Confidence            1111000         000000    00                    000000                          


Q ss_pred             ccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy1534         426 SGMAAYSQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSN  505 (587)
Q Consensus       426 ~g~~~~~~~~g~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  505 (587)
                                                                                                      
T Consensus       276 --------------------------------------------------------------------------------  275 (562)
T TIGR01628       276 --------------------------------------------------------------------------------  275 (562)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCCCCCCCCCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC-----CCeEEEEECCHHHHHHHHHHhCCCcccCc
Q psy1534         506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK-----GDIGLVRFDSEWTAKRAIDMMDRTRIDGK  580 (587)
Q Consensus       506 ~~~~~~~~~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~-----~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~  580 (587)
                       ...........+|||.|||+++|+++|+++|++||.|+.|+|..+     +|+|||+|.+.++|++||+.|||..|+|+
T Consensus       276 -~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk  354 (562)
T TIGR01628       276 -QQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK  354 (562)
T ss_pred             -hhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCc
Confidence             000000112458999999999999999999999999999999654     48999999999999999999999999999


Q ss_pred             eEEEEE
Q psy1534         581 IIDVTF  586 (587)
Q Consensus       581 ~i~v~~  586 (587)
                      +|+|.+
T Consensus       355 ~l~V~~  360 (562)
T TIGR01628       355 PLYVAL  360 (562)
T ss_pred             eeEEEe
Confidence            999975

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=2.2e-43  Score=367.51  Aligned_cols=166  Identities=21%  Similarity=0.367  Sum_probs=149.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+|||+|||.++++++| ++|++||+|.+|+|++|+ +|+++|||||+|.+.++|++||+.||+..|.|++|+|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            3578999999999999999 899999999999999997 89999999999999999999999999999999999999987


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      ....                                           ....++|||+|||..+++++|+++|++||.|..
T Consensus        82 ~~~~-------------------------------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~  118 (352)
T TIGR01661        82 PSSD-------------------------------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIIT  118 (352)
T ss_pred             cccc-------------------------------------------ccccceEEECCccccCCHHHHHHHHhccCCEEE
Confidence            3321                                           112468999999999999999999999999999


Q ss_pred             EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEccCCC
Q psy1534         189 VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMDRVAD  239 (587)
Q Consensus       189 v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a~~~~  239 (587)
                      +.++.+.. +.++|||||+|.+.++|++||+.|||..+.+  ++|.|+++....
T Consensus       119 ~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       119 SRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             EEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            99999874 8899999999999999999999999999887  567777765543

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

>KOG4212|consensus

Probab=100.00  E-value=1.7e-39  Score=316.52  Aligned_cols=242  Identities=47%  Similarity=0.781  Sum_probs=188.4

Q ss_pred             CcEEEcCCCCCCCHHHH-Hhc-ccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHL-STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F-~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      +.|||.|||++..+++| ++| ++.|+|+.|.++.|++|++||||.|||+++|.++||++.||.+.+.||+|.|+.....
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~  124 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDE  124 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCch
Confidence            34999999999999999 777 7899999999999999999999999999999999999999999999999999987733


Q ss_pred             cCCC---CC---------------------CCCCCC---CCCchhhhhccC-----CcccCC---------CCCCChhhh
Q psy1534         111 KGGR---RN---------------------MGGGGG---VDRDLSALLQNN-----SSKFGN---------TYGLSPQFL  149 (587)
Q Consensus       111 ~~~~---~~---------------------~~~~~~---~~~~~~~~~~~~-----~~~~~~---------~~~~~~~~~  149 (587)
                      +..+   ..                     +....+   .+.....+....     ...+.+         -|..+..++
T Consensus       125 q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Fl  204 (608)
T KOG4212|consen  125 QRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFL  204 (608)
T ss_pred             hhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhh
Confidence            3221   10                     000000   000000011100     011111         234555666


Q ss_pred             hccCC-CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCe
Q psy1534         150 ESLGI-NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFER  228 (587)
Q Consensus       150 ~~~~~-~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  228 (587)
                      ++... .+|...++||.||.+.+....|++.|.-.|.|+.|.+-.|+.|.++|||.|+|+.+-+|..||..|++.-+..+
T Consensus       205 r~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~~  284 (608)
T KOG4212|consen  205 RSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFDR  284 (608)
T ss_pred             hhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCccc
Confidence            65554 56667899999999999999999999999999999999999999999999999999999999999999888899


Q ss_pred             EEEEEEccCCCCCCCCCCCCCCcccccCCCCCCCchHHHHHHhhhcc
Q psy1534         229 RITVRMDRVADRLDGPVRLPEGLKSIGMGLGANGAPLQDVANWLLQE  275 (587)
Q Consensus       229 ~l~v~~a~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~~~~~~~~~  275 (587)
                      +..+++.+-.. +.....+|+.+.+.+.+.+...++|+.....++..
T Consensus       285 ~~~~Rl~~~~D-rn~g~~l~~~~~glg~gmdr~g~ele~~~~~l~~~  330 (608)
T KOG4212|consen  285 RMTVRLDRIPD-RNEGIKLPEGLGGLGIGMDRNGEELEDVAHNLPNG  330 (608)
T ss_pred             cceeecccccc-ccccccccccccceeeccCCCccHHHHhhcccCCc
Confidence            99998876654 33445678888888888889999998887665543

>KOG0144|consensus

Probab=100.00  E-value=1.4e-40  Score=324.40  Aligned_cols=172  Identities=24%  Similarity=0.363  Sum_probs=152.5

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCce-eCC--eEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFE-TKG--RKL  102 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~-l~g--r~i  102 (587)
                      .+.+..++||+.||..++|+|| ++|++||.|.+|.|++|+ ++.+||||||.|.+.++|.+|+.+||+.+ |.|  .+|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            3457779999999999999999 899999999999999998 99999999999999999999999999854 544  899


Q ss_pred             EEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHh
Q psy1534         103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRL  182 (587)
Q Consensus       103 ~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~  182 (587)
                      .|++++.++..                                          .....+|||+-|+..++|.|++++|++
T Consensus       110 qvk~Ad~E~er------------------------------------------~~~e~KLFvg~lsK~~te~evr~iFs~  147 (510)
T KOG0144|consen  110 QVKYADGERER------------------------------------------IVEERKLFVGMLSKQCTENEVREIFSR  147 (510)
T ss_pred             eecccchhhhc------------------------------------------cccchhhhhhhccccccHHHHHHHHHh
Confidence            99999844310                                          011358999999999999999999999


Q ss_pred             cCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCC--eEEEEEEccCCCCC
Q psy1534         183 AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQN-LFE--RRITVRMDRVADRL  241 (587)
Q Consensus       183 ~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~-~~g--~~l~v~~a~~~~~~  241 (587)
                      ||.|++|.|++|.++.+||||||+|.+.|.|..||+.||+.. +.|  .+|.|+|+++++.+
T Consensus       148 fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  148 FGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             hCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCc
Confidence            999999999999999999999999999999999999999864 554  58999999887643

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

Probab=100.00  E-value=3.1e-39  Score=347.10  Aligned_cols=167  Identities=20%  Similarity=0.257  Sum_probs=138.5

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEEecc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM--HRFETKGRKLVIKEAV  108 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l--~g~~l~gr~i~V~~a~  108 (587)
                      .+.|||+|||+++++++| ++|++||+|.+|+|+++     |+||||+|.+.++|++|++.+  ++..|.|++|+|.++.
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-----k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~   76 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-----KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYST   76 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-----CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecC
Confidence            468999999999999999 89999999999999974     689999999999999999864  7899999999999997


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      .++..+...                  ..+.             ........+|||.||++.+++++|+++|++||.|.+
T Consensus        77 ~~~~~~~~~------------------~~~~-------------~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~  125 (481)
T TIGR01649        77 SQEIKRDGN------------------SDFD-------------SAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLR  125 (481)
T ss_pred             CcccccCCC------------------Cccc-------------CCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEE
Confidence            543222110                  0000             001112357999999999999999999999999999


Q ss_pred             EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEccC
Q psy1534         189 VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMDRV  237 (587)
Q Consensus       189 v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a~~  237 (587)
                      |.|+++..   +++|||+|.+.++|.+|++.|||..|.+  +.|+|.|++.
T Consensus       126 v~i~~~~~---~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~  173 (481)
T TIGR01649       126 IVTFTKNN---VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKP  173 (481)
T ss_pred             EEEEecCC---ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecC
Confidence            99988642   4799999999999999999999999975  5788888775

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0117|consensus

Probab=100.00  E-value=3.5e-39  Score=316.37  Aligned_cols=162  Identities=22%  Similarity=0.355  Sum_probs=148.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETK-GRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~-gr~i~V~  105 (587)
                      ++....|||+.||.|+.|+|| .+|++.|+|.+++||+|+ +|.+||||||+|.+.++|++||+.||+++|. |+.|.|+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            356779999999999999999 899999999999999997 9999999999999999999999999999996 9999999


Q ss_pred             ecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC
Q psy1534         106 EAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK  185 (587)
Q Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~  185 (587)
                      .+..                                                 .|+|||+|||.+.++++|.+.|++.++
T Consensus       160 ~Sva-------------------------------------------------n~RLFiG~IPK~k~keeIlee~~kVte  190 (506)
T KOG0117|consen  160 VSVA-------------------------------------------------NCRLFIGNIPKTKKKEEILEEMKKVTE  190 (506)
T ss_pred             Eeee-------------------------------------------------cceeEeccCCccccHHHHHHHHHhhCC
Confidence            8873                                                 379999999999999999999999987


Q ss_pred             -eeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhC--CceeCCeEEEEEEccCCC
Q psy1534         186 -VENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLN--NQNLFERRITVRMDRVAD  239 (587)
Q Consensus       186 -i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~~a~~~~  239 (587)
                       |++|.+..+++  .++||||||+|.++..|..|-+.|-  ..++.|..+.|.||.+..
T Consensus       191 GVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~  249 (506)
T KOG0117|consen  191 GVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEE  249 (506)
T ss_pred             CeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCccc
Confidence             78888888774  8899999999999999999998873  346789999999998875

>KOG0145|consensus

Probab=100.00  E-value=6.5e-39  Score=293.15  Aligned_cols=168  Identities=21%  Similarity=0.399  Sum_probs=152.2

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....+|.|.-||.++|++|| .+|...|+|++|++++|+ +|.|.||+||.|.+++||++|+..|||..+..+.|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            345568999999999999999 799999999999999998 999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCe
Q psy1534         107 AVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKV  186 (587)
Q Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i  186 (587)
                      +.+..                                           .......|||++||..+|..||+++|++||.|
T Consensus       118 ARPSs-------------------------------------------~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrI  154 (360)
T KOG0145|consen  118 ARPSS-------------------------------------------DSIKDANLYVSGLPKTMTQKELEQIFSPFGRI  154 (360)
T ss_pred             ccCCh-------------------------------------------hhhcccceEEecCCccchHHHHHHHHHHhhhh
Confidence            98432                                           12234689999999999999999999999999


Q ss_pred             eEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEccCCC
Q psy1534         187 ENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMDRVAD  239 (587)
Q Consensus       187 ~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a~~~~  239 (587)
                      ...+|+.|.. |.+||.+||+|+..++|++||+.|||++-.|  .+|.|+++....
T Consensus       155 ItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  155 ITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             hhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcc
Confidence            9999998884 9999999999999999999999999998765  579999986654

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

Probab=100.00  E-value=8.2e-38  Score=332.69  Aligned_cols=160  Identities=22%  Similarity=0.302  Sum_probs=138.2

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK-GRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~-gr~i~V~~a  107 (587)
                      ....+|||+|||.+++|++| ++|++||+|.+|+|++|.+|++||||||+|.+.|+|++||+.||+..|. ++.|.|..+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            34579999999999999999 8999999999999999999999999999999999999999999999885 788777655


Q ss_pred             ccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC-e
Q psy1534         108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK-V  186 (587)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-i  186 (587)
                      ..                                                 .++|||+|||+++++++|.++|++++. +
T Consensus       136 ~~-------------------------------------------------~~rLFVgNLP~~~TeeeL~eeFskv~egv  166 (578)
T TIGR01648       136 VD-------------------------------------------------NCRLFVGGIPKNKKREEILEEFSKVTEGV  166 (578)
T ss_pred             cc-------------------------------------------------CceeEeecCCcchhhHHHHHHhhcccCCc
Confidence            41                                                 358999999999999999999999875 4


Q ss_pred             eEEEEeeCC--CCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEEccCC
Q psy1534         187 ENVEIALDK--DGKSRGFGTVEFDHPVEAVQSISMLNN--QNLFERRITVRMDRVA  238 (587)
Q Consensus       187 ~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~a~~~  238 (587)
                      +++.+....  .++++|||||+|.++++|.+|++.|+.  ..+.|+.|.|+|+.+.
T Consensus       167 v~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~  222 (578)
T TIGR01648       167 VDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPE  222 (578)
T ss_pred             eEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccc
Confidence            554443322  278899999999999999999998864  3578999999987654

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.

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

Probab=100.00  E-value=1.1e-35  Score=320.21  Aligned_cols=175  Identities=26%  Similarity=0.430  Sum_probs=151.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|++||+|.+|+|++|+ +++++|||||+|.+.++|++||. |+|..|.|++|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            4568999999999999999 899999999999999997 89999999999999999999995 89999999999999876


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      .+......                 ...              ......+..++|||+|||..+++++|+++|+.||.|..
T Consensus       167 ~~~~~~~~-----------------~~~--------------~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~  215 (457)
T TIGR01622       167 AEKNRAAK-----------------AAT--------------HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIED  215 (457)
T ss_pred             hhhhhhhh-----------------ccc--------------ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEE
Confidence            33211000                 000              00001223679999999999999999999999999999


Q ss_pred             EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         189 VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       189 v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      |.|++++. |+++|||||+|.+.++|.+|++.|||..|.|++|.|.++..
T Consensus       216 v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       216 VQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             EEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            99999986 79999999999999999999999999999999999999873

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.

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

Probab=100.00  E-value=9e-35  Score=309.59  Aligned_cols=178  Identities=18%  Similarity=0.306  Sum_probs=153.4

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....+|||+|||+++++++| ++|++||+|.+|+|++|+ ++++||||||+|.+.++|++|++.|||..|.||+|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            45678999999999999999 899999999999999997 9999999999999999999999999999999999999865


Q ss_pred             ccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCee
Q psy1534         108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVE  187 (587)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~  187 (587)
                      ........                                ............++|||+|||+++++++|+++|+.||.|.
T Consensus       185 ~~~p~a~~--------------------------------~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~  232 (612)
T TIGR01645       185 SNMPQAQP--------------------------------IIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIV  232 (612)
T ss_pred             cccccccc--------------------------------ccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCee
Confidence            42210000                                0000000122346999999999999999999999999999


Q ss_pred             EEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         188 NVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       188 ~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      +|+|.+++. ++++|||||+|.+.++|.+||+.||+..|+|+.|+|.++....
T Consensus       233 svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       233 KCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             EEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            999999986 8899999999999999999999999999999999999887653

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.

>KOG0127|consensus

Probab=100.00  E-value=5.4e-35  Score=292.82  Aligned_cols=193  Identities=20%  Similarity=0.268  Sum_probs=156.9

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..+|||++||+.++-++| ++|+.+|+|..|.++.++ ++.+|||+||+|+-.||+++|++.+++..|.||.|.|..+.+
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            379999999999999999 899999999999999997 889999999999999999999999999999999999999984


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                      +......   ..+.           ............+...   ....+..+|.|+||||.+.+.+|+.+|+.||.|.+|
T Consensus        85 R~r~e~~---~~~e-----------~~~veK~~~q~~~~k~---~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei  147 (678)
T KOG0127|consen   85 RARSEEV---EKGE-----------NKAVEKPIEQKRPTKA---KVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEI  147 (678)
T ss_pred             cccchhc---cccc-----------chhhhcccccCCcchh---hccCccceEEeecCCcccCcHHHHHHHhhcceEEEE
Confidence            4321100   0000           0000000000000000   001224589999999999999999999999999999


Q ss_pred             EEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCC
Q psy1534         190 EIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRL  241 (587)
Q Consensus       190 ~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~  241 (587)
                      .|++.++|+-.|||||.|.+..+|.+||+.+|+.+|.||+|.|.||-++...
T Consensus       148 ~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~y  199 (678)
T KOG0127|consen  148 VIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTY  199 (678)
T ss_pred             EcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccc
Confidence            9999888888899999999999999999999999999999999999888743

>KOG0123|consensus

Probab=100.00  E-value=5.1e-33  Score=283.90  Aligned_cols=331  Identities=23%  Similarity=0.296  Sum_probs=259.3

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccccC
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG  112 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~  112 (587)
                      .|||+   +++|+..| ++|+++|+|.+|+|++|. . |.|||||.|.++++|++|+++||...+.|++|+|.|+.+.. 
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~-   76 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP-   76 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC-
Confidence            58999   89999999 999999999999999999 5 99999999999999999999999999999999999998553 


Q ss_pred             CCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEe
Q psy1534         113 GRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIA  192 (587)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~  192 (587)
                                                                     ..|||.||+++++..+|.++|+.||+|++|++.
T Consensus        77 -----------------------------------------------~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~  109 (369)
T KOG0123|consen   77 -----------------------------------------------SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVA  109 (369)
T ss_pred             -----------------------------------------------ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEE
Confidence                                                           139999999999999999999999999999999


Q ss_pred             eCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCCCCC----CCCCCcccccCCCCCCCchHHHH
Q psy1534         193 LDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGPV----RLPEGLKSIGMGLGANGAPLQDV  268 (587)
Q Consensus       193 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~~~~~----~~~~~~~~~g~~~~~~~~~l~~~  268 (587)
                      .+.+| ++|| ||+|+++++|.+||+.|||..+.+++|.|.....+..+..+.    +.-............+...+..+
T Consensus       110 ~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~  187 (369)
T KOG0123|consen  110 TDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDL  187 (369)
T ss_pred             EcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHh
Confidence            99988 8999 999999999999999999999999999998876654332221    11233344566666777788888


Q ss_pred             HHhhhccccceeEEEEeccCccceeeeeceeeeeecCCCCCCc-eeEecCCCCCCHHHHHHHHhcCCCCCCCCCCCCCCc
Q psy1534         269 ANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA-ASVNTASKTDSTNAEKDKIGNLPNMNTNPTPTASVS  347 (587)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~fv~~~~~~~~~~~~~~ai~~l~g~~~~g~~~~~~~  347 (587)
                      |..++.+..                     -....+..+.+++ +||.    |.+.+++..|+..|++....+..+- +.
T Consensus       188 f~~~g~i~s---------------------~~v~~~~~g~~~~~gfv~----f~~~e~a~~av~~l~~~~~~~~~~~-V~  241 (369)
T KOG0123|consen  188 FSAYGSITS---------------------VAVMRDSIGKSKGFGFVN----FENPEDAKKAVETLNGKIFGDKELY-VG  241 (369)
T ss_pred             hcccCcceE---------------------EEEeecCCCCCCCcccee----ecChhHHHHHHHhccCCcCCcccee-ec
Confidence            888777522                     2233444455666 5999    7779999999999999887755554 11


Q ss_pred             hhhhhcccccccccCCCCCCCCCCcccccccCCCCCCcccccccccccccccccccCCCCCCCCCCCCCCCCCCCccccc
Q psy1534         348 TPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSG  427 (587)
Q Consensus       348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~~g  427 (587)
                      .+..     ..-.....-                            ......                            
T Consensus       242 ~aqk-----k~e~~~~l~----------------------------~~~~~~----------------------------  260 (369)
T KOG0123|consen  242 RAQK-----KSEREAELK----------------------------RKFEQE----------------------------  260 (369)
T ss_pred             cccc-----chhhHHHHh----------------------------hhhHhh----------------------------
Confidence            1110     000000000                            000000                            


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy1534         428 MAAYSQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRS  507 (587)
Q Consensus       428 ~~~~~~~~g~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  507 (587)
                                                                                                     .
T Consensus       261 -------------------------------------------------------------------------------~  261 (369)
T KOG0123|consen  261 -------------------------------------------------------------------------------F  261 (369)
T ss_pred             -------------------------------------------------------------------------------h
Confidence                                                                                           0


Q ss_pred             CCCCCCCCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC-----CCeEEEEECCHHHHHHHHHHhCCCcccCceE
Q psy1534         508 MNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK-----GDIGLVRFDSEWTAKRAIDMMDRTRIDGKII  582 (587)
Q Consensus       508 ~~~~~~~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~-----~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i  582 (587)
                      ...........|+|.||+..++.++|++.|..||+|++++|..+     +|+|||+|.+.++|.+|+..+|+..+.++.|
T Consensus       262 ~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l  341 (369)
T KOG0123|consen  262 AKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPL  341 (369)
T ss_pred             hhccccccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCch
Confidence            00000112348999999999999999999999999999988442     5999999999999999999999999999988


Q ss_pred             EEE
Q psy1534         583 DVT  585 (587)
Q Consensus       583 ~v~  585 (587)
                      .|-
T Consensus       342 ~va  344 (369)
T KOG0123|consen  342 YVA  344 (369)
T ss_pred             hhh
Confidence            764

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

Probab=100.00  E-value=2.1e-32  Score=299.00  Aligned_cols=190  Identities=15%  Similarity=0.186  Sum_probs=141.3

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccC------------CCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCce
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTV------------GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE   96 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~------------G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~   96 (587)
                      ...++|||+|||+++|+++| ++|.+|            +.|..|.+.+     .+|||||+|.+.++|.+|| .|+|..
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~-----~kg~afVeF~~~e~A~~Al-~l~g~~  246 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK-----EKNFAFLEFRTVEEATFAM-ALDSII  246 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECC-----CCCEEEEEeCCHHHHhhhh-cCCCeE
Confidence            45678999999999999999 788864            3566665544     4799999999999999999 599999


Q ss_pred             eCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHH
Q psy1534          97 TKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKL  176 (587)
Q Consensus        97 l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l  176 (587)
                      |.|++|+|......... ..  .....   ....+.......    .    ............++|||+|||+.+++++|
T Consensus       247 ~~g~~l~v~r~~~~~~~-~~--~~~~~---~~~~~~~~~~~~----~----~~~~~~~~~~~~~~l~v~nlp~~~~~~~l  312 (509)
T TIGR01642       247 YSNVFLKIRRPHDYIPV-PQ--ITPEV---SQKNPDDNAKNV----E----KLVNSTTVLDSKDRIYIGNLPLYLGEDQI  312 (509)
T ss_pred             eeCceeEecCccccCCc-cc--cCCCC---CCCCCccccccc----c----cccccccCCCCCCEEEEeCCCCCCCHHHH
Confidence            99999999765421100 00  00000   000000000000    0    00000112234579999999999999999


Q ss_pred             HHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         177 REVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       177 ~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      +++|+.||.|..+.|+++.. |.++|||||+|.+.++|..||+.|||..|.|+.|.|.++....
T Consensus       313 ~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~  376 (509)
T TIGR01642       313 KELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGA  376 (509)
T ss_pred             HHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCC
Confidence            99999999999999999874 9999999999999999999999999999999999999986543

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

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

Probab=100.00  E-value=1.5e-32  Score=302.86  Aligned_cols=285  Identities=16%  Similarity=0.244  Sum_probs=228.1

Q ss_pred             CCCCchhHHHHHHcCCCCCcc-cccc-------CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcc
Q psy1534           2 TSPVTETELVEQIAHQDFPMF-QRIE-------TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPR   72 (587)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~-~~~~-------~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~sk   72 (587)
                      .++.++..|.+.++...+..+ .++.       .......+|||+|||.++++++| ++|++||.|.+|+|+++.+|++|
T Consensus        50 ~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~sk  129 (562)
T TIGR01628        50 QNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSR  129 (562)
T ss_pred             CCHHHHHHHHHHhCCCEECCeeEEeecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcc
Confidence            455566777777766644222 1111       11123457999999999999999 89999999999999999999999


Q ss_pred             eEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhcc
Q psy1534          73 GSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESL  152 (587)
Q Consensus        73 G~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (587)
                      |||||+|.+.++|++|++.||+..+.++.|.|....++....                                      
T Consensus       130 g~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~--------------------------------------  171 (562)
T TIGR01628       130 GYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE--------------------------------------  171 (562)
T ss_pred             cEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccc--------------------------------------
Confidence            999999999999999999999999999999998766332100                                      


Q ss_pred             CCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC----Ce
Q psy1534         153 GINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF----ER  228 (587)
Q Consensus       153 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~----g~  228 (587)
                      .......++|||+|||+++++++|+++|+.||.|.++.++++.+++++|||||+|.+.++|.+|++.||+..+.    ++
T Consensus       172 ~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~  251 (562)
T TIGR01628       172 AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGK  251 (562)
T ss_pred             cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccce
Confidence            00112246899999999999999999999999999999999988999999999999999999999999999999    99


Q ss_pred             EEEEEEccCCCCCCC--------------CCCCCCCcccccCCCCCCCchHHHHHHhhhccccceeEEEEeccCccceee
Q psy1534         229 RITVRMDRVADRLDG--------------PVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLE  294 (587)
Q Consensus       229 ~l~v~~a~~~~~~~~--------------~~~~~~~~~~~g~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  294 (587)
                      .|.|.++..+..+..              .......+...+++...+.+.|+++|..++.+.                 +
T Consensus       252 ~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~-----------------~  314 (562)
T TIGR01628       252 KLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEIT-----------------S  314 (562)
T ss_pred             eeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeE-----------------E
Confidence            999988765543210              011223467789999999999999999988752                 1


Q ss_pred             eeceeeeeecCCCCCCc-eeEecCCCCCCHHHHHHHHhcCCCCCCCCCCCCCCchhh
Q psy1534         295 RWDFKLQYDKSSDENDA-ASVNTASKTDSTNAEKDKIGNLPNMNTNPTPTASVSTPA  350 (587)
Q Consensus       295 ~~~~~~~~~~~~~~~~~-~fv~~~~~~~~~~~~~~ai~~l~g~~~~g~~~~~~~~~~  350 (587)
                      .   ++..+ .++.+++ +||.    |.+.++|.+|+..|+|..+.|++|. |.++.
T Consensus       315 ~---~i~~d-~~g~~~g~gfV~----f~~~~~A~~A~~~~~g~~~~gk~l~-V~~a~  362 (562)
T TIGR01628       315 A---KVMLD-EKGVSRGFGFVC----FSNPEEANRAVTEMHGRMLGGKPLY-VALAQ  362 (562)
T ss_pred             E---EEEEC-CCCCcCCeEEEE----eCCHHHHHHHHHHhcCCeeCCceeE-EEecc
Confidence            1   34444 5677777 5999    9999999999999999999999997 65543

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

>KOG0148|consensus

Probab=100.00  E-value=7.5e-33  Score=255.42  Aligned_cols=139  Identities=24%  Similarity=0.347  Sum_probs=118.4

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...+++|||+||+.++||+.| .+|++.|+|++|+|+.|                                  .|+|.++
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~----------------------------------e~~v~wa   48 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD----------------------------------ELKVNWA   48 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh----------------------------------hhccccc
Confidence            356789999999999999998 89999999999999986                                  4566666


Q ss_pred             ccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCee
Q psy1534         108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVE  187 (587)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~  187 (587)
                      ........                +                      .....-.+||+.|...++-++|++.|.+||+|.
T Consensus        49 ~~p~nQsk----------------~----------------------t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS   90 (321)
T KOG0148|consen   49 TAPGNQSK----------------P----------------------TSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVS   90 (321)
T ss_pred             cCcccCCC----------------C----------------------ccccceeEEehhcchhcchHHHHHHhccccccc
Confidence            63311100                0                      111123799999999999999999999999999


Q ss_pred             EEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         188 NVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       188 ~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      +++|++|.. +++|||+||.|-..++|++||..|||+.|.+|.|+-.|+..+.
T Consensus        91 ~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   91 DAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             cceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            999999985 9999999999999999999999999999999999999987664

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=2e-32  Score=278.39  Aligned_cols=171  Identities=23%  Similarity=0.349  Sum_probs=153.9

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .......+|||+|||+++|+++| ++|++||+|++|+|++|. ++++||||||+|.++++|++||+.||+..|.+++|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            44557789999999999999999 899999999999999996 9999999999999999999999999999999999999


Q ss_pred             EecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcC
Q psy1534         105 KEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAG  184 (587)
Q Consensus       105 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G  184 (587)
                      .++.....                                           ....++|||+|||++++|++|+++|++||
T Consensus       182 ~~a~p~~~-------------------------------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG  218 (346)
T TIGR01659       182 SYARPGGE-------------------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYG  218 (346)
T ss_pred             eccccccc-------------------------------------------ccccceeEEeCCCCcccHHHHHHHHHhcC
Confidence            98863210                                           11235899999999999999999999999


Q ss_pred             CeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEccCCCC
Q psy1534         185 KVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMDRVADR  240 (587)
Q Consensus       185 ~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a~~~~~  240 (587)
                      .|+.|+|++++ +++++|||||+|.+.++|++||+.||+..+.+  ++|+|+++....+
T Consensus       219 ~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       219 QIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             CEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            99999999998 49999999999999999999999999999875  6889988876653

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

>KOG0148|consensus

Probab=99.97  E-value=3.2e-30  Score=238.06  Aligned_cols=177  Identities=20%  Similarity=0.314  Sum_probs=157.8

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..-|||+-|..+++-++| +.|.+||+|.+++|++|. |++||||+||.|.+.++|++||..|||.-|++|.|+-.|+.|
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            446999999999999999 889999999999999997 999999999999999999999999999999999999999998


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                      |..+.-                           ..+..+.+-.....+..|+|||+|++.-++|++|++.|++||.|.+|
T Consensus       142 Kp~e~n---------------------------~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EV  194 (321)
T KOG0148|consen  142 KPSEMN---------------------------GKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEV  194 (321)
T ss_pred             CccccC---------------------------CCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEE
Confidence            863211                           01122334445567778999999999999999999999999999999


Q ss_pred             EEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q psy1534         190 EIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADR  240 (587)
Q Consensus       190 ~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~  240 (587)
                      +|.++     +||+||+|+++|.|.+||..+|+.+|.|..++|.|-+....
T Consensus       195 RvFk~-----qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  195 RVFKD-----QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             EEecc-----cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCC
Confidence            99998     69999999999999999999999999999999999876653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=3.7e-28  Score=253.05  Aligned_cols=237  Identities=19%  Similarity=0.217  Sum_probs=166.6

Q ss_pred             CCCchhHHHHHHcCCCCCccc------cccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceE
Q psy1534           3 SPVTETELVEQIAHQDFPMFQ------RIETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGS   74 (587)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~   74 (587)
                      ++-+...|+..+++..+....      +.........+|||+|||.++++++| ++|++||+|..++++++. ++.++||
T Consensus        54 ~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~  133 (352)
T TIGR01661        54 RPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGV  133 (352)
T ss_pred             cHHHHHHHHhhcccEEECCeeEEEEeecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcE
Confidence            344556666677766553321      11111234568999999999999999 889999999999999997 8899999


Q ss_pred             EEEEECCHHHHHHHHHHhCCceeCC--eEEEEEecccccCCCCCCCCC--------CCCC------------------Cc
Q psy1534          75 AIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKEAVEDKGGRRNMGGG--------GGVD------------------RD  126 (587)
Q Consensus        75 aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~a~~~~~~~~~~~~~--------~~~~------------------~~  126 (587)
                      |||+|.+.++|++|++.||+..+.+  ++|.|.++..+.......-..        ....                  ..
T Consensus       134 ~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  213 (352)
T TIGR01661       134 GFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAA  213 (352)
T ss_pred             EEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCccc
Confidence            9999999999999999999999877  678898886333111000000        0000                  00


Q ss_pred             hhhhh--------------ccCCcccCCCCCCCh-------hhhh--ccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhc
Q psy1534         127 LSALL--------------QNNSSKFGNTYGLSP-------QFLE--SLGINCPLINKVFVANLDYKVDEKKLREVFRLA  183 (587)
Q Consensus       127 ~~~~~--------------~~~~~~~~~~~~~~~-------~~~~--~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~  183 (587)
                      .+...              .............++       ....  ........+.+|||+|||+++++++|+++|++|
T Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~f  293 (352)
T TIGR01661       214 RFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPF  293 (352)
T ss_pred             ccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhC
Confidence            00000              000000000000000       0000  000012234579999999999999999999999


Q ss_pred             CCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         184 GKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       184 G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      |.|.+|+|++|+ +++++|||||+|.+.++|.+||..|||..|.||.|+|.|+..+.
T Consensus       294 G~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       294 GAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             CCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            999999999998 59999999999999999999999999999999999999987764

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

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

Probab=99.96  E-value=3.3e-27  Score=254.04  Aligned_cols=279  Identities=17%  Similarity=0.192  Sum_probs=193.3

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEecccc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKEAVED  110 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~a~~~  110 (587)
                      +|||+||++.+++++| ++|++||+|++|+|+++..   +++|||+|.+.++|.+|++.|||..|.+  +.|+|.++...
T Consensus        98 ~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~---~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649        98 RVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN---VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC---ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence            7999999999999999 8999999999999988642   4799999999999999999999999975  58999888732


Q ss_pred             cC-------CCCCCCC-----CCCCCCch--hhhhcc---------CCcccCC----------------------C----
Q psy1534         111 KG-------GRRNMGG-----GGGVDRDL--SALLQN---------NSSKFGN----------------------T----  141 (587)
Q Consensus       111 ~~-------~~~~~~~-----~~~~~~~~--~~~~~~---------~~~~~~~----------------------~----  141 (587)
                      ..       ...+...     .+......  ....+.         ....++.                      .    
T Consensus       175 ~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  254 (481)
T TIGR01649       175 RLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPA  254 (481)
T ss_pred             CceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCccc
Confidence            21       0000000     00000000  000000         0000000                      0    


Q ss_pred             CCCChh--hhhc-cCCCCCCCcEEEEecCCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHH
Q psy1534         142 YGLSPQ--FLES-LGINCPLINKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI  217 (587)
Q Consensus       142 ~~~~~~--~~~~-~~~~~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al  217 (587)
                      +...+.  .... .....+++++|||+|||+ .+++++|+++|+.||.|.+|+|++++    +|||||+|.+.++|.+||
T Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~----~g~afV~f~~~~~A~~Ai  330 (481)
T TIGR01649       255 YEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLAL  330 (481)
T ss_pred             ccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC----CCEEEEEECCHHHHHHHH
Confidence            000000  0000 001235678999999998 69999999999999999999999874    699999999999999999


Q ss_pred             HHhCCceeCCeEEEEEEccCCCCCCCC---------------------C------------CCCCCcccccCCCCCCCch
Q psy1534         218 SMLNNQNLFERRITVRMDRVADRLDGP---------------------V------------RLPEGLKSIGMGLGANGAP  264 (587)
Q Consensus       218 ~~l~g~~~~g~~l~v~~a~~~~~~~~~---------------------~------------~~~~~~~~~g~~~~~~~~~  264 (587)
                      ..||+..|.|++|+|.+++........                     .            .....+...+++...+.+.
T Consensus       331 ~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~  410 (481)
T TIGR01649       331 THLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEED  410 (481)
T ss_pred             HHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHH
Confidence            999999999999999987554210000                     0            0012456689999999999


Q ss_pred             HHHHHHhhhccccceeEEEEeccCccceeeeeceeeeeecCCCCCCceeEecCCCCCCHHHHHHHHhcCCCCCCCCCC
Q psy1534         265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKTDSTNAEKDKIGNLPNMNTNPTP  342 (587)
Q Consensus       265 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fv~~~~~~~~~~~~~~ai~~l~g~~~~g~~  342 (587)
                      |+++|..++...+...                  ++ +.+.......+||.    |.+.++|.+||..|+|..+.++.
T Consensus       411 L~~lF~~~G~~~i~~i------------------k~-~~~~~~~~~~gfVe----F~~~e~A~~Al~~ln~~~l~~~~  465 (481)
T TIGR01649       411 LKELFAENGVHKVKKF------------------KF-FPKDNERSKMGLLE----WESVEDAVEALIALNHHQLNEPN  465 (481)
T ss_pred             HHHHHHhcCCccceEE------------------EE-ecCCCCcceeEEEE----cCCHHHHHHHHHHhcCCccCCCC
Confidence            9999999876211111                  11 12222222336999    88999999999999999998875

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).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=9e-27  Score=237.00  Aligned_cols=82  Identities=23%  Similarity=0.379  Sum_probs=76.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      .....++|||+|||++++|++|+++|+.||.|++|+|++|+. ++++|||||+|.++++|++||+.||+..|.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            344578999999999999999999999999999999999975 9999999999999999999999999999999999998


Q ss_pred             Ecc
Q psy1534         234 MDR  236 (587)
Q Consensus       234 ~a~  236 (587)
                      +++
T Consensus       183 ~a~  185 (346)
T TIGR01659       183 YAR  185 (346)
T ss_pred             ccc
Confidence            754

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

>KOG0124|consensus

Probab=99.95  E-value=3.1e-26  Score=219.27  Aligned_cols=176  Identities=18%  Similarity=0.309  Sum_probs=152.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      -..+|||+.|.+++.|+.| ..|..||+|++|.+-.|+ |+++||||||+|+-+|.|+.|++.||+..++||.|+|.+..
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            4578999999999999999 689999999999999998 99999999999999999999999999999999999998554


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      ...                                ...+.......+...-++|||..+.++++|+||+.+|+.||+|.+
T Consensus       192 Nmp--------------------------------QAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~  239 (544)
T KOG0124|consen  192 NMP--------------------------------QAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVK  239 (544)
T ss_pred             CCc--------------------------------ccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceee
Confidence            211                                111111111122333579999999999999999999999999999


Q ss_pred             EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         189 VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       189 v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      |.+.++++ +.++||+||+|.+..+...||..||=..++|..|+|-.+-..
T Consensus       240 C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  240 CQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             EEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCC
Confidence            99999997 889999999999999999999999999999999999765443

>KOG0147|consensus

Probab=99.94  E-value=9.1e-27  Score=235.77  Aligned_cols=179  Identities=25%  Similarity=0.363  Sum_probs=149.6

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +.++||+-.|....+..+| ++|+.+|+|.+|.|+.|+ ++++||.|||+|.+.+....|| .|.|+.+.|.+|.|+...
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccH
Confidence            3448999999999999999 899999999999999997 9999999999999999999999 789999999999999887


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      ..+.....                 ....+          . . .....+...|||+||.+++++++|+.+|++||.|..
T Consensus       257 aeknr~a~-----------------~s~a~----------~-~-k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~  307 (549)
T KOG0147|consen  257 AEKNRAAN-----------------ASPAL----------Q-G-KGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIEN  307 (549)
T ss_pred             HHHHHHHh-----------------ccccc----------c-c-cccccchhhhhhcccccCchHHHHhhhccCccccee
Confidence            44321000                 00000          0 0 000112234999999999999999999999999999


Q ss_pred             EEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         189 VEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       189 v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      |.+++|. +|.++||+||+|.+.++|.+|++.|||.+|-|+.|+|..-....
T Consensus       308 v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  308 VQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             eeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            9999998 59999999999999999999999999999999999998754443

>KOG0131|consensus

Probab=99.94  E-value=4.2e-27  Score=205.61  Aligned_cols=170  Identities=25%  Similarity=0.344  Sum_probs=153.7

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....+|||+||+..++++.| ++|-+.|+|.+++|.+|+ +...+|||||+|.++|+|+-|++-||..++.||+|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            35679999999999999999 999999999999999998 8899999999999999999999999999999999999998


Q ss_pred             ccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCee
Q psy1534         108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVE  187 (587)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~  187 (587)
                      .....                                          ..+.+.+|||+||.+.++|..|.+.|+.||.+.
T Consensus        87 s~~~~------------------------------------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~  124 (203)
T KOG0131|consen   87 SAHQK------------------------------------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLI  124 (203)
T ss_pred             ccccc------------------------------------------cccccccccccccCcchhHHHHHHHHHhccccc
Confidence            82211                                          122346899999999999999999999999975


Q ss_pred             E-EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCC
Q psy1534         188 N-VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRL  241 (587)
Q Consensus       188 ~-v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~  241 (587)
                      . -+|+++.+ |.++||+||.|.+.|.+.+|+..+|++.++.++++|.++..+..+
T Consensus       125 ~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  125 SPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             cCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            5 48999987 999999999999999999999999999999999999999877644

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

Probab=99.94  E-value=2.3e-25  Score=237.67  Aligned_cols=194  Identities=20%  Similarity=0.228  Sum_probs=153.0

Q ss_pred             CCCCchhHHHHHHcCCCCCcccccc-CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCC-eEEEEEeeCC--CCCcceEEE
Q psy1534           2 TSPVTETELVEQIAHQDFPMFQRIE-TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGD-VTYVEILNDD--TGKPRGSAI   76 (587)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~-V~~v~i~~d~--~g~skG~aF   76 (587)
                      +++-++..|+..+++..+...+... .......+|||+|||.++++++| ++|+++++ |+++.++..+  +++++||||
T Consensus       107 ~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAF  186 (578)
T TIGR01648       107 CGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAF  186 (578)
T ss_pred             CCHHHHHHHHHHcCCCeecCCccccccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEE
Confidence            4455667778888876663221111 11234678999999999999999 88999874 5565554332  567899999


Q ss_pred             EEECCHHHHHHHHHHhCC--ceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCC
Q psy1534          77 VEFQSPDLVRKAVNKMHR--FETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGI  154 (587)
Q Consensus        77 V~F~~~e~A~~Al~~l~g--~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (587)
                      |+|.+.++|.+|++.|+.  ..+.|+.|.|.|+.++.....                                      .
T Consensus       187 VeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~--------------------------------------~  228 (578)
T TIGR01648       187 VEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDE--------------------------------------D  228 (578)
T ss_pred             EEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccc--------------------------------------c
Confidence            999999999999998864  568899999999985431100                                      0


Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhc--CCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLA--GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      .....++|||+|||+++++++|+++|++|  |.|++|.+++       +||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus       229 ~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V  301 (578)
T TIGR01648       229 VMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-------DYAFVHFEDREDAVKAMDELNGKELEGSEIEV  301 (578)
T ss_pred             ccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            11234689999999999999999999999  9999998764       59999999999999999999999999999999


Q ss_pred             EEccCCCC
Q psy1534         233 RMDRVADR  240 (587)
Q Consensus       233 ~~a~~~~~  240 (587)
                      .++++..+
T Consensus       302 ~~Akp~~~  309 (578)
T TIGR01648       302 TLAKPVDK  309 (578)
T ss_pred             EEccCCCc
Confidence            99987653

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.

>KOG0123|consensus

Probab=99.94  E-value=3.3e-25  Score=226.56  Aligned_cols=282  Identities=16%  Similarity=0.243  Sum_probs=226.6

Q ss_pred             CCCCCchhHHHHHHcCCCCCcc-ccccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEE
Q psy1534           1 MTSPVTETELVEQIAHQDFPMF-QRIETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVE   78 (587)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~   78 (587)
                      |+.|-++..|...++...+..+ .|+-....++..|||+||+.+++.++| ++|+.||+|.+|++.+|.+| +||| ||+
T Consensus        44 f~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~  121 (369)
T KOG0123|consen   44 FQQPADAERALDTMNFDVLKGKPIRIMWSQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQ  121 (369)
T ss_pred             cCCHHHHHHHHHHcCCcccCCcEEEeehhccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEE
Confidence            4677788888999888877553 333344445555999999999999999 89999999999999999999 9999 999


Q ss_pred             ECCHHHHHHHHHHhCCceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCC
Q psy1534          79 FQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPL  158 (587)
Q Consensus        79 F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (587)
                      |+++++|++|++.+||..+.+++|.|....+++.....                    ..               .....
T Consensus       122 f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~--------------------~~---------------~~~~~  166 (369)
T KOG0123|consen  122 FESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAP--------------------LG---------------EYKKR  166 (369)
T ss_pred             eCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhccc--------------------cc---------------chhhh
Confidence            99999999999999999999999999998855421100                    00               01122


Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      -+.++|.|++.+++++.|.++|..+|.|.++.++.+..+++++|+||.|.++++|..|++.|++..+.+..+.|..+..+
T Consensus       167 ~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk  246 (369)
T KOG0123|consen  167 FTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKK  246 (369)
T ss_pred             hhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999988876653


Q ss_pred             CCCCC--------------CCCCCCCcccccCCCCCCCchHHHHHHhhhccccceeEEEEeccCccceeeeeceeeeeec
Q psy1534         239 DRLDG--------------PVRLPEGLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDK  304 (587)
Q Consensus       239 ~~~~~--------------~~~~~~~~~~~g~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  304 (587)
                      .....              ....-..+...++....+.+.|+..|..++.+..                    ..+.. .
T Consensus       247 ~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s--------------------~kv~~-~  305 (369)
T KOG0123|consen  247 SEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITS--------------------AKVMV-D  305 (369)
T ss_pred             hhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceee--------------------EEEEe-c
Confidence            22111              0112234455677778888999999988887632                    12222 3


Q ss_pred             CCCCCCc-eeEecCCCCCCHHHHHHHHhcCCCCCCCCCCCC
Q psy1534         305 SSDENDA-ASVNTASKTDSTNAEKDKIGNLPNMNTNPTPTA  344 (587)
Q Consensus       305 ~~~~~~~-~fv~~~~~~~~~~~~~~ai~~l~g~~~~g~~~~  344 (587)
                      ..+.+.+ +||.    |++++++.+|+..+++..+.++++.
T Consensus       306 ~~g~skG~gfV~----fs~~eeA~~A~~~~n~~~i~~k~l~  342 (369)
T KOG0123|consen  306 ENGKSKGFGFVE----FSSPEEAKKAMTEMNGRLIGGKPLY  342 (369)
T ss_pred             cCCCccceEEEE----cCCHHHHHHHHHhhChhhhcCCchh
Confidence            3445555 6999    9999999999999999999999987

>KOG0105|consensus

Probab=99.94  E-value=3e-25  Score=193.81  Aligned_cols=78  Identities=23%  Similarity=0.376  Sum_probs=69.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||.++.|.||+++|.+||.|..|.|...+  ....||||+|+++.+|+.||..-+|..+.|..|+|++++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            36899999999999999999999999999999876533  2357999999999999999999999999999999988643

>KOG0117|consensus

Probab=99.93  E-value=7.7e-24  Score=208.70  Aligned_cols=190  Identities=20%  Similarity=0.252  Sum_probs=158.2

Q ss_pred             hhHHHHHHcCCCCCcccccc-CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCC-eEEEEEeeCC--CCCcceEEEEEECC
Q psy1534           7 ETELVEQIAHQDFPMFQRIE-TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGD-VTYVEILNDD--TGKPRGSAIVEFQS   81 (587)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~-V~~v~i~~d~--~g~skG~aFV~F~~   81 (587)
                      +++|+..+++.++..-+++. .-.....+|||+|||.+.++++| +.|++.++ |++|.|..++  +.++||||||+|++
T Consensus       138 Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~  217 (506)
T KOG0117|consen  138 AQEAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYES  217 (506)
T ss_pred             HHHHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeec
Confidence            46677788888774332222 22246679999999999999999 88999997 8999998886  56789999999999


Q ss_pred             HHHHHHHHHHhCC--ceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCC
Q psy1534          82 PDLVRKAVNKMHR--FETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLI  159 (587)
Q Consensus        82 ~e~A~~Al~~l~g--~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (587)
                      ...|..|.+.|-.  ..+-|..+.|.|+.++..-.                                      .......
T Consensus       218 H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~d--------------------------------------ed~ms~V  259 (506)
T KOG0117|consen  218 HRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPD--------------------------------------EDTMSKV  259 (506)
T ss_pred             chhHHHHHhhccCCceeecCCcceeeccCcccCCC--------------------------------------hhhhhhe
Confidence            9999999988765  55679999999999554210                                      0122235


Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      +.|||+||+.++|||.|+++|++||.|+.|+.++|       ||||+|.+.++|.+|++.+|+++|.|..|.|.+|++..
T Consensus       260 KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~  332 (506)
T KOG0117|consen  260 KVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVD  332 (506)
T ss_pred             eeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChh
Confidence            78999999999999999999999999999998876       99999999999999999999999999999999999876


Q ss_pred             CC
Q psy1534         240 RL  241 (587)
Q Consensus       240 ~~  241 (587)
                      ++
T Consensus       333 k~  334 (506)
T KOG0117|consen  333 KK  334 (506)
T ss_pred             hh
Confidence            44

>KOG0146|consensus

Probab=99.93  E-value=7.3e-26  Score=208.42  Aligned_cols=81  Identities=26%  Similarity=0.275  Sum_probs=75.3

Q ss_pred             CCCCCCCCCCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCC------CeEEEEECCHHHHHHHHHHhCCCcccC
Q psy1534         506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKG------DIGLVRFDSEWTAKRAIDMMDRTRIDG  579 (587)
Q Consensus       506 ~~~~~~~~~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~------g~g~v~f~~~~~a~~Ai~~l~g~~~~g  579 (587)
                      -...|++++++|+|||++||.+..+.||...|-+||.|++++|+.||      .+|||.|+++.+|+.||..|||+.|+-
T Consensus       275 ~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGM  354 (371)
T KOG0146|consen  275 LPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGM  354 (371)
T ss_pred             hhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhh
Confidence            35557899999999999999999999999999999999999997764      789999999999999999999999999


Q ss_pred             ceEEEEE
Q psy1534         580 KIIDVTF  586 (587)
Q Consensus       580 ~~i~v~~  586 (587)
                      +||+|.+
T Consensus       355 KRLKVQL  361 (371)
T KOG0146|consen  355 KRLKVQL  361 (371)
T ss_pred             hhhhhhh
Confidence            9999864

>KOG0110|consensus

Probab=99.93  E-value=9.9e-25  Score=226.69  Aligned_cols=200  Identities=22%  Similarity=0.279  Sum_probs=141.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..+.|+|+|||..+..++| ++|..||+|..|.+.  +.|   -.|+|+|.++.+|++|++.|....+...++.+.|+..
T Consensus       384 s~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G---~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~  458 (725)
T KOG0110|consen  384 SDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGG---TGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPE  458 (725)
T ss_pred             hcceeeeccCccccccHHHHHHhhcccccceeecC--ccc---ceeeeeecCccchHHHHHHhchhhhccCccccccChh
Confidence            5567999999999999999 889999999999444  444   2499999999999999999999999999999999884


Q ss_pred             ccCCCCCCC-CCCCCCCch-hhhhccC----CcccCCCCC--CChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHH
Q psy1534         110 DKGGRRNMG-GGGGVDRDL-SALLQNN----SSKFGNTYG--LSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFR  181 (587)
Q Consensus       110 ~~~~~~~~~-~~~~~~~~~-~~~~~~~----~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~  181 (587)
                      ......... .-....... ...+...    .....+...  ...... .........++|||.||+++++.++|..+|.
T Consensus       459 dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a-~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~  537 (725)
T KOG0110|consen  459 DVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLA-RVAEDEETETKLFVKNLNFDTTLEDLEDLFS  537 (725)
T ss_pred             hhccCCccccccccccccccccCcceecccccccccccCCccccccch-hhhhccccchhhhhhcCCcccchhHHHHHHH
Confidence            433211000 000000000 0000000    000000000  000000 0001112234499999999999999999999


Q ss_pred             hcCCeeEEEEeeCCCCC----cceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         182 LAGKVENVEIALDKDGK----SRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       182 ~~G~i~~v~i~~~~~g~----~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..|.|.+|.|.+.++..    +.|||||+|.++++|++|++.|+|+.|.|+.|.|+++.
T Consensus       538 k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  538 KQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            99999999998877533    45999999999999999999999999999999999987

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

Probab=99.93  E-value=1.1e-24  Score=232.70  Aligned_cols=78  Identities=27%  Similarity=0.546  Sum_probs=73.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|+|++|+. ++++|||||+|.+.++|++||+.|||..|.||+|+|.+
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            3468999999999999999999999999999999999985 99999999999999999999999999999999999973

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.

>KOG4211|consensus

Probab=99.93  E-value=1.8e-23  Score=209.15  Aligned_cols=172  Identities=23%  Similarity=0.268  Sum_probs=135.3

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ...+...-|=+++|||++|++|| ++|+-++ |+++.+.+ .+|+..|-|||+|.++|++++|++. +...+..|.|.|.
T Consensus         5 ~e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf   81 (510)
T KOG4211|consen    5 NEGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR-RNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVF   81 (510)
T ss_pred             cCCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec-cCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEE
Confidence            44556666778999999999999 8888886 67765554 4799999999999999999999976 8899999999999


Q ss_pred             ecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCC-CCCCCcEEEEecCCCCCcHHHHHHHHHhcC
Q psy1534         106 EAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGI-NCPLINKVFVANLDYKVDEKKLREVFRLAG  184 (587)
Q Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~V~nLp~~~te~~l~~~F~~~G  184 (587)
                      .+..++....-                                 ..... .......|-+++||+.||++||.+||+..-
T Consensus        82 ~~~~~e~d~~~---------------------------------~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~  128 (510)
T KOG4211|consen   82 TAGGAEADWVM---------------------------------RPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLE  128 (510)
T ss_pred             ccCCccccccc---------------------------------cCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCc
Confidence            98744321100                                 00000 112345899999999999999999999874


Q ss_pred             CeeE-EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         185 KVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       185 ~i~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .|.. |.++.++.+++.|.|||.|++.+.|++|+.. |...|.-|-|.|-.+
T Consensus       129 Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  129 IVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             ccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            4433 5677788899999999999999999999976 778888888888653

>KOG0109|consensus

Probab=99.92  E-value=4.3e-25  Score=206.22  Aligned_cols=151  Identities=21%  Similarity=0.356  Sum_probs=140.2

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      ..+|||+|||.++++.+| .+|++||+|.+|.|+++       ||||+.++...|+.||+.||+.+|+|..|.|+.++.+
T Consensus         2 ~~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    2 PVKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             ccchhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            468999999999999999 78999999999999975       9999999999999999999999999999999998855


Q ss_pred             cCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEE
Q psy1534         111 KGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVE  190 (587)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~  190 (587)
                      ..                                             .+++|+|+||.+.++.++|+..|++||.|.+|+
T Consensus        75 sk---------------------------------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecd  109 (346)
T KOG0109|consen   75 SK---------------------------------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECD  109 (346)
T ss_pred             CC---------------------------------------------CccccccCCCCccccCHHHhhhhcccCCceeee
Confidence            21                                             246899999999999999999999999999999


Q ss_pred             EeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCC
Q psy1534         191 IALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRL  241 (587)
Q Consensus       191 i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~  241 (587)
                      |++|       |+||.|+-.++|..|++.|+++++.|++++|.++..+-+.
T Consensus       110 ivkd-------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrt  153 (346)
T KOG0109|consen  110 IVKD-------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT  153 (346)
T ss_pred             eecc-------eeEEEEeeccchHHHHhcccccccccceeeeeeecccccc
Confidence            9975       9999999999999999999999999999999998777643

>KOG0145|consensus

Probab=99.92  E-value=4.6e-24  Score=195.89  Aligned_cols=235  Identities=20%  Similarity=0.197  Sum_probs=170.4

Q ss_pred             CCCchhHHHHHHcCCCCCcc------ccccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceE
Q psy1534           3 SPVTETELVEQIAHQDFPMF------QRIETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGS   74 (587)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~   74 (587)
                      +|-++..|++.+++-.+..+      -|-.+..-...+|||++||..+|..|| .+|++||.|..-+|+.|. +|.+||.
T Consensus        92 ~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGV  171 (360)
T KOG0145|consen   92 RPKDAEKAINTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGV  171 (360)
T ss_pred             ChHHHHHHHhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecce
Confidence            56677777887777655332      122233345568999999999999999 689999999999999997 9999999


Q ss_pred             EEEEECCHHHHHHHHHHhCCceeCC--eEEEEEecccccCCCCC--------CCCCCC-CCC----chhhhhccCCcccC
Q psy1534          75 AIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKEAVEDKGGRRN--------MGGGGG-VDR----DLSALLQNNSSKFG  139 (587)
Q Consensus        75 aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~a~~~~~~~~~--------~~~~~~-~~~----~~~~~~~~~~~~~~  139 (587)
                      +||.|...++|+.||+.|||.+-.|  .+|.|+++........-        ....+. +..    ...... .......
T Consensus       172 gFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~-~~~~~~~  250 (360)
T KOG0145|consen  172 GFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLD-NLLNPHA  250 (360)
T ss_pred             eEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccc-cccchhh
Confidence            9999999999999999999987665  78999998843221110        000000 000    000000 0000000


Q ss_pred             CCCCCChhh---h-----hccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCH
Q psy1534         140 NTYGLSPQF---L-----ESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP  210 (587)
Q Consensus       140 ~~~~~~~~~---~-----~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~  210 (587)
                      .....+|..   +     ...........+|||-||.++.+|.-|.++|.+||.|..|+|++|.+ .+++||+||.+.+.
T Consensus       251 ~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNY  330 (360)
T KOG0145|consen  251 AQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNY  330 (360)
T ss_pred             hhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecch
Confidence            000000000   0     01111233468999999999999999999999999999999999997 99999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         211 VEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       211 ~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      ++|..||..|||..+.+|.|.|.+...+
T Consensus       331 dEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  331 DEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             HHHHHHHHHhcCccccceEEEEEEecCC
Confidence            9999999999999999999999997654

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

Probab=99.92  E-value=1.3e-23  Score=229.83  Aligned_cols=191  Identities=18%  Similarity=0.176  Sum_probs=147.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+|||+|||+++++++| ++|++||+|..|.|+++. +|.++|||||+|.+.++|.+|++.|||..|.|++|.|+++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            4578999999999999999 899999999999999996 99999999999999999999999999999999999999987


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhh-ccCCCCCCCcEEEEecCCCC--C--------cHHHHH
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLE-SLGINCPLINKVFVANLDYK--V--------DEKKLR  177 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~V~nLp~~--~--------te~~l~  177 (587)
                      .........         ....    .....   ........ .......++++|+|.||...  +        ..++|+
T Consensus       374 ~~~~~~~~~---------~~~~----~~~~~---~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~  437 (509)
T TIGR01642       374 VGANQATID---------TSNG----MAPVT---LLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVK  437 (509)
T ss_pred             cCCCCCCcc---------cccc----ccccc---cccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHH
Confidence            332111000         0000    00000   00000000 00112345789999999642  1        236899


Q ss_pred             HHHHhcCCeeEEEEeeCC-C---CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         178 EVFRLAGKVENVEIALDK-D---GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       178 ~~F~~~G~i~~v~i~~~~-~---g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ++|++||.|+.|.|+++. +   +...|++||+|.+.++|++||..|||..|.|+.|.|.|...
T Consensus       438 ~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       438 TEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            999999999999999863 2   45679999999999999999999999999999999998654

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

>KOG0127|consensus

Probab=99.91  E-value=2.1e-23  Score=209.94  Aligned_cols=208  Identities=22%  Similarity=0.256  Sum_probs=152.8

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      .-+|.|+|||+.+...+| .+|+.||.|.+|.|++.++|+..|||||+|....+|.+|++.+|+..|.||+|-|.|+..+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            568999999999999999 7899999999999998887777799999999999999999999999999999999999833


Q ss_pred             cC-CCCC---------------------CCCCCCCCCchhhhhccCC-------------------cccCC--CCCCChh
Q psy1534         111 KG-GRRN---------------------MGGGGGVDRDLSALLQNNS-------------------SKFGN--TYGLSPQ  147 (587)
Q Consensus       111 ~~-~~~~---------------------~~~~~~~~~~~~~~~~~~~-------------------~~~~~--~~~~~~~  147 (587)
                      .. ....                     ..+......+.........                   .....  +....+.
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence            21 1100                     0000000000000000000                   00000  0000000


Q ss_pred             ----hhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHh--
Q psy1534         148 ----FLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML--  220 (587)
Q Consensus       148 ----~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l--  220 (587)
                          +.........-..+|||+|||+++||++|.+.|++||+|.++.|+.++. ++++|.|||.|.+..+|++||+.-  
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Asp  356 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASP  356 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCc
Confidence                0000111223358999999999999999999999999999999999996 999999999999999999999876  


Q ss_pred             ---CC-ceeCCeEEEEEEccCCC
Q psy1534         221 ---NN-QNLFERRITVRMDRVAD  239 (587)
Q Consensus       221 ---~g-~~~~g~~l~v~~a~~~~  239 (587)
                         .+ ..|.||.|.|..+-.+.
T Consensus       357 a~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  357 ASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             cCCCceEEEeccEEeeeeccchH
Confidence               23 67889999999886654

>KOG0146|consensus

Probab=99.90  E-value=1.2e-23  Score=193.80  Aligned_cols=209  Identities=23%  Similarity=0.378  Sum_probs=158.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC-ceeCC--eEEEEEe
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR-FETKG--RKLVIKE  106 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g-~~l~g--r~i~V~~  106 (587)
                      +.++|||+-|...-.|+|+ .+|..||+|++|.+++.++|.+||||||.|.+.-+|..||..|+| ..+-|  ..|.|++
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            6689999999999999998 899999999999999999999999999999999999999999999 44544  7899999


Q ss_pred             cccccCC--CCC--------------------------------------------------------------------
Q psy1534         107 AVEDKGG--RRN--------------------------------------------------------------------  116 (587)
Q Consensus       107 a~~~~~~--~~~--------------------------------------------------------------------  116 (587)
                      ++.++..  |+-                                                                    
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A~  177 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAAA  177 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccccC
Confidence            8843321  110                                                                    


Q ss_pred             -----C-C-CCCCC---CC----------chhhhhcc-------------------------------------------
Q psy1534         117 -----M-G-GGGGV---DR----------DLSALLQN-------------------------------------------  133 (587)
Q Consensus       117 -----~-~-~~~~~---~~----------~~~~~~~~-------------------------------------------  133 (587)
                           . . ....-   ..          ......+.                                           
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence                 0 0 00000   00          00000000                                           


Q ss_pred             --CCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCH
Q psy1534         134 --NSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP  210 (587)
Q Consensus       134 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~  210 (587)
                        ........+..++........+.+.+|+|||-.||.+..+.||.+.|-+||.|++.++..|+. +.+|+|+||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence              000000000111111222223567899999999999999999999999999999999999994 99999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         211 VEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       211 ~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      .+|+.||..|||..|+-++|+|.+.+++.
T Consensus       338 ~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            99999999999999999999999988875

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

Probab=99.89  E-value=1.3e-21  Score=211.04  Aligned_cols=205  Identities=16%  Similarity=0.154  Sum_probs=145.7

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+|||+|||.++++++| ++|++||.|..|.|++++ +|+++|||||+|.+.++|.+|++.|||..|.|++|.|.++.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            3578999999999999999 899999999999999997 78999999999999999999999999999999999999976


Q ss_pred             cccCCCCC--------C--CCCCC-CCCchhhh---------------hccC-----CcccCCC-------------CCC
Q psy1534         109 EDKGGRRN--------M--GGGGG-VDRDLSAL---------------LQNN-----SSKFGNT-------------YGL  144 (587)
Q Consensus       109 ~~~~~~~~--------~--~~~~~-~~~~~~~~---------------~~~~-----~~~~~~~-------------~~~  144 (587)
                      ........        .  ..+.. ........               +...     ...+...             ...
T Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (457)
T TIGR01622       265 DSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGAL  344 (457)
T ss_pred             CCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccccccccc
Confidence            22111000        0  00000 00000000               0000     0000000             000


Q ss_pred             Chhhhh---ccCCCCCCCcEEEEecCCCCCc----------HHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHH
Q psy1534         145 SPQFLE---SLGINCPLINKVFVANLDYKVD----------EKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPV  211 (587)
Q Consensus       145 ~~~~~~---~~~~~~~~~~~l~V~nLp~~~t----------e~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~  211 (587)
                      ......   .......+.++|+|.||....+          .+||++.|++||.|++|.|...   ...|++||+|.+.+
T Consensus       345 ~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~---~~~G~~fV~F~~~e  421 (457)
T TIGR01622       345 AIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK---NSAGKIYLKFSSVD  421 (457)
T ss_pred             ccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC---CCceeEEEEECCHH
Confidence            000000   0000235678999999955433          3689999999999999998743   35799999999999


Q ss_pred             HHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         212 EAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       212 ~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      +|.+|++.|||+.|.|+.|.|.+....
T Consensus       422 ~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       422 AALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             HHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            999999999999999999999986543

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0144|consensus

Probab=99.88  E-value=2.6e-22  Score=196.94  Aligned_cols=210  Identities=20%  Similarity=0.321  Sum_probs=157.3

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC-ceeCC--eEEEEE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR-FETKG--RKLVIK  105 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g-~~l~g--r~i~V~  105 (587)
                      +.+++|||+-|+..++|.|+ ++|++||.|++|.|++|+.+.|||||||+|.+.|.|..||+.||+ .++.|  .+|.|+
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            56889999999999999999 899999999999999999999999999999999999999999999 44554  899999


Q ss_pred             ecccccCCCCC-------------CCCC--------------------------CC---C------CCc-----------
Q psy1534         106 EAVEDKGGRRN-------------MGGG--------------------------GG---V------DRD-----------  126 (587)
Q Consensus       106 ~a~~~~~~~~~-------------~~~~--------------------------~~---~------~~~-----------  126 (587)
                      +++.++.+..+             +++.                          ..   .      ...           
T Consensus       202 FADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~  281 (510)
T KOG0144|consen  202 FADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALA  281 (510)
T ss_pred             ecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhh
Confidence            99944322110             0000                          00   0      000           


Q ss_pred             --------------h------hh-----hhcc---------------------------CCcccC-------CC------
Q psy1534         127 --------------L------SA-----LLQN---------------------------NSSKFG-------NT------  141 (587)
Q Consensus       127 --------------~------~~-----~~~~---------------------------~~~~~~-------~~------  141 (587)
                                    .      ..     .+..                           .+..+.       ..      
T Consensus       282 ~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~a  361 (510)
T KOG0144|consen  282 AAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVA  361 (510)
T ss_pred             hhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCccc
Confidence                          0      00     0000                           000000       00      


Q ss_pred             --------CCCChhh-------------------------------------hhccCCCCCCCcEEEEecCCCCCcHHHH
Q psy1534         142 --------YGLSPQF-------------------------------------LESLGINCPLINKVFVANLDYKVDEKKL  176 (587)
Q Consensus       142 --------~~~~~~~-------------------------------------~~~~~~~~~~~~~l~V~nLp~~~te~~l  176 (587)
                              .+..+..                                     ......+.+.+..|||.+||.+.-+.||
T Consensus       362 a~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~l  441 (510)
T KOG0144|consen  362 ASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQDL  441 (510)
T ss_pred             ccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHHH
Confidence                    0000000                                     0000113567889999999999999999


Q ss_pred             HHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         177 REVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       177 ~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      -..|..||.|++.++..|+ ++-++.|+||.|++..+|.+||..|||..|..++++|...+.+.
T Consensus       442 ~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~  505 (510)
T KOG0144|consen  442 IATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRN  505 (510)
T ss_pred             HHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccC
Confidence            9999999999999999998 59999999999999999999999999999999999999887665

>KOG0110|consensus

Probab=99.87  E-value=6.4e-22  Score=205.91  Aligned_cols=175  Identities=23%  Similarity=0.388  Sum_probs=148.9

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCC----CcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTG----KPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g----~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      .+.+|||+||++++|.++| .+|.+.|.|.+|.|.+.++.    .|.|||||+|.++++|+.|++.|+|+.|.|+.|.|+
T Consensus       514 ~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  514 TETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             cchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEE
Confidence            3445999999999999999 78999999999998877644    366999999999999999999999999999999999


Q ss_pred             ecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC
Q psy1534         106 EAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK  185 (587)
Q Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~  185 (587)
                      ++..+.....                       +           .........++|+|+|||+..+..+++++|..||.
T Consensus       594 ~S~~k~~~~~-----------------------g-----------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGq  639 (725)
T KOG0110|consen  594 ISENKPASTV-----------------------G-----------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQ  639 (725)
T ss_pred             eccCcccccc-----------------------c-----------cccccccccceeeeeccchHHHHHHHHHHHhcccc
Confidence            9982221000                       0           00001122579999999999999999999999999


Q ss_pred             eeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         186 VENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       186 i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      |.+|+|++... +-++|||||+|-++.+|.+|++.|..+.++||.|.++|+....
T Consensus       640 lksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  640 LKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             eeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            99999998743 7789999999999999999999999999999999999987664

>KOG4205|consensus

Probab=99.86  E-value=1e-21  Score=193.56  Aligned_cols=175  Identities=23%  Similarity=0.344  Sum_probs=152.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+|||++|+++++++.| ++|+.||+|.+|.+++|+ +++++||+||+|++++...+++.. ..+.|.++.|.++.+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            6789999999999999999 889999999999999998 999999999999999999999954 6788999999999998


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      +.......                                     .......+|||+.||.++++++++++|++||.|..
T Consensus        84 ~r~~~~~~-------------------------------------~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~  126 (311)
T KOG4205|consen   84 SREDQTKV-------------------------------------GRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVAD  126 (311)
T ss_pred             Cccccccc-------------------------------------ccccceeEEEecCcCCCCchHHHhhhhhccceeEe
Confidence            54321110                                     01113679999999999999999999999999999


Q ss_pred             EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCCCC
Q psy1534         189 VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRLDGP  244 (587)
Q Consensus       189 v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~~~~  244 (587)
                      +.++.|.+ .+++||+||.|.+++.+++++. ..-+.|+++.+.|+.|.++......
T Consensus       127 ~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~~~  182 (311)
T KOG4205|consen  127 VVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQST  182 (311)
T ss_pred             eEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhcccc
Confidence            99999986 9999999999999999999885 4788999999999999888754433

>KOG0109|consensus

Probab=99.85  E-value=6.1e-21  Score=178.54  Aligned_cols=68  Identities=35%  Similarity=0.470  Sum_probs=65.5

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .+|+|.||.+.++-+||+..|.+||.|+.|+|.++  ++||.|+-.++|..||+.||+.+|.|+++.|.+
T Consensus        79 tkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   79 TKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             cccccCCCCccccCHHHhhhhcccCCceeeeeecc--eeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            38999999999999999999999999999999988  999999999999999999999999999999975

>KOG0105|consensus

Probab=99.83  E-value=2e-19  Score=157.56  Aligned_cols=174  Identities=22%  Similarity=0.311  Sum_probs=135.6

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ...+|||+|||.++.+.|| ++|.+||.|.+|.|...+ + ...||||+|+++.+|+.||..-+|..+.|..|+|+++.-
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~-g-~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP-G-PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC-C-CCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            5678999999999999999 789999999999876432 2 247999999999999999999999999999999999882


Q ss_pred             ccC--CCCC---CCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcC
Q psy1534         110 DKG--GRRN---MGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAG  184 (587)
Q Consensus       110 ~~~--~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G  184 (587)
                      -..  .+..   +++..+........++....+                      ..|.|.+||.+.+|+||++...+.|
T Consensus        83 gr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe----------------------~RVvVsGLp~SgSWQDLKDHmReaG  140 (241)
T KOG0105|consen   83 GRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSE----------------------YRVVVSGLPPSGSWQDLKDHMREAG  140 (241)
T ss_pred             CCcccccccccCCCCCCCCCCCcccCCcccccc----------------------eeEEEecCCCCCchHHHHHHHHhhC
Confidence            221  1111   111111222222223333333                      4899999999999999999999999


Q ss_pred             CeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEEE
Q psy1534         185 KVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF--ERRITVRM  234 (587)
Q Consensus       185 ~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~~  234 (587)
                      .|....+.+|      |++.|+|...|+.+-|+..|+...+.  |....+.+
T Consensus       141 dvCfadv~rD------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  141 DVCFADVQRD------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             Ceeeeeeecc------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            9999999886      58999999999999999999887764  55544444

>KOG1190|consensus

Probab=99.82  E-value=1.1e-18  Score=170.41  Aligned_cols=198  Identities=17%  Similarity=0.122  Sum_probs=130.8

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR--FETKGRKLVI  104 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g--~~l~gr~i~V  104 (587)
                      .....+-|.++|||++++|+|| +++.+||+|+.+.+++-     +..||++|.+.++|..-+.....  -.+.+++|.|
T Consensus        24 ~~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkG-----knQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yi   98 (492)
T KOG1190|consen   24 MAEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKG-----KNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYI   98 (492)
T ss_pred             ccCCcceeEeccCCccccHHHHHHhcccccceeeeeeecc-----chhhhhhhcchhhhhheeecccccCccccCcceee
Confidence            3446677899999999999998 99999999999988875     45899999999999885543332  4467999999


Q ss_pred             EecccccCCCCCCCC-CCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhc
Q psy1534         105 KEAVEDKGGRRNMGG-GGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLA  183 (587)
Q Consensus       105 ~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~  183 (587)
                      +++............ .++. ...   ...........................+--+++|.|+-+-++-+-|.++|++|
T Consensus        99 q~sn~~~lkt~s~p~q~r~~-~vy---~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~f  174 (492)
T KOG1190|consen   99 QYSNHSELKTDSQPNQIRGQ-AVY---QAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKF  174 (492)
T ss_pred             hhhhHHHHhccCchhhhhhh-hHH---hhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhc
Confidence            998743322111000 0000 000   00000000000000000011111122234567899999999999999999999


Q ss_pred             CCeeEEEEeeCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         184 GKVENVEIALDKDGKSRGF-GTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       184 G~i~~v~i~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      |.|.+|.-....    .+| |.|.|.+.+.|..|...|+|+.|..-.+.+++...+
T Consensus       175 G~VlKIiTF~Kn----n~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  175 GFVLKIITFTKN----NGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             ceeEEEEEEecc----cchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            999888655432    344 899999999999999999999998665566555444

>KOG0131|consensus

Probab=99.81  E-value=2.1e-19  Score=157.61  Aligned_cols=79  Identities=37%  Similarity=0.491  Sum_probs=74.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ...+|||+||+..++++-|.++|-+.|.|++++|++|+. ..++|||||+|.++|+|+-||+.||..++.||+|+|+.+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            457999999999999999999999999999999999995 7899999999999999999999999999999999998765

>KOG4211|consensus

Probab=99.79  E-value=1.7e-17  Score=166.59  Aligned_cols=149  Identities=17%  Similarity=0.130  Sum_probs=112.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ....|-+++|||++|++||.+||+.+ .|+++.+.+. +|++.|-|||+|.+.|++++|+++ +...+..|.|.|-.+..
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR-NGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGG   85 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc-CCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCC
Confidence            34578899999999999999999999 5888666553 589999999999999999999965 88888999999988766


Q ss_pred             CCCCCCCCCCC------C-CcccccCCCCCCCchHHHHHHhhhccccceeEEEEeccCccceeeeeceeeeeecCCCCCC
Q psy1534         238 ADRLDGPVRLP------E-GLKSIGMGLGANGAPLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDEND  310 (587)
Q Consensus       238 ~~~~~~~~~~~------~-~~~~~g~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  310 (587)
                      .+.....++..      . -++-+|||++|+++++.++|..|..+..  -+.                  ...+...++.
T Consensus        86 ~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~--gi~------------------l~~d~rgR~t  145 (510)
T KOG4211|consen   86 AEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPD--GIL------------------LPMDQRGRPT  145 (510)
T ss_pred             ccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCccccc--cee------------------eeccCCCCcc
Confidence            65433222221      1 1234899999999999999988766422  000                  1223344455


Q ss_pred             c-eeEecCCCCCCHHHHHHHHhcC
Q psy1534         311 A-ASVNTASKTDSTNAEKDKIGNL  333 (587)
Q Consensus       311 ~-~fv~~~~~~~~~~~~~~ai~~l  333 (587)
                      + +||.    |.+.+.+++|++..
T Consensus       146 GEAfVq----F~sqe~ae~Al~rh  165 (510)
T KOG4211|consen  146 GEAFVQ----FESQESAEIALGRH  165 (510)
T ss_pred             cceEEE----ecCHHHHHHHHHHH
Confidence            5 6999    88888999998743

>KOG1190|consensus

Probab=99.77  E-value=1e-16  Score=156.87  Aligned_cols=195  Identities=17%  Similarity=0.236  Sum_probs=136.1

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEecc--
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKEAV--  108 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~a~--  108 (587)
                      +++|.++-+.++.+.| .+|++||.|..|.-.....+   -.|+|+|.+.+.|+.|...|+|+.|..  ..|+|.++.  
T Consensus       152 r~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~---FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt  228 (492)
T KOG1190|consen  152 RTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNG---FQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLT  228 (492)
T ss_pred             EEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccc---hhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcc
Confidence            6889999999999999 88999999999866654333   359999999999999999999998875  566666665  


Q ss_pred             --------cc--cCCCCCCCCCCCCCCchhhhhccCCcccC-------CCCCCCh----hhhhccCCCCC-CCcEEEEec
Q psy1534         109 --------ED--KGGRRNMGGGGGVDRDLSALLQNNSSKFG-------NTYGLSP----QFLESLGINCP-LINKVFVAN  166 (587)
Q Consensus       109 --------~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~----~~~~~~~~~~~-~~~~l~V~n  166 (587)
                              .+  .+.++.-..+.+..    .........+.       .....+.    .....-....+ ..+.|-|.|
T Consensus       229 ~LnvKynndkSRDyTnp~LP~gd~~p----~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsn  304 (492)
T KOG1190|consen  229 DLNVKYNNDKSRDYTNPDLPVGDGQP----SLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSN  304 (492)
T ss_pred             cceeeccccccccccCCCCCCCcccc----ccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEec
Confidence                    11  11111111110000    00000000110       0011111    11111011111 258899999


Q ss_pred             CCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         167 LDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       167 Lp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      |.. .+|++.|..+|.-||+|.+|+|+.++    +--|.|.|.+...|+-|++.|+|+.|.|++|+|.+++...
T Consensus       305 ln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  305 LNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             CchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            976 59999999999999999999999876    3469999999999999999999999999999999987665

>KOG0124|consensus

Probab=99.77  E-value=2.1e-18  Score=165.72  Aligned_cols=75  Identities=28%  Similarity=0.562  Sum_probs=72.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      -|+|||+.|.+.+.|+.|+..|.+||.|.+|.+-+|+ +++++|||||+|+-+|.|+-|++.|||..++||.|+|.
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            5899999999999999999999999999999999999 49999999999999999999999999999999999986

>KOG0147|consensus

Probab=99.77  E-value=3.7e-18  Score=173.58  Aligned_cols=199  Identities=17%  Similarity=0.212  Sum_probs=138.2

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccccc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK  111 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~  111 (587)
                      +|||+||..++++++| .+|+.||.|+.|.+.+|. ||++|||+||+|.+.++|++|++.|||.+|.||.|+|.....+.
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            3999999999999999 789999999999999996 99999999999999999999999999999999999998876222


Q ss_pred             CCCC--------C----CCCC--CCC-CCchhhhhccCCcccCCCC--------CCChhhhhc------cCCCC------
Q psy1534         112 GGRR--------N----MGGG--GGV-DRDLSALLQNNSSKFGNTY--------GLSPQFLES------LGINC------  156 (587)
Q Consensus       112 ~~~~--------~----~~~~--~~~-~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~------~~~~~------  156 (587)
                      ....        +    .+-.  .++ ....+...+......-.+.        .+.......      ...+.      
T Consensus       360 ~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~  439 (549)
T KOG0147|consen  360 DTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAF  439 (549)
T ss_pred             ccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcccccccc
Confidence            1110        0    0000  000 0011111110000000000        000000000      00111      


Q ss_pred             -CCCcEEEEecC--CCCCcH--------HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy1534         157 -PLINKVFVANL--DYKVDE--------KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL  225 (587)
Q Consensus       157 -~~~~~l~V~nL--p~~~te--------~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  225 (587)
                       .++.++.+.|+  |...|+        +|+.+.|.+||.|.+|.+-+.    +-|+.||.|.+.+.|..|+.+|||++|
T Consensus       440 ~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n----s~g~VYvrc~s~~~A~~a~~alhgrWF  515 (549)
T KOG0147|consen  440 DIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN----SAGCVYVRCPSAEAAGTAVKALHGRWF  515 (549)
T ss_pred             CCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC----CCceEEEecCcHHHHHHHHHHHhhhhh
Confidence             44556667776  222222        688899999999999888664    349999999999999999999999999


Q ss_pred             CCeEEEEEEcc
Q psy1534         226 FERRITVRMDR  236 (587)
Q Consensus       226 ~g~~l~v~~a~  236 (587)
                      .|+.|+++|-.
T Consensus       516 ~gr~Ita~~~~  526 (549)
T KOG0147|consen  516 AGRMITAKYLP  526 (549)
T ss_pred             ccceeEEEEee
Confidence            99999999853

>KOG4206|consensus

Probab=99.74  E-value=9.6e-17  Score=146.93  Aligned_cols=194  Identities=18%  Similarity=0.254  Sum_probs=143.9

Q ss_pred             cEEEcCCCCCCCHHHH-H----hcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          34 PVVMDLIQGDASLYQI-S----HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~----~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +|||.||...+..++| +    +|++||+|.+|...+  +.+.||.|||.|.+.+.|..|++.|+|..|.|++++|+++.
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            9999999999999988 3    799999999987654  56789999999999999999999999999999999999998


Q ss_pred             cccCC--CCCC------CCCCCCCCchhhhhccCCcccC--CCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHH
Q psy1534         109 EDKGG--RRNM------GGGGGVDRDLSALLQNNSSKFG--NTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLRE  178 (587)
Q Consensus       109 ~~~~~--~~~~------~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~  178 (587)
                      .+..-  +..+      .....+.......+......+.  .....++++   .....++...||+.|||..++.+.|..
T Consensus        89 s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~---~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   89 SDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPF---LAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             CccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCc---cccCCCCceEEEEecCCcchhHHHHHH
Confidence            44321  1110      0000000000000000001110  111122222   133567889999999999999999999


Q ss_pred             HHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEEcc
Q psy1534         179 VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF-ERRITVRMDR  236 (587)
Q Consensus       179 ~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~a~  236 (587)
                      +|..|....+|+++...    ++.|||+|.+...|..|...+.+..|. ...+.|.+++
T Consensus       166 lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999999888754    679999999999999999999998886 7778777654

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

Probab=99.73  E-value=3.8e-17  Score=145.77  Aligned_cols=93  Identities=18%  Similarity=0.314  Sum_probs=82.2

Q ss_pred             CccccccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCcee
Q psy1534          20 PMFQRIETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFET   97 (587)
Q Consensus        20 ~~~~~~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l   97 (587)
                      |......+......+|||+|||+++++++| ++|++||+|++|+|++|+ ++++||||||+|.+.++|++|++.||+..|
T Consensus        22 ~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i  101 (144)
T PLN03134         22 PVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKEL  101 (144)
T ss_pred             ccccccccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            333334444556779999999999999999 899999999999999997 999999999999999999999999999999


Q ss_pred             CCeEEEEEecccccC
Q psy1534          98 KGRKLVIKEAVEDKG  112 (587)
Q Consensus        98 ~gr~i~V~~a~~~~~  112 (587)
                      .|++|+|.++..+..
T Consensus       102 ~Gr~l~V~~a~~~~~  116 (144)
T PLN03134        102 NGRHIRVNPANDRPS  116 (144)
T ss_pred             CCEEEEEEeCCcCCC
Confidence            999999999985543

>KOG4307|consensus

Probab=99.70  E-value=1e-15  Score=158.38  Aligned_cols=182  Identities=12%  Similarity=0.051  Sum_probs=110.0

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEE-EEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTY-VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...-|||..||..+++.++ ++|.+--.|++ |.|-+.++++-++.|||+|..++++.+|...-+.+.++.|.|+|....
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            4457999999999999988 89998888888 767677899999999999999999999987666777888999999876


Q ss_pred             cccC-CCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhh-ccCCCCCCCcEEEEecCC-CCCcHHHHHHHHHhcCC
Q psy1534         109 EDKG-GRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLE-SLGINCPLINKVFVANLD-YKVDEKKLREVFRLAGK  185 (587)
Q Consensus       109 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~V~nLp-~~~te~~l~~~F~~~G~  185 (587)
                      ++.. .+..       ............++.       +..+. ..........+-.+.+.+ ++.+.-+.+.+-.  +.
T Consensus       513 ~~~m~~ek~-------~~~~~~lq~~~~dqr-------e~~l~~p~~~v~~~~~~~~~~~~~~F~~~~rr~~~e~~--~~  576 (944)
T KOG4307|consen  513 DYAMMMEKN-------GEQGIKLQQSDKDQR-------ETALDGPIPSVSMVPSKEQRSHEDDFDKKSRRSRWENT--SP  576 (944)
T ss_pred             hHHHHHHHh-------HHHHHHHhhhhhHHH-------HHhhcCCccchhhhhhhhhhccCcccccchHHHHhhhc--CC
Confidence            3322 0000       000000000000000       00000 000000001122344555 4666555554433  23


Q ss_pred             ee---EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeE
Q psy1534         186 VE---NVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR  229 (587)
Q Consensus       186 i~---~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  229 (587)
                      +.   .+.+.+|..+++++-+||.|.+...+.+-+. ++-..+.+++
T Consensus       577 ~~~~n~~p~~~dN~~~~~~~~~v~~~n~p~~r~~~~-~~~~~vnn~p  622 (944)
T KOG4307|consen  577 IRSPNRSPLRRDNRDRSRSRSPVRRRNSPRRREEHT-RWCVQVNNVP  622 (944)
T ss_pred             ccCccccccccccCCcccccCccccCCCccccchhh-hhhhcccCcc
Confidence            32   3456667668888889999998777766552 2334444444

>KOG1456|consensus

Probab=99.70  E-value=1.2e-14  Score=140.73  Aligned_cols=165  Identities=18%  Similarity=0.240  Sum_probs=128.0

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHH--HhCCceeCCeEEEEEe
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVN--KMHRFETKGRKLVIKE  106 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~--~l~g~~l~gr~i~V~~  106 (587)
                      +...-|.|++|-..++|.+| +..+.||+|..|..+..     +..|.|+|++.+.|+.|+.  +-+...+.|+.-.+.+
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~-----~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~Ny  103 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH-----KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNY  103 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc-----cceeeeeeccccchhhheehhccCcccccCchhhccc
Confidence            34556899999999999999 89999999999988764     5689999999999999984  2234667888888888


Q ss_pred             cccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEE--EecCCCCCcHHHHHHHHHhcC
Q psy1534         107 AVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVF--VANLDYKVDEKKLREVFRLAG  184 (587)
Q Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--V~nLp~~~te~~l~~~F~~~G  184 (587)
                      +..+...|..                                    .++..+.+.|.  |-|--+.+|-+-|..++...|
T Consensus       104 Stsq~i~R~g------------------------------------~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~G  147 (494)
T KOG1456|consen  104 STSQCIERPG------------------------------------DESATPNKVLLFTILNPQYPITVDVLYTICNPQG  147 (494)
T ss_pred             chhhhhccCC------------------------------------CCCCCCCeEEEEEeecCccccchhhhhhhcCCCC
Confidence            8755443321                                    00112233444  345456799999999999999


Q ss_pred             CeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEccCCC
Q psy1534         185 KVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMDRVAD  239 (587)
Q Consensus       185 ~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a~~~~  239 (587)
                      +|.+|.|++. +|   --|.|+|++.+.|++|...|||..|+.  ++|+|++|++..
T Consensus       148 kVlRIvIfkk-ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  148 KVLRIVIFKK-NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             ceEEEEEEec-cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            9999999985 22   259999999999999999999999873  567788877654

>KOG1548|consensus

Probab=99.70  E-value=6.3e-16  Score=148.65  Aligned_cols=199  Identities=20%  Similarity=0.234  Sum_probs=144.1

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEE--------EEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTY--------VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~--------v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      ..|||.|||.++|.+++ ++|++||-|..        |+|.++..|..||-|+|.|...|+++.|++.|++..|.|+.|+
T Consensus       135 t~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~r  214 (382)
T KOG1548|consen  135 TSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKLR  214 (382)
T ss_pred             ceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEEE
Confidence            35999999999999999 89999998874        8999999999999999999999999999999999999999999


Q ss_pred             EEecccccCCCCCCCCCC-CCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCC----CCCc------
Q psy1534         104 IKEAVEDKGGRRNMGGGG-GVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLD----YKVD------  172 (587)
Q Consensus       104 V~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp----~~~t------  172 (587)
                      |+.|.-...+...-.... +..............    .+++.+...  ........++|.+.|+=    ...+      
T Consensus       215 VerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k----~~dw~pd~~--~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~d  288 (382)
T KOG1548|consen  215 VERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQK----LLDWRPDRD--DPSKARADRTVILKNMFTPEDFEKNPDLLND  288 (382)
T ss_pred             EehhhhhhccCcCcccccccccccHHHHHHHHHh----hcccCCCcc--ccccccCCcEEEeeecCCHHHhccCHHHHHH
Confidence            999982222111100000 000111111100001    111111110  01122346789999972    1223      


Q ss_pred             -HHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q psy1534         173 -EKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADR  240 (587)
Q Consensus       173 -e~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~  240 (587)
                       .++|++-+++||.|.+|.|.-.   .+.|.+-|.|.+.++|..||+.|+|+.+.||.|...+...+.+
T Consensus       289 lkedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t~  354 (382)
T KOG1548|consen  289 LKEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKTK  354 (382)
T ss_pred             HHHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcce
Confidence             3678888999999999987643   3578999999999999999999999999999999998766653

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

Probab=99.69  E-value=6.8e-16  Score=137.75  Aligned_cols=85  Identities=29%  Similarity=0.524  Sum_probs=79.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||++++|++|+++|++||.|.+|.|++|+. ++++|||||+|.+.++|++||+.||++.|.|++|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34567999999999999999999999999999999999985 99999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      +..+..
T Consensus       111 a~~~~~  116 (144)
T PLN03134        111 ANDRPS  116 (144)
T ss_pred             CCcCCC
Confidence            876654

>KOG4212|consensus

Probab=99.68  E-value=7.5e-16  Score=151.66  Aligned_cols=82  Identities=32%  Similarity=0.557  Sum_probs=76.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHh-cCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRL-AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .+.+||.|||+++.|+||+++|.+ .|+|+.|.++.|.+|+++|||.|+|+++|.+++|++.||.+.+.||+|.|+-...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            456999999999999999999975 8999999999999999999999999999999999999999999999999988766


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      ..+
T Consensus       124 ~q~  126 (608)
T KOG4212|consen  124 EQR  126 (608)
T ss_pred             hhh
Confidence            543

>KOG0106|consensus

Probab=99.68  E-value=1.2e-16  Score=148.13  Aligned_cols=69  Identities=29%  Similarity=0.685  Sum_probs=63.5

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEE
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT  585 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~  585 (587)
                      +.++++|.+|+..+.|+||+++|.++|++.+...  .++++||+|.++++|.+||..|++..+.+++|+|.
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence            3689999999999999999999999999966655  45799999999999999999999999999999884

>KOG0106|consensus

Probab=99.65  E-value=2.6e-16  Score=145.84  Aligned_cols=165  Identities=27%  Similarity=0.382  Sum_probs=132.4

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK  111 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~  111 (587)
                      .+|||++||+.+.+.+| ++|.+||.|.+|.+..       ||+||+|.+..+|..|+..||+..|.+-.+.|.++....
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN-------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec-------ccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            57999999999999999 6899999999997764       899999999999999999999999999888888888544


Q ss_pred             CCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEE
Q psy1534         112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEI  191 (587)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i  191 (587)
                      ..+..   +.++....|.                    .....+....+.++|.+++..+.+.+|.+.|.++|.+....+
T Consensus        75 ~~~g~---~~~g~r~~~~--------------------~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~  131 (216)
T KOG0106|consen   75 RGRGR---PRGGDRRSDS--------------------RRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA  131 (216)
T ss_pred             cccCC---CCCCCccchh--------------------hccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh
Confidence            33311   0110000000                    011112334678999999999999999999999999855554


Q ss_pred             eeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         192 ALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       192 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .       ++++||+|++.++|.+|++.|++..+.++.|.+..
T Consensus       132 ~-------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  132 R-------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             h-------ccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            2       56899999999999999999999999999999944

>KOG1456|consensus

Probab=99.62  E-value=1e-12  Score=127.44  Aligned_cols=201  Identities=21%  Similarity=0.224  Sum_probs=138.8

Q ss_pred             CCCCcEE---EcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC--eEEE
Q psy1534          30 PLEVPVV---MDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG--RKLV  103 (587)
Q Consensus        30 ~~~~~vf---V~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~  103 (587)
                      ...++|.   |-|--+.+|.+.| .+....|+|.+|.|++. +|   =.|.|||++.+.|++|.+.|||..|..  ..|+
T Consensus       117 ~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLK  192 (494)
T KOG1456|consen  117 ATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLK  192 (494)
T ss_pred             CCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cc---eeeEEeechhHHHHHHHhhcccccccccceeEE
Confidence            3444444   4566788999999 88999999999988875 55   369999999999999999999988873  7888


Q ss_pred             EEecccccCC--C--------------CCCCCCCCC-CCchh-hhhccCCcccCC-------------CCCCChhhhhc-
Q psy1534         104 IKEAVEDKGG--R--------------RNMGGGGGV-DRDLS-ALLQNNSSKFGN-------------TYGLSPQFLES-  151 (587)
Q Consensus       104 V~~a~~~~~~--~--------------~~~~~~~~~-~~~~~-~~~~~~~~~~~~-------------~~~~~~~~~~~-  151 (587)
                      |+++++.+..  +              .....+++. .+... .-....+..|+.             ....+...... 
T Consensus       193 IeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~  272 (494)
T KOG1456|consen  193 IEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGY  272 (494)
T ss_pred             EEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCcccc
Confidence            9988832210  0              000011110 00000 000001111110             00011111000 


Q ss_pred             -------cCCCCCCCcEEEEecCCCC-CcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q psy1534         152 -------LGINCPLINKVFVANLDYK-VDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ  223 (587)
Q Consensus       152 -------~~~~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~  223 (587)
                             ......+++.+.|-+|... ++-+.|..+|..||.|++|++++.+    .|-|.|++.+..+.++|+..||+.
T Consensus       273 ~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~  348 (494)
T KOG1456|consen  273 RDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNI  348 (494)
T ss_pred             ccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccC
Confidence                   0123567899999999975 7778899999999999999999986    578999999999999999999999


Q ss_pred             eeCCeEEEEEEccCC
Q psy1534         224 NLFERRITVRMDRVA  238 (587)
Q Consensus       224 ~~~g~~l~v~~a~~~  238 (587)
                      .+-|.+|.|.+++..
T Consensus       349 ~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  349 PLFGGKLNVCVSKQN  363 (494)
T ss_pred             ccccceEEEeecccc
Confidence            999999999887654

>KOG4205|consensus

Probab=99.60  E-value=2.7e-15  Score=148.29  Aligned_cols=81  Identities=27%  Similarity=0.460  Sum_probs=72.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||++|+|+++++.|++.|+.||+|.+|.+++|+. ++++||+||+|++++...++|.. .-+.|.|+.|.++.+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            357999999999999999999999999999999999996 99999999999999988888754 5678899998887765


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      +..
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            554

>PF00076 RRM_1: RNA recognition motif

Probab=99.59  E-value=5.4e-15  Score=115.41  Aligned_cols=69  Identities=23%  Similarity=0.469  Sum_probs=66.6

Q ss_pred             EEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          35 VVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        35 vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      |||+|||.++++++| ++|++||+|..++++.+.++.++++|||+|.+.++|++|++.|++..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999 899999999999999988889999999999999999999999999999999985

(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 ....

>KOG1457|consensus

Probab=99.59  E-value=3.5e-14  Score=128.53  Aligned_cols=193  Identities=18%  Similarity=0.198  Sum_probs=127.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeC-C-CCCcceEEEEEECCHHHHHHHHHHhCCceeC---CeEEEE
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILND-D-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETK---GRKLVI  104 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d-~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~---gr~i~V  104 (587)
                      .-++|||.+||.|+.-.|| .+|..|---+.+.|... + ....+-+|||+|.+..+|..|+..|||..|+   +..|++
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            3578999999999999999 88999887777766554 3 3346689999999999999999999999997   789999


Q ss_pred             EecccccC-CCCCCCCCCCCC----Cchhhhhcc------------CCccc---CC---------CCC--------CCh-
Q psy1534         105 KEAVEDKG-GRRNMGGGGGVD----RDLSALLQN------------NSSKF---GN---------TYG--------LSP-  146 (587)
Q Consensus       105 ~~a~~~~~-~~~~~~~~~~~~----~~~~~~~~~------------~~~~~---~~---------~~~--------~~~-  146 (587)
                      +.++.... .+.+..+..+..    .+.......            .+...   ..         ++.        +.| 
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            99883222 222222111100    000000000            00000   00         000        000 


Q ss_pred             -----hhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy1534         147 -----QFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN  221 (587)
Q Consensus       147 -----~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  221 (587)
                           +.............+|||.||..+++|++|+.+|+.|-....++|.. +.|  ...||++|++.+.|..|+..|+
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~~g--~~vaf~~~~~~~~at~am~~lq  269 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-RGG--MPVAFADFEEIEQATDAMNHLQ  269 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-CCC--cceEeecHHHHHHHHHHHHHhh
Confidence                 00000111223457899999999999999999999997655555432 223  3479999999999999999999


Q ss_pred             CceeC
Q psy1534         222 NQNLF  226 (587)
Q Consensus       222 g~~~~  226 (587)
                      |..|.
T Consensus       270 g~~~s  274 (284)
T KOG1457|consen  270 GNLLS  274 (284)
T ss_pred             cceec
Confidence            87764

>KOG1365|consensus

Probab=99.59  E-value=8.4e-15  Score=142.17  Aligned_cols=167  Identities=20%  Similarity=0.221  Sum_probs=115.1

Q ss_pred             EEEcCCCCCCCHHHHHhcccCCCeEE-EEEee-CCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccccC
Q psy1534          35 VVMDLIQGDASLYQISHLSTVGDVTY-VEILN-DDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG  112 (587)
Q Consensus        35 vfV~nlp~~~t~~~l~~F~~~G~V~~-v~i~~-d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~  112 (587)
                      |-.++|||..+..+|..|-+-=.|.. -..+. ...|+..|++.|.|.++|.-+.|++. +...+.+|.|.|-.+.-.+.
T Consensus        63 vRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~ge~f  141 (508)
T KOG1365|consen   63 VRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKATGEEF  141 (508)
T ss_pred             EEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccCchhh
Confidence            34578999999999954322222222 12222 23677779999999999999999987 88889999999998874443


Q ss_pred             CCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhc----CCeeE
Q psy1534         113 GRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLA----GKVEN  188 (587)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~  188 (587)
                      -...++...            ....|          .     +...--.|.+++||+++++.|+.++|.+-    |..+.
T Consensus       142 ~~iagg~s~------------e~~~f----------l-----sk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~eg  194 (508)
T KOG1365|consen  142 LKIAGGTSN------------EAAPF----------L-----SKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEG  194 (508)
T ss_pred             eEecCCccc------------cCCCC----------C-----CcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccc
Confidence            222111000            00000          0     00112357788999999999999999632    34577


Q ss_pred             EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q psy1534         189 VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRI  230 (587)
Q Consensus       189 v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  230 (587)
                      |.+++.++|+..|-|||.|..+++|+.||.+ |...|+-|.|
T Consensus       195 vLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  195 VLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             eEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            8888878899999999999999999999976 5555554443

>KOG0120|consensus

Probab=99.56  E-value=5.9e-14  Score=145.35  Aligned_cols=184  Identities=20%  Similarity=0.248  Sum_probs=138.1

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccC-----------C-CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCcee
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTV-----------G-DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET   97 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~-----------G-~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l   97 (587)
                      ..+++||+++|..++++.. .+|..-           | .|..|.|-..     +.|||++|.+.++|..|+ .+++..+
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~-----~nfa~ie~~s~~~at~~~-~~~~~~f  247 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLE-----KNFAFIEFRSISEATEAM-ALDGIIF  247 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeeccc-----ccceeEEecCCCchhhhh-cccchhh
Confidence            4558999999999999987 455332           3 3777776554     689999999999999999 5689999


Q ss_pred             CCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHH
Q psy1534          98 KGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLR  177 (587)
Q Consensus        98 ~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~  177 (587)
                      .|+++++...........           ..... .....+...+        .........+++||++||..+++..++
T Consensus       248 ~g~~~~~~r~~d~~~~p~-----------~~~~~-~~~~~~~~~~--------~~t~~~~~~~ki~v~~lp~~l~~~q~~  307 (500)
T KOG0120|consen  248 EGRPLKIRRPHDYQPVPG-----------ITLSP-SQLGKVGLLP--------ASTDVPDSPNKIFVGGLPLYLTEDQVK  307 (500)
T ss_pred             CCCCceecccccccCCcc-----------chhhh-ccccccCCcc--------cccCcccccchhhhccCcCccCHHHHH
Confidence            999998876552210000           00000 0000000000        011123345789999999999999999


Q ss_pred             HHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q psy1534         178 EVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADR  240 (587)
Q Consensus       178 ~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~  240 (587)
                      ++...||.+....+..+.. |.++||||.+|.++.....|+..|||..+.+++|.|..|-....
T Consensus       308 Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~  371 (500)
T KOG0120|consen  308 ELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGAS  371 (500)
T ss_pred             HHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccch
Confidence            9999999999999999986 89999999999999999999999999999999999998876653

>KOG0120|consensus

Probab=99.55  E-value=2.1e-14  Score=148.62  Aligned_cols=197  Identities=16%  Similarity=0.204  Sum_probs=146.5

Q ss_pred             CccccccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCcee
Q psy1534          20 PMFQRIETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFET   97 (587)
Q Consensus        20 ~~~~~~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l   97 (587)
                      +...+.........++||++||...++.++ |+.+.||++....++.|. +|.+|||||.+|.++-....|++.|||+.+
T Consensus       277 ~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~l  356 (500)
T KOG0120|consen  277 GLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQL  356 (500)
T ss_pred             CCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhh
Confidence            344455556667889999999999999998 899999999999999996 899999999999999999999999999999


Q ss_pred             CCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCC-CChhhh-hccCCCCCCCcEEEEecC--CCCC-c
Q psy1534          98 KGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYG-LSPQFL-ESLGINCPLINKVFVANL--DYKV-D  172 (587)
Q Consensus        98 ~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~~l~V~nL--p~~~-t  172 (587)
                      ++++|.|+.+......-.                     .+.+... ..+... ........++..|.+.|+  |.++ +
T Consensus       357 gd~~lvvq~A~~g~~~~~---------------------~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkd  415 (500)
T KOG0120|consen  357 GDKKLVVQRAIVGASNAN---------------------VNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKD  415 (500)
T ss_pred             cCceeEeehhhccchhcc---------------------ccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcc
Confidence            999999999883321100                     0000000 000000 000112334445555553  1111 1


Q ss_pred             H-------HHHHHHHHhcCCeeEEEEeeC-CC---CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         173 E-------KKLREVFRLAGKVENVEIALD-KD---GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       173 e-------~~l~~~F~~~G~i~~v~i~~~-~~---g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +       |+++..|.+||.|..|.|+++ .+   ....|..||+|.+.+++++|+++|+|.++.+|.|...|-..
T Consensus       416 d~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  416 DEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             hHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            1       467778889999999999998 43   44567899999999999999999999999999999988544

>KOG0125|consensus

Probab=99.55  E-value=1e-14  Score=139.30  Aligned_cols=80  Identities=20%  Similarity=0.280  Sum_probs=75.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...+++|+|+|||+...+.|| .+|++||+|.+|.|+.++.| ||||+||+|++++||++|.++|||..+.||+|.|..+
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            346789999999999999999 78999999999999999877 8999999999999999999999999999999999999


Q ss_pred             cc
Q psy1534         108 VE  109 (587)
Q Consensus       108 ~~  109 (587)
                      ..
T Consensus       172 Ta  173 (376)
T KOG0125|consen  172 TA  173 (376)
T ss_pred             ch
Confidence            83

>PF00076 RRM_1: RNA recognition motif

Probab=99.54  E-value=3.7e-14  Score=110.67  Aligned_cols=70  Identities=33%  Similarity=0.619  Sum_probs=67.3

Q ss_pred             EEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       162 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      |||+|||+++++++|+++|++||.|..+.+..+..++.+++|||+|.+.++|++|++.|++..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999999999999987789999999999999999999999999999999885

(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 ....

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.51  E-value=1e-13  Score=108.26  Aligned_cols=69  Identities=28%  Similarity=0.446  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          35 VVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        35 vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      |||+|||+++++++| ++|+.||.|..|++..+++++++++|||+|.++++|++|++.+++..|.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999 899999999999999997789999999999999999999999999999999885

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 ....

>KOG0107|consensus

Probab=99.51  E-value=3e-14  Score=124.64  Aligned_cols=75  Identities=20%  Similarity=0.281  Sum_probs=70.5

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ....+|||+||+.++++.|| ..|.+||+|.+|+|.+.    ..|||||||+++.||+.|+..|+|..|+|..|+|+.+.
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            35789999999999999999 57999999999999986    36899999999999999999999999999999999998

>KOG4206|consensus

Probab=99.51  E-value=1.6e-12  Score=119.40  Aligned_cols=80  Identities=18%  Similarity=0.340  Sum_probs=72.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHH----HHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~----~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      +..+|||.||...+..++|++    +|++||.|..|...+.  .+.+|-|||.|.+.+.|-.|+..|+|..+.|++++|.
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt--~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT--PKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC--CCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            344999999999999999988    9999999999887754  4678999999999999999999999999999999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      ||+.+.
T Consensus        86 yA~s~s   91 (221)
T KOG4206|consen   86 YAKSDS   91 (221)
T ss_pred             cccCcc
Confidence            998775

>KOG0149|consensus

Probab=99.51  E-value=1.9e-14  Score=132.06  Aligned_cols=78  Identities=15%  Similarity=0.247  Sum_probs=72.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      -.-.||||++|+|++..++| ++|++||+|++..|+.|+ +|+||||+||+|.+.|.|++|++. ..-.|+||+..|..+
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLA   88 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchh
Confidence            34568999999999999999 899999999999999998 999999999999999999999976 567799999999988


Q ss_pred             c
Q psy1534         108 V  108 (587)
Q Consensus       108 ~  108 (587)
                      .
T Consensus        89 ~   89 (247)
T KOG0149|consen   89 S   89 (247)
T ss_pred             h
Confidence            7

>KOG1457|consensus

Probab=99.50  E-value=8.4e-13  Score=119.67  Aligned_cols=88  Identities=13%  Similarity=0.198  Sum_probs=74.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeC---CeEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLF---ERRITV  232 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~v  232 (587)
                      ..++|||.+||.++...+|..+|..|-.-+.+.|.....  ...+-+|||+|.+..+|..|+..|||..|+   +..|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            468999999999999999999999987777777665443  345579999999999999999999999986   889999


Q ss_pred             EEccCCCCCCCCC
Q psy1534         233 RMDRVADRLDGPV  245 (587)
Q Consensus       233 ~~a~~~~~~~~~~  245 (587)
                      ++++...+..+.+
T Consensus       113 ElAKSNtK~kr~k  125 (284)
T KOG1457|consen  113 ELAKSNTKRKRRK  125 (284)
T ss_pred             eehhcCcccccCC
Confidence            9998887654433

>KOG0126|consensus

Probab=99.49  E-value=7.6e-15  Score=128.78  Aligned_cols=105  Identities=14%  Similarity=0.249  Sum_probs=88.1

Q ss_pred             CCchhHHHHHHcCCCCCccccc--cC--CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEE
Q psy1534           4 PVTETELVEQIAHQDFPMFQRI--ET--GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIV   77 (587)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV   77 (587)
                      |++.-..+.+++.+++......  ..  .=.+.--|||+|||+++||.|| -.|++||+|++|.+++|+ ||+|+||||+
T Consensus         3 plt~vk~i~~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFL   82 (219)
T KOG0126|consen    3 PLTNVKNIQKLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFL   82 (219)
T ss_pred             hhHHHHHHHHhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEE
Confidence            6666677777777766443211  11  1124456999999999999998 889999999999999997 9999999999


Q ss_pred             EECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          78 EFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        78 ~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .|++..+...|+..|||..|.||.|+|....
T Consensus        83 cYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   83 CYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             EecCccceEEEEeccCCceecceeEEeeecc
Confidence            9999999999999999999999999999876

>KOG0122|consensus

Probab=99.47  E-value=1.3e-13  Score=126.88  Aligned_cols=80  Identities=21%  Similarity=0.270  Sum_probs=76.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ++.+|=|.||+.+++|++| ++|.+||.|..|.|.+|+ ||.+||||||.|.+.++|.+||+.|||+-+..-.|+|+|+.
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            5667999999999999999 899999999999999997 99999999999999999999999999999999999999997


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            43

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

Probab=99.47  E-value=4e-13  Score=134.62  Aligned_cols=167  Identities=22%  Similarity=0.343  Sum_probs=119.6

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..+|||+|||+++++++| ++|.+||+|..|.|..|+ +++++|||||+|.+.++|..|++.+++..|.|++|.|.+...
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            589999999999999999 899999999999999996 999999999999999999999999999999999999999752


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                      ....+...       ...      ....+      .................+++.+++..++..++...|..+|.+...
T Consensus       195 ~~~~~~~~-------~~~------~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (306)
T COG0724         195 ASQPRSEL-------SNN------LDASF------AKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRA  255 (306)
T ss_pred             cccccccc-------ccc------cchhh------hccccccccccccccceeeccccccccchhHHHHhccccccceee
Confidence            00000000       000      00000      000001111134456789999999999999999999999999777


Q ss_pred             EEeeCCC-CCcceEEEEEecCHHHHHHHH
Q psy1534         190 EIALDKD-GKSRGFGTVEFDHPVEAVQSI  217 (587)
Q Consensus       190 ~i~~~~~-g~~~g~afV~f~~~~~A~~Al  217 (587)
                      .+..... .......++.+.....+....
T Consensus       256 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (306)
T COG0724         256 SLPPSKDGKIPKSRSFVGNEASKDALESN  284 (306)
T ss_pred             eccCCCCCcccccccccchhHHHhhhhhh
Confidence            6666554 223333444444443333333

>KOG0107|consensus

Probab=99.47  E-value=1.6e-13  Score=120.06  Aligned_cols=79  Identities=28%  Similarity=0.472  Sum_probs=74.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+||+..+++.||..+|..||.|.+|+|.+.+    .|||||+|+++.+|+.|+..|+|+.|+|..|+|+++..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            36899999999999999999999999999999999854    79999999999999999999999999999999999887


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      ..+
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            765

>KOG0125|consensus

Probab=99.46  E-value=2e-13  Score=130.56  Aligned_cols=82  Identities=27%  Similarity=0.460  Sum_probs=75.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|+|+|||+...|.||+.+|++||.|.+|.|+.+.. -+|||+||+|++.+||++|.++|||..+.||+|+|+.+.+
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNER-GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNER-GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccC-CCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            357999999999999999999999999999999998765 4699999999999999999999999999999999999877


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      +-.
T Consensus       174 rV~  176 (376)
T KOG0125|consen  174 RVH  176 (376)
T ss_pred             hhc
Confidence            643

>KOG0122|consensus

Probab=99.46  E-value=2.2e-13  Score=125.45  Aligned_cols=81  Identities=31%  Similarity=0.399  Sum_probs=77.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|-|.||+.+++|++|+++|.+||.|..|.|.+|+. |.++|||||.|.+.++|.+||..|||+-++.--|.|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            467899999999999999999999999999999999996 9999999999999999999999999999999999999998


Q ss_pred             CC
Q psy1534         237 VA  238 (587)
Q Consensus       237 ~~  238 (587)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            75

>KOG0121|consensus

Probab=99.45  E-value=1e-13  Score=114.68  Aligned_cols=80  Identities=20%  Similarity=0.167  Sum_probs=74.9

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      -....+|||+||++-++|++| ++|+++|+|..|.+=.|+ +..+.|||||+|.+.++|+.|++-+++..+..++|+|.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            346789999999999999999 999999999999888887 888899999999999999999999999999999999998


Q ss_pred             cc
Q psy1534         107 AV  108 (587)
Q Consensus       107 a~  108 (587)
                      ..
T Consensus       113 D~  114 (153)
T KOG0121|consen  113 DA  114 (153)
T ss_pred             cc
Confidence            76

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.45  E-value=5.1e-13  Score=104.30  Aligned_cols=70  Identities=36%  Similarity=0.621  Sum_probs=65.2

Q ss_pred             EEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       162 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      |||+|||+++++++|+++|+.||.|..+.+.+++++.++++|||+|.+.++|.+|++.+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999999988789999999999999999999999999999999874

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 ....

>KOG0149|consensus

Probab=99.44  E-value=2.3e-13  Score=124.96  Aligned_cols=79  Identities=24%  Similarity=0.470  Sum_probs=73.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      -++|||++|+|.+..++|+++|++||+|++..|+.|+. |++|||+||+|.|.++|.+|++. -.-.|+||+..|++|..
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            47999999999999999999999999999999999996 99999999999999999999975 45789999999999876


Q ss_pred             C
Q psy1534         238 A  238 (587)
Q Consensus       238 ~  238 (587)
                      .
T Consensus        91 g   91 (247)
T KOG0149|consen   91 G   91 (247)
T ss_pred             c
Confidence            3

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.43  E-value=4.4e-13  Score=127.76  Aligned_cols=75  Identities=21%  Similarity=0.256  Sum_probs=69.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|+.||+|++|.|++|+.  ++|||||+|.++++|+.|| .|+|..|.|++|.|.++.
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEecc
Confidence            3579999999999999999 8999999999999998853  4699999999999999999 599999999999999986

>KOG0121|consensus

Probab=99.43  E-value=3.2e-13  Score=111.78  Aligned_cols=81  Identities=23%  Similarity=0.382  Sum_probs=75.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..+++|||+||++.++||.|.++|+++|+|..|.+-.|+. ..+.|||||+|.+.++|+.|++.+++..+..++|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            3578999999999999999999999999999998888885 788999999999999999999999999999999999986


Q ss_pred             cC
Q psy1534         236 RV  237 (587)
Q Consensus       236 ~~  237 (587)
                      ..
T Consensus       114 ~G  115 (153)
T KOG0121|consen  114 AG  115 (153)
T ss_pred             cc
Confidence            54

>KOG1548|consensus

Probab=99.43  E-value=1.7e-11  Score=118.49  Aligned_cols=83  Identities=18%  Similarity=0.311  Sum_probs=76.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCee--------EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVE--------NVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR  229 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  229 (587)
                      ..+.|||.|||.++|.+++.++|++||.|.        .|+|.++..|+.+|-|.|.|...+++.-|++.|++..+.|+.
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            356799999999999999999999999874        489999999999999999999999999999999999999999


Q ss_pred             EEEEEccCCCC
Q psy1534         230 ITVRMDRVADR  240 (587)
Q Consensus       230 l~v~~a~~~~~  240 (587)
                      |+|+.|+-..+
T Consensus       213 ~rVerAkfq~K  223 (382)
T KOG1548|consen  213 LRVERAKFQMK  223 (382)
T ss_pred             EEEehhhhhhc
Confidence            99999877654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.42  E-value=1.1e-12  Score=125.08  Aligned_cols=78  Identities=22%  Similarity=0.452  Sum_probs=71.7

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .++|||+|||+.++|++|+++|+.||.|.+|.|++++.  ++|||||+|.++++|+.|| .|||..|.|+.|.|.++..-
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccCC
Confidence            46999999999999999999999999999999998863  5799999999999999999 59999999999999998654


Q ss_pred             C
Q psy1534         239 D  239 (587)
Q Consensus       239 ~  239 (587)
                      .
T Consensus        81 ~   81 (260)
T PLN03120         81 Q   81 (260)
T ss_pred             C
Confidence            3

>KOG4207|consensus

Probab=99.41  E-value=2.3e-13  Score=121.93  Aligned_cols=79  Identities=24%  Similarity=0.233  Sum_probs=75.7

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .....|-|.||.+-++-++| .+|++||.|-+|.|.+|+ |+.++|||||.|.+..||+.|+++|+|..|+|+.|.|+.+
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            45668999999999999999 899999999999999998 9999999999999999999999999999999999999998


Q ss_pred             c
Q psy1534         108 V  108 (587)
Q Consensus       108 ~  108 (587)
                      .
T Consensus        91 r   91 (256)
T KOG4207|consen   91 R   91 (256)
T ss_pred             h
Confidence            8

>PLN03213 repressor of silencing 3; Provisional

Probab=99.37  E-value=1.4e-12  Score=130.70  Aligned_cols=78  Identities=19%  Similarity=0.252  Sum_probs=71.7

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCH--HHHHHHHHHhCCceeCCeEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSP--DLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~--e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ......+|||+||++++++++| ..|+.||.|.+|.|++ .+|  ||||||+|.+.  +++.+||+.|||..+.|+.|+|
T Consensus         6 s~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR-ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKV   82 (759)
T PLN03213          6 SGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR-TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRL   82 (759)
T ss_pred             cCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec-ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEE
Confidence            3446689999999999999999 7899999999999994 377  89999999988  7899999999999999999999


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      ..+.
T Consensus        83 NKAK   86 (759)
T PLN03213         83 EKAK   86 (759)
T ss_pred             eecc
Confidence            9998

>KOG0113|consensus

Probab=99.37  E-value=1.4e-12  Score=123.49  Aligned_cols=78  Identities=17%  Similarity=0.347  Sum_probs=73.9

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +=.+|||.-|+++++|..| +.|++||+|+.|+|++|. ||++||||||+|+++.+...|.+..+|..|.|+.|.|.+-.
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvER  179 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVER  179 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecc
Confidence            4458999999999999999 789999999999999997 99999999999999999999999999999999999998765

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.36  E-value=3e-12  Score=120.06  Aligned_cols=76  Identities=18%  Similarity=0.219  Sum_probs=69.9

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +...+|||+||++++|+++| ++|+.||+|.+|+|++|  +.+++||||+|+++++|+.|+ .|+|..|.+++|.|..+.
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            35578999999999999999 89999999999999998  445689999999999999999 789999999999999877

>KOG0130|consensus

Probab=99.36  E-value=8.3e-13  Score=110.26  Aligned_cols=75  Identities=17%  Similarity=0.329  Sum_probs=72.9

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      -|||.++..+++|++| +.|..||+|+++++-.|+ ||-.||||+|+|++.++|++|++.+||..|.+++|.|.|+.
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            4999999999999999 889999999999999996 99999999999999999999999999999999999999998

>smart00362 RRM_2 RNA recognition motif

Probab=99.35  E-value=4.1e-12  Score=98.92  Aligned_cols=71  Identities=27%  Similarity=0.425  Sum_probs=66.7

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      +|||+|||..++.++| ++|++||+|.++++..++ +.++|+|||+|.+.++|++|++.+++..+.|++|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            5999999999999999 889999999999999887 7788999999999999999999999999999999873

>KOG0114|consensus

Probab=99.35  E-value=3.7e-12  Score=101.53  Aligned_cols=80  Identities=15%  Similarity=0.215  Sum_probs=71.2

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ++..+-|||+|||+++|.++. ++|.+||+|..|+|=..  ...+|.|||.|++..+|++|++.|+|..+.++.+.|.+.
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~--k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT--KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc--cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            345567999999999999998 99999999999998654  345799999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      ...
T Consensus        93 q~~   95 (124)
T KOG0114|consen   93 QPE   95 (124)
T ss_pred             CHH
Confidence            833

>KOG4207|consensus

Probab=99.35  E-value=3.3e-12  Score=114.53  Aligned_cols=82  Identities=30%  Similarity=0.482  Sum_probs=77.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ...|.|-||.+.++.++|+.+|++||.|-+|.|++|+. ..++|||||.|.+..+|+.|+++|+|..++|+.|.|.+|+.
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            46899999999999999999999999999999999995 99999999999999999999999999999999999999877


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      ...
T Consensus        93 gr~   95 (256)
T KOG4207|consen   93 GRP   95 (256)
T ss_pred             CCC
Confidence            654

>KOG0113|consensus

Probab=99.35  E-value=6.7e-12  Score=118.87  Aligned_cols=95  Identities=28%  Similarity=0.441  Sum_probs=84.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ...+-+||||+-|+.+++|.+|+..|+.||.|..|.|++|+ +|+++|||||+|+++.+...|.+..+|.+|.|+.|.|.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            34678999999999999999999999999999999999997 59999999999999999999999999999999999999


Q ss_pred             EccCCCCCCCCCCCCCCcc
Q psy1534         234 MDRVADRLDGPVRLPEGLK  252 (587)
Q Consensus       234 ~a~~~~~~~~~~~~~~~~~  252 (587)
                      +.+....+   .++|..|.
T Consensus       177 vERgRTvk---gW~PRRLG  192 (335)
T KOG0113|consen  177 VERGRTVK---GWLPRRLG  192 (335)
T ss_pred             eccccccc---cccccccc
Confidence            98766533   45555553

>KOG0114|consensus

Probab=99.32  E-value=8.6e-12  Score=99.46  Aligned_cols=71  Identities=25%  Similarity=0.457  Sum_probs=66.1

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeec---CCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEEC
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG---KGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF  587 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~---~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~  587 (587)
                      .-|||+|||+++|.++.-|+|-.||.|..++|.-   .+|+|||.|++-.+|.+||++|+|+.+.++.+.|-+|
T Consensus        19 riLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   19 RILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             eeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            4789999999999999999999999999999943   3699999999999999999999999999999999875

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.31  E-value=1.1e-11  Score=116.15  Aligned_cols=76  Identities=21%  Similarity=0.268  Sum_probs=69.8

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +.+|||+||++.+||++|+++|+.||+|.+|+|++|.  +.++||||+|.++++|+.|+ .|+|..|.+++|.|.....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~--et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG--EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC--CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            5799999999999999999999999999999999884  55689999999999999999 7899999999999987553

>smart00362 RRM_2 RNA recognition motif

Probab=99.31  E-value=1.3e-11  Score=95.99  Aligned_cols=72  Identities=40%  Similarity=0.616  Sum_probs=67.6

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      +|||+|||..+++++|+++|++||.|..+.+..++ +.++++|||+|.+.++|++|++.+++..+.|++|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999999877 7788999999999999999999999999999998873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.31  E-value=8e-12  Score=125.31  Aligned_cols=78  Identities=22%  Similarity=0.283  Sum_probs=71.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCH--HHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHP--VEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~--~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...+|||+||+++++++||+.+|+.||.|.+|.|++.. |  ||||||+|.+.  .++.+||..|||..+.|+.|+|..|
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET-G--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK-G--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc-C--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            45799999999999999999999999999999999543 5  89999999987  7899999999999999999999988


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      ++.
T Consensus        86 KP~   88 (759)
T PLN03213         86 KEH   88 (759)
T ss_pred             cHH
Confidence            765

>KOG4454|consensus

Probab=99.31  E-value=3e-13  Score=122.25  Aligned_cols=145  Identities=23%  Similarity=0.313  Sum_probs=125.7

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .++..++|||.|+-..++|+.| |+|-+-|+|..|.|..+++++.| ||||.|+++-.+..|++.+||..+.+++|+|++
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            4567789999999999999999 89999999999999998888888 999999999999999999999999999887754


Q ss_pred             cccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEec----CCCCCcHHHHHHHHHh
Q psy1534         107 AVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVAN----LDYKVDEKKLREVFRL  182 (587)
Q Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----Lp~~~te~~l~~~F~~  182 (587)
                      -                                                        .++    |...++++.+.+.|+.
T Consensus        84 r--------------------------------------------------------~G~shapld~r~~~ei~~~v~s~  107 (267)
T KOG4454|consen   84 R--------------------------------------------------------CGNSHAPLDERVTEEILYEVFSQ  107 (267)
T ss_pred             c--------------------------------------------------------cCCCcchhhhhcchhhheeeecc
Confidence            3                                                        333    5667889999999999


Q ss_pred             cCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeE
Q psy1534         183 AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR  229 (587)
Q Consensus       183 ~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  229 (587)
                      .+.+..+++.++.+|+++-++|+.+.-....-.++....+....=++
T Consensus       108 a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~  154 (267)
T KOG4454|consen  108 AGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKK  154 (267)
T ss_pred             cCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCCCC
Confidence            99999999999999999999999998887777888776655444333

>KOG1365|consensus

Probab=99.29  E-value=3.5e-12  Score=124.18  Aligned_cols=188  Identities=18%  Similarity=0.166  Sum_probs=134.4

Q ss_pred             EEEcCCCCCCCHHHH-Hhccc----CCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          35 VVMDLIQGDASLYQI-SHLST----VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        35 vfV~nlp~~~t~~~l-~~F~~----~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      |-.++||+++++.|+ ++|..    -|-++.|-.++.++|+..|-|||.|..+++|+.|+.+ |...|+-|.|.+.++..
T Consensus       164 vRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRSTa  242 (508)
T KOG1365|consen  164 VRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRSTA  242 (508)
T ss_pred             EEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHhH
Confidence            345799999999998 78852    2356678888888999999999999999999999977 77888888888887763


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCC--CCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC-e
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGN--TYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK-V  186 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-i  186 (587)
                      .+....-         .+.     .......  +...-+..............+|.+++||+..+.|||.++|..|-. |
T Consensus       243 aEvqqvl---------nr~-----~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i  308 (508)
T KOG1365|consen  243 AEVQQVL---------NRE-----VSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDI  308 (508)
T ss_pred             HHHHHHH---------Hhh-----ccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhc
Confidence            3211100         000     0000000  000000000111112333568999999999999999999999865 4


Q ss_pred             eE--EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         187 EN--VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       187 ~~--v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..  |.+..+..|++.|.|||+|.+.|+|..|....+++....|.|.|--+..
T Consensus       309 ~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~  361 (508)
T KOG1365|consen  309 RFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSV  361 (508)
T ss_pred             ccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccH
Confidence            33  7888888899999999999999999999998888888889988866443

>KOG0108|consensus

Probab=99.29  E-value=4.6e-12  Score=130.95  Aligned_cols=77  Identities=31%  Similarity=0.434  Sum_probs=75.0

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..|||+|||+++++++| ++|+..|.|.+++++.|+ +|++||||||+|.+.++|++|++.||+.++.||+|+|.|+..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            88999999999999999 899999999999999997 999999999999999999999999999999999999999983

>smart00360 RRM RNA recognition motif

Probab=99.28  E-value=1.3e-11  Score=95.57  Aligned_cols=69  Identities=30%  Similarity=0.478  Sum_probs=64.9

Q ss_pred             EcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          37 MDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        37 V~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      |+|||..+++++| ++|++||+|.+|++..++ ++.++|+|||+|.+.++|.+|++.+++..+.+++|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6899999999999 889999999999999987 78999999999999999999999999999999999873

>KOG0111|consensus

Probab=99.28  E-value=2.9e-12  Score=115.79  Aligned_cols=83  Identities=20%  Similarity=0.275  Sum_probs=77.9

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++|||++|-.+++|..| ..|-+||.|++|.|+.|- ++++||||||+|.-.|||..||..||+.+|.||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45689999999999999999 789999999999999994 9999999999999999999999999999999999999999


Q ss_pred             ccccC
Q psy1534         108 VEDKG  112 (587)
Q Consensus       108 ~~~~~  112 (587)
                      .+.+.
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            96653

>KOG0111|consensus

Probab=99.27  E-value=3.5e-12  Score=115.29  Aligned_cols=86  Identities=33%  Similarity=0.556  Sum_probs=80.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||++|..+++|.-|...|-+||.|..|.++.|.. +++|||+||+|...|+|..||..||+.++.||.|+|.+++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            357999999999999999999999999999999999985 9999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q psy1534         237 VADRLDG  243 (587)
Q Consensus       237 ~~~~~~~  243 (587)
                      +.+.+..
T Consensus        89 P~kikeg   95 (298)
T KOG0111|consen   89 PEKIKEG   95 (298)
T ss_pred             CccccCC
Confidence            8765443

>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=99.25  E-value=4.9e-11  Score=93.29  Aligned_cols=73  Identities=26%  Similarity=0.374  Sum_probs=68.3

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      +|||++||..+++++| ++|+.||+|..+.+..++...++++|||+|.+.++|..|++.+++..+.+++|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999 889999999999999988667889999999999999999999999999999999864

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).

>KOG0126|consensus

Probab=99.24  E-value=1.1e-12  Score=115.31  Aligned_cols=79  Identities=23%  Similarity=0.442  Sum_probs=74.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +.-|||+|||+++||.||..+|++||+|+.|.+++|+. |+++||||+.|++..+..-|+..|||..|.||.|+|.....
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            46899999999999999999999999999999999996 99999999999999999999999999999999999986433

>smart00360 RRM RNA recognition motif

Probab=99.22  E-value=5.2e-11  Score=92.20  Aligned_cols=70  Identities=43%  Similarity=0.666  Sum_probs=65.7

Q ss_pred             EecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       164 V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      |+|||..+++++|+++|++||.|..+.+..++. +.++++|||+|.+.++|.+|++.+++..+.++.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            579999999999999999999999999999875 8899999999999999999999999999999998873

>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=99.22  E-value=1.1e-10  Score=91.28  Aligned_cols=74  Identities=43%  Similarity=0.634  Sum_probs=69.6

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      +|+|+|||..+++++|+++|+.||.|..+.+..++...++++|||+|.+.++|..|++.+++..+.++.+.|++
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999987777899999999999999999999999999999999864

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).

>KOG0130|consensus

Probab=99.22  E-value=2.9e-11  Score=101.15  Aligned_cols=81  Identities=25%  Similarity=0.430  Sum_probs=77.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +-.|||.++...++|++|.+.|..||+|..+.+-.|+. |..+|||+|+|++.++|++|+..+||..+.+.+|.|.|+..
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            45899999999999999999999999999999999985 99999999999999999999999999999999999999877


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus       152 ~g  153 (170)
T KOG0130|consen  152 KG  153 (170)
T ss_pred             cC
Confidence            65

>PF13893 RRM_5: RNA recognition motif

Probab=99.20  E-value=5.9e-11  Score=88.09  Aligned_cols=54  Identities=31%  Similarity=0.488  Sum_probs=49.3

Q ss_pred             HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          50 SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        50 ~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ++|++||+|.+|++..+.    +++|||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus         3 ~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    3 KLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             HHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            679999999999998763    589999999999999999999999999999999985

(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 ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.18  E-value=7.8e-11  Score=91.72  Aligned_cols=59  Identities=19%  Similarity=0.301  Sum_probs=52.0

Q ss_pred             HHHH-Hhcc----cCCCeEEEE-EeeCC-C--CCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          46 LYQI-SHLS----TVGDVTYVE-ILNDD-T--GKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        46 ~~~l-~~F~----~~G~V~~v~-i~~d~-~--g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      +++| ++|+    +||+|.+|. |+.++ +  +.++|||||+|.+.++|.+|++.|||..+.||+|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            3455 5676    999999996 77765 5  899999999999999999999999999999999987

>KOG0108|consensus

Probab=99.18  E-value=4e-11  Score=124.04  Aligned_cols=82  Identities=29%  Similarity=0.502  Sum_probs=78.4

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      +.|||+|+|++++|++|.++|+..|.|.+++++.|++ |+++||+|++|.+.++|.+|++.|||.++.||+|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            7999999999999999999999999999999999996 999999999999999999999999999999999999998776


Q ss_pred             CCC
Q psy1534         239 DRL  241 (587)
Q Consensus       239 ~~~  241 (587)
                      ...
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            643

>KOG0129|consensus

Probab=99.16  E-value=6e-10  Score=113.66  Aligned_cols=171  Identities=18%  Similarity=0.206  Sum_probs=119.8

Q ss_pred             ccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC--CC--Ccce---EEEEEECCHHHHHHHHHHhCCce
Q psy1534          25 IETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD--TG--KPRG---SAIVEFQSPDLVRKAVNKMHRFE   96 (587)
Q Consensus        25 ~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~--~g--~skG---~aFV~F~~~e~A~~Al~~l~g~~   96 (587)
                      ....+.-.++|||++||++++|++| ..|..||.|. |.-....  .+  -++|   |+|+.|+++..++.-+.++.-  
T Consensus       252 ~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~--  328 (520)
T KOG0129|consen  252 GYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE--  328 (520)
T ss_pred             CCCccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh--
Confidence            3344456679999999999999999 7799999864 3333211  11  3556   999999999999887765432  


Q ss_pred             eCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHH
Q psy1534          97 TKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKL  176 (587)
Q Consensus        97 l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l  176 (587)
                       ....+.++...+....+                    ..+..........+........++.+||||++||.-++-++|
T Consensus       329 -~~~~~yf~vss~~~k~k--------------------~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eL  387 (520)
T KOG0129|consen  329 -GEGNYYFKVSSPTIKDK--------------------EVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEEL  387 (520)
T ss_pred             -cccceEEEEecCccccc--------------------ceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHH
Confidence             44444443333111100                    000000011111222333445677899999999999999999


Q ss_pred             HHHHH-hcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHH
Q psy1534         177 REVFR-LAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM  219 (587)
Q Consensus       177 ~~~F~-~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~  219 (587)
                      -.+|+ .||.|..+-|-.|++ +.++|-|-|+|.+..+-.+||.+
T Consensus       388 A~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  388 AMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             HHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            99999 699999999999976 89999999999999999999975

>PF13893 RRM_5: RNA recognition motif

Probab=99.11  E-value=3.2e-10  Score=84.13  Aligned_cols=56  Identities=32%  Similarity=0.490  Sum_probs=51.2

Q ss_pred             HHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         176 LREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       176 l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      |+++|++||+|.++.+.++.    +++|||+|.+.++|.+|++.||+..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999998764    589999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=99.10  E-value=3.7e-10  Score=113.02  Aligned_cols=79  Identities=41%  Similarity=0.623  Sum_probs=75.8

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|..||.|..+.+..++ .++++|||||+|.+.++|..|++.+++..|.|++|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            5899999999999999999999999999999999997 599999999999999999999999999999999999999765

>smart00361 RRM_1 RNA recognition motif

Probab=99.06  E-value=7.6e-10  Score=86.14  Aligned_cols=60  Identities=22%  Similarity=0.400  Sum_probs=53.7

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EeeCC-C--CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         173 EKKLREVFR----LAGKVENVE-IALDK-D--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       173 e~~l~~~F~----~~G~i~~v~-i~~~~-~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      +++|+++|+    +||.|.+|. |+.++ +  ++++||+||+|.+.++|.+|++.|||+.+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999999995 66655 3  889999999999999999999999999999999986

>KOG4208|consensus

Probab=99.03  E-value=6.4e-10  Score=100.62  Aligned_cols=86  Identities=22%  Similarity=0.268  Sum_probs=76.0

Q ss_pred             ccCCCCCCCcEEEcCCCCCCCHHHH-HhcccC-CCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeE
Q psy1534          25 IETGAPLEVPVVMDLIQGDASLYQI-SHLSTV-GDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK  101 (587)
Q Consensus        25 ~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~-G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~  101 (587)
                      .......+.-+||+.+|.-+.+.+| .+|.+| |.|..+++-|++ ||.|||||||+|+++|.|+-|-+.||++.|.++.
T Consensus        42 ~~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~l  121 (214)
T KOG4208|consen   42 EKPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHL  121 (214)
T ss_pred             cCCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhe
Confidence            3444556667999999999999888 678887 789999998986 9999999999999999999999999999999999


Q ss_pred             EEEEecccc
Q psy1534         102 LVIKEAVED  110 (587)
Q Consensus       102 i~V~~a~~~  110 (587)
                      |.|.+..+.
T Consensus       122 L~c~vmppe  130 (214)
T KOG4208|consen  122 LECHVMPPE  130 (214)
T ss_pred             eeeEEeCch
Confidence            999998744

>KOG0128|consensus

Probab=98.95  E-value=9.4e-11  Score=125.63  Aligned_cols=146  Identities=18%  Similarity=0.292  Sum_probs=126.1

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeC-CCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      .++||+||++.+.+.+| ..|..+|.+..|+|... .+++.||+|||+|..++++.+||.-.+...+ |          +
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~-g----------K  736 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF-G----------K  736 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh-h----------h
Confidence            37999999999999999 67999999888887744 3888999999999999999999976443333 2          1


Q ss_pred             cCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEE
Q psy1534         111 KGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVE  190 (587)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~  190 (587)
                                                                       ..|+|.|+|+..|.++|+.+|+.+|.+.++.
T Consensus       737 -------------------------------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~  767 (881)
T KOG0128|consen  737 -------------------------------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLR  767 (881)
T ss_pred             -------------------------------------------------hhhheeCCCCCCchHHHHhhccccCCccccc
Confidence                                                             2799999999999999999999999999999


Q ss_pred             EeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         191 IALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       191 i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      ++..+.|+++|.+||.|.+..++.+++...+...+.-+.+.|.++.+.
T Consensus       768 ~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  768 LVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             hhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            999889999999999999999999999888877777777777776553

>KOG0415|consensus

Probab=98.92  E-value=2.4e-09  Score=103.65  Aligned_cols=82  Identities=18%  Similarity=0.245  Sum_probs=76.7

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHHH-hcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQIS-HLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l~-~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...|+++-|||=.|.+-+|.++|+ +|+.||+|.+|.|++|. ||.+.-||||+|++.+++++|.-.|++..|.++.|.|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            445788899999999999999996 59999999999999996 9999999999999999999999999999999999999


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      .++.
T Consensus       314 DFSQ  317 (479)
T KOG0415|consen  314 DFSQ  317 (479)
T ss_pred             ehhh
Confidence            9987

>KOG0415|consensus

Probab=98.90  E-value=2.7e-09  Score=103.33  Aligned_cols=85  Identities=25%  Similarity=0.380  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..||.+.|||-.|.+.++.+||.-+|+.||.|.+|.|++|.. |.+..||||+|++.+++++|.-.|++..|..+.|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            467899999999999999999999999999999999999985 9999999999999999999999999999999999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      ++....
T Consensus       315 FSQSVs  320 (479)
T KOG0415|consen  315 FSQSVS  320 (479)
T ss_pred             hhhhhh
Confidence            876554

>KOG0226|consensus

Probab=98.89  E-value=1e-09  Score=102.05  Aligned_cols=169  Identities=17%  Similarity=0.217  Sum_probs=130.4

Q ss_pred             cEEEcCCCCCCCHHH-H---HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          34 PVVMDLIQGDASLYQ-I---SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~-l---~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..|+.++-.++.-+- |   ..|+.|-.....+++++.-+.-++++|+.|.....-.++-..-+++++.-++|++.....
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            455666544443332 2   458888888888999998777889999999988888887766666777777655443331


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                                        |.++..  ..                 -.....+||++.|..+++++-|...|.+|-.....
T Consensus       178 ------------------wedPsl--~e-----------------w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~a  220 (290)
T KOG0226|consen  178 ------------------WEDPSL--AE-----------------WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKA  220 (290)
T ss_pred             ------------------cCCccc--cc-----------------CccccceeecccccccccHHHHHHHHHhccchhhc
Confidence                              111110  01                 11224589999999999999999999999888889


Q ss_pred             EEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         190 EIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       190 ~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      ++++|+. |+++||+||.|.+.+++.+|+..|+|+.++.|+|+++.+..+.
T Consensus       221 kviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  221 KVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             cccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            9999985 9999999999999999999999999999999999998776655

>KOG4210|consensus

Probab=98.83  E-value=5.4e-09  Score=103.61  Aligned_cols=176  Identities=15%  Similarity=0.197  Sum_probs=134.9

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++|++++.+++.+.++ .+|.++|.+..+.+.... ...++|+++|.|+..+.+..|+...-...+.++.+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            3568999999999988877 678999988888777765 88899999999999999999997633345555555444443


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEE-EecCCCCCcHHHHHHHHHhcCCee
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVF-VANLDYKVDEKKLREVFRLAGKVE  187 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nLp~~~te~~l~~~F~~~G~i~  187 (587)
                      .... +..                    .        +.    .........++| |++|++.+++++|+..|..+|.|.
T Consensus       167 ~~~~-~~~--------------------n--------~~----~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~  213 (285)
T KOG4210|consen  167 RRGL-RPK--------------------N--------KL----SRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEIT  213 (285)
T ss_pred             cccc-ccc--------------------c--------hh----cccccCccccceeecccccccchHHHhhhccCcCcce
Confidence            2210 000                    0        00    000111223445 999999999999999999999999


Q ss_pred             EEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q psy1534         188 NVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADR  240 (587)
Q Consensus       188 ~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~  240 (587)
                      .++++.++. +.++||++|.|.....+..++.. ....+.++++.+....+...
T Consensus       214 ~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  214 SVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             eeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            999998886 99999999999999999999977 78899999999988877653

>KOG0132|consensus

Probab=98.76  E-value=1.6e-08  Score=107.46  Aligned_cols=79  Identities=15%  Similarity=0.275  Sum_probs=73.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++||||+.|+..++|.||..+|+.||+|.+|.++..     ++||||.+....+|.+|+.+|+...+.++.|+|.|+..
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            4789999999999999999999999999999988764     79999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy1534         238 ADRL  241 (587)
Q Consensus       238 ~~~~  241 (587)
                      +..+
T Consensus       495 ~G~k  498 (894)
T KOG0132|consen  495 KGPK  498 (894)
T ss_pred             CCcc
Confidence            7543

>KOG4307|consensus

Probab=98.73  E-value=3.1e-06  Score=89.20  Aligned_cols=194  Identities=11%  Similarity=0.028  Sum_probs=130.8

Q ss_pred             CcEE--EcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          33 VPVV--MDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        33 ~~vf--V~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .++|  +++.+++..+.|+ ++|.- =.|..+.|..+. .+...|-++|+|....++++|+.. |...+-.|.|.|..+.
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g-~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPG-RNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPG  387 (944)
T ss_pred             hhheeeecccccccccchhhhhcCc-ccccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCC
Confidence            3455  6789999999999 45422 146677777776 333368999999999999999976 7788889999998877


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhh---hccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFL---ESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK  185 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~  185 (587)
                      .....-...   ......    +......++..........   .....+...+..|||..||..+++.++.++|...-.
T Consensus       388 ~~~~~~a~~---~~~~~~----~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~  460 (944)
T KOG4307|consen  388 NLGRNGAPP---FQAGVP----PPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAA  460 (944)
T ss_pred             ccccccCcc---ccccCC----CCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhh
Confidence            333211100   000000    0000000000000000000   011224556789999999999999999999998767


Q ss_pred             eeE-EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         186 VEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       186 i~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      |++ |.|-+.++++-++.|||.|..++++..|+..-+.+.+..|.|+|.-.
T Consensus       461 Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  461 VEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             hhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            776 77877778888999999999999999998776777777888888743

>KOG4661|consensus

Probab=98.72  E-value=2.8e-08  Score=101.69  Aligned_cols=80  Identities=16%  Similarity=0.275  Sum_probs=73.3

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++|||.+|...+.-.+| .+|++||+|+-.+|+++. +--.+.|+||++.+.++|.+||+.|+.+.|.|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            35678999999999999999 799999999999999995 5556789999999999999999999999999999999998


Q ss_pred             cc
Q psy1534         108 VE  109 (587)
Q Consensus       108 ~~  109 (587)
                      +.
T Consensus       483 KN  484 (940)
T KOG4661|consen  483 KN  484 (940)
T ss_pred             cc
Confidence            83

>KOG0153|consensus

Probab=98.71  E-value=4.6e-08  Score=95.15  Aligned_cols=78  Identities=19%  Similarity=0.307  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML-NNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~  233 (587)
                      +....++|||++|-..++|.+|++.|.+||+|.++.++..     +++|||+|.+.+.|+.|.+.. |...|.|++|+|.
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            3445689999999999999999999999999999998875     579999999999999998765 5567899999999


Q ss_pred             EccC
Q psy1534         234 MDRV  237 (587)
Q Consensus       234 ~a~~  237 (587)
                      |.++
T Consensus       299 Wg~~  302 (377)
T KOG0153|consen  299 WGRP  302 (377)
T ss_pred             eCCC
Confidence            9887

>KOG0132|consensus

Probab=98.70  E-value=2.7e-08  Score=105.85  Aligned_cols=75  Identities=17%  Similarity=0.336  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         512 SNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       512 ~~~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      ..+...||+|.+||.+++++||+++|+.||+|.++++...++||||.+.++.+|++|+.+|+...+..+.|+|.|
T Consensus       417 isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            456678999999999999999999999999999999999999999999999999999999999999999999876

>KOG0533|consensus

Probab=98.69  E-value=3.7e-08  Score=93.99  Aligned_cols=81  Identities=20%  Similarity=0.252  Sum_probs=76.0

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..+.+|+|.|||+.++.+|| ++|..||+++.+-|-.|++|++.|+|=|.|...+||.+|++.+++..+.|++|++....
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            45578999999999999999 89999999999999999999999999999999999999999999999999999999887


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      ..
T Consensus       161 ~~  162 (243)
T KOG0533|consen  161 SP  162 (243)
T ss_pred             Cc
Confidence            43

>KOG0153|consensus

Probab=98.69  E-value=4.6e-08  Score=95.14  Aligned_cols=76  Identities=20%  Similarity=0.322  Sum_probs=67.9

Q ss_pred             CCCCCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCC-cccCceEEEEE
Q psy1534         511 SSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT-RIDGKIIDVTF  586 (587)
Q Consensus       511 ~~~~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~-~~~g~~i~v~~  586 (587)
                      -.+..-.+|+|.+|-+.++++||+|||.+||+|.++.+...++||||+|.++++|+.|.++.-.. -|.|++|+|.|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~W  299 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKW  299 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEe
Confidence            34555679999999889999999999999999999999988899999999999999999876554 57999999975

>KOG4208|consensus

Probab=98.68  E-value=5.9e-08  Score=88.05  Aligned_cols=83  Identities=23%  Similarity=0.322  Sum_probs=74.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhc-CCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLA-GKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~-G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ......++|..+|.-+.+.++..+|.+| |.|..+++-|++ +|.++|||||+|++++.|.-|-+.||+..+.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3445689999999999999999999998 667888887887 49999999999999999999999999999999999999


Q ss_pred             EccCC
Q psy1534         234 MDRVA  238 (587)
Q Consensus       234 ~a~~~  238 (587)
                      +-.+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            87665

>KOG0128|consensus

Probab=98.65  E-value=1.3e-09  Score=117.07  Aligned_cols=157  Identities=20%  Similarity=0.188  Sum_probs=119.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH--HhcccCCCeEEEEEeeCCCCCcce-EEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI--SHLSTVGDVTYVEILNDDTGKPRG-SAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l--~~F~~~G~V~~v~i~~d~~g~skG-~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      .-...+.++.++.+...+.++  ..|..+|.|+.|++.......+.. +.++++....+++.|... .+.-+.++.+.|.
T Consensus       568 ~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~p-a~~~~a~~~~av~  646 (881)
T KOG0128|consen  568 PLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVP-AGGALANRSAAVG  646 (881)
T ss_pred             hhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccc-cccccCCccccCC
Confidence            345667888999888877766  679999999999998743333333 899999999999999954 7888888888888


Q ss_pred             ecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC
Q psy1534         106 EAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK  185 (587)
Q Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~  185 (587)
                      .+..+.....                    .+      ..+.       .....+++||+||+..+.++||...|..+|.
T Consensus       647 ~ad~~~~~~~--------------------~k------vs~n-------~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~  693 (881)
T KOG0128|consen  647 LADAEEKEEN--------------------FK------VSPN-------EIRDLIKIFVSNLSPKMSEEDLSERFSPSGT  693 (881)
T ss_pred             CCCchhhhhc--------------------cC------cCch-------HHHHHHHHHHhhcchhhcCchhhhhcCccch
Confidence            7774432110                    00      0000       0112368999999999999999999999999


Q ss_pred             eeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHH
Q psy1534         186 VENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISM  219 (587)
Q Consensus       186 i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~  219 (587)
                      +..++|.-.. .++.+|+||++|..++++.+||..
T Consensus       694 ~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f  728 (881)
T KOG0128|consen  694 IEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF  728 (881)
T ss_pred             hhhHHHHHHhhccccccceeeEeecCCchhhhhhh
Confidence            8887776333 388899999999999999999854

>KOG0533|consensus

Probab=98.65  E-value=1.2e-07  Score=90.56  Aligned_cols=83  Identities=27%  Similarity=0.398  Sum_probs=76.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ....+|+|.|||+.++++||+++|..||.+..+.+..++.|.+.|.|-|.|...++|.+|++.+|+..+.|+++++....
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            33478999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ...
T Consensus       161 ~~~  163 (243)
T KOG0533|consen  161 SPS  163 (243)
T ss_pred             Ccc
Confidence            554

>KOG0112|consensus

Probab=98.59  E-value=3.8e-08  Score=106.38  Aligned_cols=161  Identities=12%  Similarity=0.127  Sum_probs=133.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++||++||+..+++.+| ..|..+|.|.+|.|.+-.-++---|+||.|.+.+.+-+|+..+.+..|..-.+++.+..
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            35568999999999999999 68999999999998776444445699999999999999999988887775555554443


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      .+                                             ..+.+.+|+++|+..+....|...|..||.|..
T Consensus       450 ~k---------------------------------------------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~  484 (975)
T KOG0112|consen  450 PK---------------------------------------------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRI  484 (975)
T ss_pred             cc---------------------------------------------cccceeeccCCCCCCChHHHHHHHhhccCccee
Confidence            11                                             123578999999999999999999999999998


Q ss_pred             EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEEEccCCCC
Q psy1534         189 VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF--ERRITVRMDRVADR  240 (587)
Q Consensus       189 v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~~a~~~~~  240 (587)
                      |.+-..     .-|++|.|++...|+.|++.|.+..|.  .+++.|.++.....
T Consensus       485 Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  485 IDYRHG-----QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             eecccC-----CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence            877543     349999999999999999999999997  46788888776553

>KOG4661|consensus

Probab=98.56  E-value=1.6e-07  Score=96.24  Aligned_cols=82  Identities=23%  Similarity=0.366  Sum_probs=73.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..+++|||.+|...+.-.||+.+|++||+|+-.+++.+.. --.++|+||++.+.++|.+||+.||...|.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            3468899999999999999999999999999999998763 345789999999999999999999999999999999987


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      +..
T Consensus       483 KNE  485 (940)
T KOG4661|consen  483 KNE  485 (940)
T ss_pred             ccC
Confidence            654

>KOG0129|consensus

Probab=98.47  E-value=2.8e-06  Score=87.37  Aligned_cols=56  Identities=29%  Similarity=0.369  Sum_probs=51.9

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHh-hcCCeeEEEeecC------CCeEEEEECCHHHHHHHHHH
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFR-NCGDIKFAEIKGK------GDIGLVRFDSEWTAKRAIDM  571 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~-~~G~v~~~~~~~~------~g~g~v~f~~~~~a~~Ai~~  571 (587)
                      ..||||.+||--++.++|..+|. -||.|+++-|+.|      +|-|-|.|.+..+--+||.+
T Consensus       370 rrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  370 RRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            46999999999999999999999 8999999999665      58899999999999999986

>KOG0151|consensus

Probab=98.45  E-value=6.1e-07  Score=94.73  Aligned_cols=87  Identities=22%  Similarity=0.322  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC----CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRI  230 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  230 (587)
                      ..+.+++|||+||++.++|+.|...|..||.|..++|+..+.    .+.+-|+||.|-+..+|++|++.|+|..+....+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            466789999999999999999999999999999999998763    5567799999999999999999999999999999


Q ss_pred             EEEEccCCCCC
Q psy1534         231 TVRMDRVADRL  241 (587)
Q Consensus       231 ~v~~a~~~~~~  241 (587)
                      ++-|.++..-.
T Consensus       250 K~gWgk~V~ip  260 (877)
T KOG0151|consen  250 KLGWGKAVPIP  260 (877)
T ss_pred             eeccccccccC
Confidence            99998665543

>KOG4454|consensus

Probab=98.45  E-value=7.9e-08  Score=87.59  Aligned_cols=77  Identities=25%  Similarity=0.273  Sum_probs=72.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..++|||.|+...++|+-|.++|-+.|.|..|.|..+++++.+ ||||.|.++....-|++.+||..+.++.+.|++-
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            3579999999999999999999999999999999999998888 9999999999999999999999999999988774

>KOG0226|consensus

Probab=98.43  E-value=1.2e-07  Score=88.35  Aligned_cols=78  Identities=14%  Similarity=0.254  Sum_probs=73.0

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+||.+.|--+++.+.| ..|.+|-.-...++++|. ||++|||+||.|.+++++..|+++|+|..++.|+|++..+.
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            5568999999999999999 789999999999999996 99999999999999999999999999999999999998776

>KOG4209|consensus

Probab=98.39  E-value=5e-07  Score=86.72  Aligned_cols=80  Identities=25%  Similarity=0.324  Sum_probs=73.8

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ...+...|||+|+.+.+|.+++ .+|+.||.|..|.|++|. ++.+|||+||+|.+.+.+++|+. ||+..|.++.|.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            3457789999999999999999 569999999999999998 77899999999999999999997 99999999999999


Q ss_pred             ecc
Q psy1534         106 EAV  108 (587)
Q Consensus       106 ~a~  108 (587)
                      +..
T Consensus       176 ~~r  178 (231)
T KOG4209|consen  176 LKR  178 (231)
T ss_pred             eee
Confidence            877

>KOG0116|consensus

Probab=98.37  E-value=4.9e-07  Score=93.40  Aligned_cols=74  Identities=23%  Similarity=0.311  Sum_probs=65.9

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .|||+|||.+++..+| +.|..||+|+...|.... .++...||||+|.+.++++.||++ +-..+++++|.|+.-.
T Consensus       290 ~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  290 GIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             ceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            4999999999999999 789999999998887754 455559999999999999999987 6888999999998755

>KOG0116|consensus

Probab=98.36  E-value=1.6e-06  Score=89.63  Aligned_cols=82  Identities=27%  Similarity=0.363  Sum_probs=69.9

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ...|||+|||.++++++|+++|..||.|+...|.... .++..+||||+|.+.++++.||++ +-..+.+++|.|+-.+.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            4559999999999999999999999999988877654 345459999999999999999987 67788999999998776


Q ss_pred             CCCC
Q psy1534         238 ADRL  241 (587)
Q Consensus       238 ~~~~  241 (587)
                      ..+.
T Consensus       367 ~~~g  370 (419)
T KOG0116|consen  367 GFRG  370 (419)
T ss_pred             cccc
Confidence            5443

>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=98.33  E-value=1.2e-06  Score=73.41  Aligned_cols=70  Identities=17%  Similarity=0.427  Sum_probs=48.1

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCC-----cccCceEEEEE
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT-----RIDGKIIDVTF  586 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~-----~~~g~~i~v~~  586 (587)
                      +.|+|.+++..++.++|+++|++||.|.|+++.+....|+|.|.+.+.|+.|++.+.-.     .|.+..+++++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            57899999999999999999999999999999988899999999999999999987655     56666666654

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

>KOG4660|consensus

Probab=98.25  E-value=7.5e-07  Score=92.22  Aligned_cols=72  Identities=25%  Similarity=0.338  Sum_probs=65.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      .....+|+|-|||.++++++|+++|+.||+|..|+.-+.+    +|.+||+|-|..+|++|+++|++..|.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~----~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK----RGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc----CceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3456799999999999999999999999999997765543    68999999999999999999999999999887

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

Probab=98.25  E-value=8.5e-06  Score=66.68  Aligned_cols=80  Identities=18%  Similarity=0.311  Sum_probs=68.0

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHh--cCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeC----CeEEEE
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRL--AGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLF----ERRITV  232 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~--~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~----g~~l~v  232 (587)
                      ++|-|+|||...+.++|.+++..  .|...-+.++.|.. +.+.|||||.|.+++.|.+-.+.++|+.+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            58999999999999999998876  35567778888874 788999999999999999999999999886    567788


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      .+|+-+.
T Consensus        82 ~yAriQG   88 (97)
T PF04059_consen   82 SYARIQG   88 (97)
T ss_pred             ehhHhhC
Confidence            8876553

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

>KOG0151|consensus

Probab=98.24  E-value=1.9e-06  Score=91.13  Aligned_cols=82  Identities=11%  Similarity=0.177  Sum_probs=74.0

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC----CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD----TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK  101 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~----~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~  101 (587)
                      .+.|...+|||+||+..++++.| ..|..||+|..|+|+.-+    ..+.+-|+||-|-+..||++|++.|+|..+..++
T Consensus       169 dgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  169 DGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE  248 (877)
T ss_pred             CCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee
Confidence            45677789999999999999999 789999999999999754    3356689999999999999999999999999999


Q ss_pred             EEEEecc
Q psy1534         102 LVIKEAV  108 (587)
Q Consensus       102 i~V~~a~  108 (587)
                      +++.|..
T Consensus       249 ~K~gWgk  255 (877)
T KOG0151|consen  249 MKLGWGK  255 (877)
T ss_pred             eeecccc
Confidence            9999986

>KOG4660|consensus

Probab=98.24  E-value=8.5e-07  Score=91.81  Aligned_cols=177  Identities=14%  Similarity=0.105  Sum_probs=107.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....+.|+|-|||.++++++| ++|+.||+|++|+.-+.    .+|.+||+|.|..+|+.|+++|++.+|.|+.|+....
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~  147 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGG  147 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCc
Confidence            345568999999999999999 89999999999765443    4689999999999999999999999999999882211


Q ss_pred             ccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCee
Q psy1534         108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVE  187 (587)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~  187 (587)
                      .+....-.     .  ....|       ..+...      .......... ...+|+ .|++..+..-++..|.-+|.+.
T Consensus       148 ~~~~~~~~-----~--~~~~~-------~~~~~p------~a~s~pgg~~-~~~~~g-~l~P~~s~~~~~~~~~~~~~~~  205 (549)
T KOG4660|consen  148 ARRAMGLQ-----S--GTSFL-------NHFGSP------LANSPPGGWP-RGQLFG-MLSPTRSSILLEHISSVDGSSP  205 (549)
T ss_pred             ccccchhc-----c--cchhh-------hhccch------hhcCCCCCCc-CCccee-eeccchhhhhhhcchhccCccc
Confidence            11110000     0  00111       011000      0000000111 123333 3888888877777777788765


Q ss_pred             EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         188 NVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       188 ~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      . +.....    .---|++|.+..++..+...+ |..+.+....+.++.+
T Consensus       206 ~-~~~~~~----~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  206 G-RETPLL----NHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             c-ccccch----hhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            4 211111    113567777777775554432 4555555555555444

>KOG4209|consensus

Probab=98.23  E-value=1.6e-06  Score=83.22  Aligned_cols=80  Identities=26%  Similarity=0.389  Sum_probs=74.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ....+||+|+.+.++.+++...|+.||.|..+.|+.|+. +.++||+||+|.+.+.+++|+. |++..|.++.+.|.+.+
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            456899999999999999999999999999999999997 7899999999999999999997 99999999999999876


Q ss_pred             CC
Q psy1534         237 VA  238 (587)
Q Consensus       237 ~~  238 (587)
                      ..
T Consensus       179 ~~  180 (231)
T KOG4209|consen  179 TN  180 (231)
T ss_pred             ee
Confidence            65

>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=98.22  E-value=5.8e-06  Score=64.16  Aligned_cols=65  Identities=29%  Similarity=0.452  Sum_probs=46.2

Q ss_pred             eEEEeCCCCCCChHHH----HHHHhhcC-CeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         518 TVVVKNLPPTITWQEL----RDKFRNCG-DIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       518 ~v~V~~Lp~~~~~~~l----~~~f~~~G-~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .|+|+|||.+.+...+    +.++..+| +|..+    ..++|+|.|.+++.|++|.++|+|..+.|++|.|.+
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            6899999999987665    45555777 57654    247999999999999999999999999999999975

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

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.20  E-value=4.3e-06  Score=64.91  Aligned_cols=69  Identities=17%  Similarity=0.277  Sum_probs=48.6

Q ss_pred             CcEEEcCCCCCCCHHHH-----HhcccCC-CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          33 VPVVMDLIQGDASLYQI-----SHLSTVG-DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-----~~F~~~G-~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .-|||.|||.+.+-..|     .++.-|| +|.+|.         .+.|+|.|.+.+.|++|.+.|+|..+.|++|.|.+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            35899999999987765     5677777 787762         37899999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            8733

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

>KOG2193|consensus

Probab=98.09  E-value=3.5e-07  Score=90.90  Aligned_cols=151  Identities=17%  Similarity=0.212  Sum_probs=119.7

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCC-CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC-ceeCCeEEEEEeccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVG-DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR-FETKGRKLVIKEAVE  109 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G-~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g-~~l~gr~i~V~~a~~  109 (587)
                      +++|++||....+-.+| .+|..-- ....-.+++      .||+||.+.+...|.+|++.+++ ..+.|+++.|..+..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            57999999999999998 5674431 111122333      38999999999999999999998 568899999998875


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                      ++.                                             .++++-|.|+|+...++-|..+...||.++.|
T Consensus        76 kkq---------------------------------------------rsrk~Qirnippql~wevld~Ll~qyg~ve~~  110 (584)
T KOG2193|consen   76 KKQ---------------------------------------------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENC  110 (584)
T ss_pred             HHH---------------------------------------------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHh
Confidence            532                                             13578899999999999999999999999988


Q ss_pred             EEee-CCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         190 EIAL-DKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       190 ~i~~-~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .... +..   .-..-|+|...+.+..||..|++..+....++|.|-..
T Consensus       111 eqvnt~~e---tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen  111 EQVNTDSE---TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPD  156 (584)
T ss_pred             hhhccchH---HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCch
Confidence            6543 321   22345788999999999999999999999999988544

>KOG1995|consensus

Probab=98.02  E-value=2.9e-05  Score=76.70  Aligned_cols=71  Identities=24%  Similarity=0.325  Sum_probs=61.5

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEE------------e--ecCCCeEEEEECCHHHHHHHHHHhCCCcccCce
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAE------------I--KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKI  581 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~------------~--~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~  581 (587)
                      .-+|||.+||+.++.++|.++|.++|.|..-+            +  ...++.|.|.|++...|+.||..+++..|++..
T Consensus        66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~  145 (351)
T KOG1995|consen   66 NETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNT  145 (351)
T ss_pred             cccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCC
Confidence            45999999999999999999999999884222            1  122589999999999999999999999999999


Q ss_pred             EEEEE
Q psy1534         582 IDVTF  586 (587)
Q Consensus       582 i~v~~  586 (587)
                      |+|.+
T Consensus       146 ikvs~  150 (351)
T KOG1995|consen  146 IKVSL  150 (351)
T ss_pred             chhhh
Confidence            99864

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

Probab=97.99  E-value=3.7e-05  Score=62.94  Aligned_cols=76  Identities=17%  Similarity=0.110  Sum_probs=63.5

Q ss_pred             CcEEEcCCCCCCCHHHH-Hhcc--cCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeC----CeEEEE
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLS--TVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETK----GRKLVI  104 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~--~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~----gr~i~V  104 (587)
                      .+|-|+|||...|.++| +++.  -.|...-+.++.|. ++.+.|||||-|.+++.|.+-.+.++|..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            57999999999999987 4332  24677778999995 8889999999999999999999999998886    466677


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7776

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

>KOG0112|consensus

Probab=97.79  E-value=2e-05  Score=85.84  Aligned_cols=71  Identities=17%  Similarity=0.274  Sum_probs=63.3

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccC--ceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDG--KIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g--~~i~v~~  586 (587)
                      ..+++|.+|+.-+....|...|..||.|.-+++....-++.|.|++...++.|++.|-|..|++  ++|+|.|
T Consensus       455 ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  455 TTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             ceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            3589999999999999999999999999999988777899999999999999999999999985  5566653

>KOG1995|consensus

Probab=97.72  E-value=2.2e-05  Score=77.58  Aligned_cols=81  Identities=16%  Similarity=0.232  Sum_probs=73.9

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeE--------EEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCC
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVT--------YVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG   99 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~--------~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g   99 (587)
                      ....+|||-+||..+++++| ++|.++|.|.        .|+|-+|+ |++.||-|.|.|.++..|+.|+..++++.|.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            46678999999999999999 7899999887        37888886 99999999999999999999999999999999


Q ss_pred             eEEEEEecccc
Q psy1534         100 RKLVIKEAVED  110 (587)
Q Consensus       100 r~i~V~~a~~~  110 (587)
                      .+|+|..+.+.
T Consensus       144 n~ikvs~a~~r  154 (351)
T KOG1995|consen  144 NTIKVSLAERR  154 (351)
T ss_pred             CCchhhhhhhc
Confidence            99999988844

>KOG4676|consensus

Probab=97.72  E-value=3.7e-05  Score=76.19  Aligned_cols=187  Identities=14%  Similarity=0.071  Sum_probs=123.1

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC----CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD----TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~----~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..-|-|-||.+.++.+++ .+|.-.|+|.+++|+...    -......|||.|.+...+.-|- .|.+++|-++.|.|.+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEe
Confidence            346889999999999999 789999999999998753    2244579999999999999887 6789999999999988


Q ss_pred             cccccCCCC-------CCC-CCCCCCCchhhhhccCCc-c-------cCCCCCCChhhhhccCCCCCCCcEEEEecCCCC
Q psy1534         107 AVEDKGGRR-------NMG-GGGGVDRDLSALLQNNSS-K-------FGNTYGLSPQFLESLGINCPLINKVFVANLDYK  170 (587)
Q Consensus       107 a~~~~~~~~-------~~~-~~~~~~~~~~~~~~~~~~-~-------~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~  170 (587)
                      +........       ... ..+-...+. -.+...+. .       ...+..+++.... ... .....+++|.+|+..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg-~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A-~kl-eeirRt~~v~sl~~~  162 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDG-VLPGDRPLTKINHSPNAILKTPELPPQAAA-KKL-EEIRRTREVQSLISA  162 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCC-ccCCCCccccccCCccceecCCCCChHhhh-hhh-HHHHhhhhhhcchhh
Confidence            762211100       000 000001111 11111110 1       1111112221111 111 112378999999999


Q ss_pred             CcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy1534         171 VDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF  226 (587)
Q Consensus       171 ~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  226 (587)
                      +...++-+.|..+|+|....+....   ..-+|-|+|........|+.. +|..+.
T Consensus       163 ~~l~e~~e~f~r~Gev~ya~~ask~---~s~~c~~sf~~qts~~halr~-~gre~k  214 (479)
T KOG4676|consen  163 AILPESGESFERKGEVSYAHTASKS---RSSSCSHSFRKQTSSKHALRS-HGRERK  214 (479)
T ss_pred             hcchhhhhhhhhcchhhhhhhhccC---CCcchhhhHhhhhhHHHHHHh-cchhhh
Confidence            9999999999999998877654432   345778999998888888865 777665

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

Probab=97.71  E-value=5.7e-05  Score=63.34  Aligned_cols=70  Identities=19%  Similarity=0.321  Sum_probs=44.2

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCc-----eeCCeEEEEEE
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ-----NLFERRITVRM  234 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~-----~~~g~~l~v~~  234 (587)
                      +.|+|.+++..++.++|+++|+.||.|..|.+.+..     ..|||.|.+.+.|++|+..+.-.     .+.+..+.+++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-----~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-----TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-----CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            579999999999999999999999999999887753     37999999999999999877433     44555555443

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

>KOG2314|consensus

Probab=97.61  E-value=0.00012  Score=75.87  Aligned_cols=78  Identities=19%  Similarity=0.238  Sum_probs=64.0

Q ss_pred             CCCcEEEcCCCCCC--CHHHH-----HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC-CeEE
Q psy1534          31 LEVPVVMDLIQGDA--SLYQI-----SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK-GRKL  102 (587)
Q Consensus        31 ~~~~vfV~nlp~~~--t~~~l-----~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~-gr~i  102 (587)
                      -..-|+|.|+|---  ..+-|     ++|+++|+|..+.++.++.|.++||.|++|.+..+|+.|++.|||+.|. .+.+
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            33468999998533  33332     6899999999999999987779999999999999999999999999887 5677


Q ss_pred             EEEecc
Q psy1534         103 VIKEAV  108 (587)
Q Consensus       103 ~V~~a~  108 (587)
                      .|...+
T Consensus       137 ~v~~f~  142 (698)
T KOG2314|consen  137 FVRLFK  142 (698)
T ss_pred             Eeehhh
Confidence            776654

>KOG0115|consensus

Probab=97.59  E-value=0.00016  Score=68.17  Aligned_cols=89  Identities=26%  Similarity=0.335  Sum_probs=80.6

Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEE
Q psy1534          83 DLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV  162 (587)
Q Consensus        83 e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  162 (587)
                      .-|+.|..+|++....++.++|.++..                                                  ..|
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~--------------------------------------------------a~l   34 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH--------------------------------------------------AEL   34 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc--------------------------------------------------ceE
Confidence            357778888999999999999999984                                                  279


Q ss_pred             EEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy1534         163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN  221 (587)
Q Consensus       163 ~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  221 (587)
                      ||.||+..++.+.|.+.|+.||.|....+.-|..+++.+-++|.|...-.|.+|+..++
T Consensus        35 ~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   35 YVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             EEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            99999999999999999999999999888888889999999999999999999998774

>KOG4676|consensus

Probab=97.58  E-value=9.2e-05  Score=73.48  Aligned_cols=75  Identities=19%  Similarity=0.226  Sum_probs=62.4

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC----CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..|.|.||.+.++.+.++.+|.-.|+|.++.|+...+    ....-.|||.|.+...+..|- .|.+..+-++.|.|...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence            3899999999999999999999999999999887543    344568999999998888875 56777888888777654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.55  E-value=8.5e-05  Score=72.16  Aligned_cols=78  Identities=9%  Similarity=0.093  Sum_probs=61.7

Q ss_pred             CcEEEcCCCCCCCHHH----H---HhcccCCCeEEEEEeeCC-CCCc-ceEE--EEEECCHHHHHHHHHHhCCceeCCeE
Q psy1534          33 VPVVMDLIQGDASLYQ----I---SHLSTVGDVTYVEILNDD-TGKP-RGSA--IVEFQSPDLVRKAVNKMHRFETKGRK  101 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~----l---~~F~~~G~V~~v~i~~d~-~g~s-kG~a--FV~F~~~e~A~~Al~~l~g~~l~gr~  101 (587)
                      .-|||-+||..+-.++    |   ++|.+||.|..|.|-+.. .-.+ .+.+  ||+|.+.|||.+||.+.+|..++||.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            3588999988775554    3   789999999998776553 2221 2334  99999999999999999999999999


Q ss_pred             EEEEecccc
Q psy1534         102 LVIKEAVED  110 (587)
Q Consensus       102 i~V~~a~~~  110 (587)
                      |+..+-..+
T Consensus       195 lkatYGTTK  203 (480)
T COG5175         195 LKATYGTTK  203 (480)
T ss_pred             EeeecCchH
Confidence            999987744

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

Probab=97.53  E-value=0.00023  Score=51.54  Aligned_cols=52  Identities=19%  Similarity=0.346  Sum_probs=44.8

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHH
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAI  569 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai  569 (587)
                      +.|.|.+.|.+..+ ++..+|..||+|+...+.......+|.|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            47899999988774 45558999999999999866689999999999999985

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

Probab=97.49  E-value=0.00014  Score=52.71  Aligned_cols=52  Identities=12%  Similarity=0.183  Sum_probs=45.2

Q ss_pred             CcEEEcCCCCCCCHHHHHhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHH
Q psy1534          33 VPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAV   89 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al   89 (587)
                      +.|-|.+.+.+..+..|++|..||+|.++.+..     .+.+.||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            457899999999888889999999999988762     2468999999999999996

>KOG2193|consensus

Probab=97.49  E-value=1.1e-05  Score=80.48  Aligned_cols=69  Identities=16%  Similarity=0.498  Sum_probs=57.4

Q ss_pred             eEEEeCCCCCCChHHHHHHHhhcCCeeEEEeec-CCCeEE--EEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG-KGDIGL--VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       518 ~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~-~~g~g~--v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .+-|+|+|....|+=|..|...||.|..|++.. +.-.+.  |.|.+.+.++.||.+|||..|...-++|-|
T Consensus        82 k~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Y  153 (584)
T KOG2193|consen   82 KIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGY  153 (584)
T ss_pred             hhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhccc
Confidence            577889999999999999999999999888843 333333  588999999999999999999877776654

>KOG2314|consensus

Probab=97.26  E-value=0.001  Score=69.29  Aligned_cols=78  Identities=27%  Similarity=0.362  Sum_probs=65.9

Q ss_pred             CCcEEEEecCCCCCc------HHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CeEE
Q psy1534         158 LINKVFVANLDYKVD------EKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF-ERRI  230 (587)
Q Consensus       158 ~~~~l~V~nLp~~~t------e~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l  230 (587)
                      -.+.|+|-|+|.--.      ..-|..+|+++|+|....++.+..|..+||.|++|.+..+|+.|++.|||+.+. .++.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            357899999986422      234678999999999999999988889999999999999999999999999986 6777


Q ss_pred             EEEEc
Q psy1534         231 TVRMD  235 (587)
Q Consensus       231 ~v~~a  235 (587)
                      .|+.-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77653

>KOG4210|consensus

Probab=97.21  E-value=0.00033  Score=69.81  Aligned_cols=79  Identities=20%  Similarity=0.336  Sum_probs=71.6

Q ss_pred             CCCcEE-EcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          31 LEVPVV-MDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        31 ~~~~vf-V~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++| |++++.++++++| ++|..+|.|..+++..++ ++.++|||||.|.+...+.+|+.. ....+.++++.+.+.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            444677 9999999999999 699999999999999997 999999999999999999999977 788999999999988


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      .+.
T Consensus       262 ~~~  264 (285)
T KOG4210|consen  262 EPR  264 (285)
T ss_pred             CCC
Confidence            744

>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=97.13  E-value=0.0017  Score=53.59  Aligned_cols=65  Identities=23%  Similarity=0.366  Sum_probs=50.7

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEE-------------eecCCCeEEEEECCHHHHHHHHHHhCCCcccCceE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAE-------------IKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKII  582 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~-------------~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i  582 (587)
                      ..-|.|.+.|.. .-..+.++|+.||.|+...             +.....--.|.|+++.+|++|+.+ ||..|.|..+
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEE
Confidence            568999999988 4577899999999997664             444557899999999999999998 9999998654

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.

>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=97.09  E-value=0.0013  Score=54.29  Aligned_cols=77  Identities=17%  Similarity=0.112  Sum_probs=53.6

Q ss_pred             CCCcEEEcCCCCCCCHHHHHhcccCCCeEEEE-EeeC-------CCCCcceEEEEEECCHHHHHHHHHHhCCceeCCe-E
Q psy1534          31 LEVPVVMDLIQGDASLYQISHLSTVGDVTYVE-ILND-------DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR-K  101 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l~~F~~~G~V~~v~-i~~d-------~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr-~  101 (587)
                      .+.-|.|=+.|...+...|++|++||+|.+.. +.++       +.-.....-.|+|.++.+|++||.+ ||..|.|. .
T Consensus         5 ~~~wVtVFGfp~~~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPSASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GGGHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEE
T ss_pred             CCeEEEEEccCHHHHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEE
Confidence            34558888999998888889999999998875 1111       1001246889999999999999976 99999985 5


Q ss_pred             EEEEecc
Q psy1534         102 LVIKEAV  108 (587)
Q Consensus       102 i~V~~a~  108 (587)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            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.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.00  E-value=0.0016  Score=63.65  Aligned_cols=80  Identities=16%  Similarity=0.258  Sum_probs=63.3

Q ss_pred             CcEEEEecCCCCCcHHHH------HHHHHhcCCeeEEEEeeCCC--CCcce-E-EEEEecCHHHHHHHHHHhCCceeCCe
Q psy1534         159 INKVFVANLDYKVDEKKL------REVFRLAGKVENVEIALDKD--GKSRG-F-GTVEFDHPVEAVQSISMLNNQNLFER  228 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l------~~~F~~~G~i~~v~i~~~~~--g~~~g-~-afV~f~~~~~A~~Al~~l~g~~~~g~  228 (587)
                      .+-+||-+||+.+-.|++      .++|.+||.|..|.|-+.-.  ....+ + .||+|.+.|+|.+||...+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            457899999988766652      58999999999988866431  11122 2 49999999999999999999999999


Q ss_pred             EEEEEEccCC
Q psy1534         229 RITVRMDRVA  238 (587)
Q Consensus       229 ~l~v~~a~~~  238 (587)
                      .|+..|...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999886544

>KOG2202|consensus

Probab=96.91  E-value=0.0003  Score=66.56  Aligned_cols=56  Identities=14%  Similarity=0.236  Sum_probs=50.3

Q ss_pred             ccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        53 ~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .+||+|++++|..+-.-.-+|-+||.|...|+|++|++.||+..+.|++|...+..
T Consensus        91 ~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   91 DKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            39999999988776544567999999999999999999999999999999999887

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

Probab=96.86  E-value=0.0054  Score=53.75  Aligned_cols=72  Identities=22%  Similarity=0.323  Sum_probs=54.6

Q ss_pred             CCCCCCeEEEeCCC----CC-CChH----HHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceE
Q psy1534         512 SNIERDTVVVKNLP----PT-ITWQ----ELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKII  582 (587)
Q Consensus       512 ~~~~~~~v~V~~Lp----~~-~~~~----~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i  582 (587)
                      .+++..||.|+=+.    .+ ...+    +|.+.|..||+|+-+++..+  +=+|.|.+-++|-+|+.. +|.+++|+.|
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--~mwVTF~dg~sALaals~-dg~~v~g~~l   99 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--TMWVTFRDGQSALAALSL-DGIQVNGRTL   99 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--CEEEEESSCHHHHHHHHG-CCSEETTEEE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--eEEEEECccHHHHHHHcc-CCcEECCEEE
Confidence            34557799998444    21 2222    78889999999998888775  899999999999999985 9999999999


Q ss_pred             EEEE
Q psy1534         583 DVTF  586 (587)
Q Consensus       583 ~v~~  586 (587)
                      +|++
T Consensus       100 ~i~L  103 (146)
T PF08952_consen  100 KIRL  103 (146)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            9985

; PDB: 1UFW_A 2DNR_A.

>KOG4849|consensus

Probab=96.85  E-value=0.00088  Score=65.57  Aligned_cols=75  Identities=16%  Similarity=0.320  Sum_probs=65.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCC--eeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGK--VENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~--i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..++||+||-|.+|++||.+.....|.  +.+++++.++. |.++|||+|...+....++.++.|-.++|.|..-.|.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            357899999999999999999887764  67888888885 9999999999999999999999999999998765553

>KOG1855|consensus

Probab=96.81  E-value=0.00082  Score=67.82  Aligned_cols=62  Identities=24%  Similarity=0.419  Sum_probs=54.7

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC-------------------CCeEEEEECCHHHHHHHHHHhCCC
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK-------------------GDIGLVRFDSEWTAKRAIDMMDRT  575 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~-------------------~g~g~v~f~~~~~a~~Ai~~l~g~  575 (587)
                      +.++|.++|||.+-..|.|.++|..+|.|..++|-..                   +-||+|+|+..+.|.+|.+.||..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            4579999999999999999999999999999998433                   257999999999999999998665


Q ss_pred             c
Q psy1534         576 R  576 (587)
Q Consensus       576 ~  576 (587)
                      .
T Consensus       310 ~  310 (484)
T KOG1855|consen  310 Q  310 (484)
T ss_pred             h
Confidence            4

>KOG1855|consensus

Probab=96.73  E-value=0.0013  Score=66.46  Aligned_cols=70  Identities=17%  Similarity=0.274  Sum_probs=58.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeC---CC---CCc--------ceEEEEEecCHHHHHHHHHHhC
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD---KD---GKS--------RGFGTVEFDHPVEAVQSISMLN  221 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~---g~~--------~g~afV~f~~~~~A~~Al~~l~  221 (587)
                      ..++++|.+-|||.+-.-+.|.++|+.+|.|..|+|...   +.   +.+        +-+|+|+|...+.|.+|.+.|+
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            346889999999999999999999999999999999887   31   222        4579999999999999999886


Q ss_pred             Ccee
Q psy1534         222 NQNL  225 (587)
Q Consensus       222 g~~~  225 (587)
                      ...-
T Consensus       308 ~e~~  311 (484)
T KOG1855|consen  308 PEQN  311 (484)
T ss_pred             hhhh
Confidence            5443

>KOG2202|consensus

Probab=96.73  E-value=0.00073  Score=64.00  Aligned_cols=66  Identities=20%  Similarity=0.238  Sum_probs=54.6

Q ss_pred             HHHHHHHH-hcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         174 KKLREVFR-LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       174 ~~l~~~F~-~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      +||...|+ +||+|++++|-.+..-.-+|-++|.|...++|++|++.||+..+.|++|.+.+..-..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCc
Confidence            45555666 8999999877765545557889999999999999999999999999999999865443

>KOG0115|consensus

Probab=96.62  E-value=0.005  Score=58.35  Aligned_cols=76  Identities=24%  Similarity=0.256  Sum_probs=64.9

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC----ceeCCeEEEEEec
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR----FETKGRKLVIKEA  107 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g----~~l~gr~i~V~~a  107 (587)
                      ..|||.||..-+..+.| +.|+.||+|+...++.|..++..+-++|+|...-.|.+|++.+.-    ....+++.-|.+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            67999999999999988 789999999998888888888889999999999999999998753    3345677777665


Q ss_pred             c
Q psy1534         108 V  108 (587)
Q Consensus       108 ~  108 (587)
                      .
T Consensus       112 e  112 (275)
T KOG0115|consen  112 E  112 (275)
T ss_pred             h
Confidence            5

>KOG4849|consensus

Probab=96.62  E-value=0.0012  Score=64.71  Aligned_cols=75  Identities=11%  Similarity=0.185  Sum_probs=65.7

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCC--CeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVG--DVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G--~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .+||+||-|-+|.+|| +....-|  .+.+++++.++ +|+|||||+|..-+....++-++.|-.++|+|+.-.|....
T Consensus        82 ~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   82 CCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            5899999999988888 7666656  67888999887 89999999999999999999999999999999877776665

>KOG1996|consensus

Probab=96.61  E-value=0.0046  Score=59.42  Aligned_cols=62  Identities=21%  Similarity=0.116  Sum_probs=51.3

Q ss_pred             HhcccCCCeEEEEEeeCCCC-Cc-ceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccccc
Q psy1534          50 SHLSTVGDVTYVEILNDDTG-KP-RGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK  111 (587)
Q Consensus        50 ~~F~~~G~V~~v~i~~d~~g-~s-kG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~  111 (587)
                      +.+++||.|..|.|..+++- .. -=--||+|+..++|.+|+-.|||..|+||.++.++..-.+
T Consensus       305 eEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~ek  368 (378)
T KOG1996|consen  305 EECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLEK  368 (378)
T ss_pred             HHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHHh
Confidence            56999999999998887522 11 1236999999999999999999999999999999887443

>KOG3152|consensus

Probab=96.59  E-value=0.0015  Score=61.67  Aligned_cols=72  Identities=26%  Similarity=0.340  Sum_probs=60.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC---------CCcc----eEEEEEecCHHHHHHHHHHhCCce
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---------GKSR----GFGTVEFDHPVEAVQSISMLNNQN  224 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---------g~~~----g~afV~f~~~~~A~~Al~~l~g~~  224 (587)
                      ..-.||+++||+.+...-|+++|+.||.|-.|.+.....         |.++    --|.|+|.+...|.++...||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            346899999999999999999999999999988876431         1222    237899999999999999999999


Q ss_pred             eCCeE
Q psy1534         225 LFERR  229 (587)
Q Consensus       225 ~~g~~  229 (587)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG1996|consensus

Probab=96.51  E-value=0.008  Score=57.82  Aligned_cols=64  Identities=23%  Similarity=0.165  Sum_probs=52.6

Q ss_pred             HHHHHHHHHhcCCeeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         173 EKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       173 e~~l~~~F~~~G~i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ++++++.+++||.|..|.|..++.  -...---||+|+..++|.+|+-.|||+.|+||.+...+-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            357889999999999999888764  1112237999999999999999999999999998876643

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

Probab=96.35  E-value=0.028  Score=49.33  Aligned_cols=78  Identities=21%  Similarity=0.179  Sum_probs=53.0

Q ss_pred             CCCCCcEEEEecCCC------CCcH---HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy1534         155 NCPLINKVFVANLDY------KVDE---KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL  225 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~------~~te---~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  225 (587)
                      ..|+..+|.|.=+.+      ...+   .+|.+.|..||++.-|++.-+       .-+|+|.+-+.|.+|+ .++|.++
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaal-s~dg~~v   94 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAAL-SLDGIQV   94 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHH-HGCCSEE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHH-ccCCcEE
Confidence            455666777775551      2222   367888999999888887754       4799999999999999 5699999


Q ss_pred             CCeEEEEEEccCCCC
Q psy1534         226 FERRITVRMDRVADR  240 (587)
Q Consensus       226 ~g~~l~v~~a~~~~~  240 (587)
                      .|+.|+|+...+..-
T Consensus        95 ~g~~l~i~LKtpdW~  109 (146)
T PF08952_consen   95 NGRTLKIRLKTPDWL  109 (146)
T ss_dssp             TTEEEEEEE------
T ss_pred             CCEEEEEEeCCccHH
Confidence            999999999776653

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.92  E-value=0.051  Score=40.42  Aligned_cols=54  Identities=17%  Similarity=0.213  Sum_probs=45.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhc---CCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLA---GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML  220 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~---G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l  220 (587)
                      .+|+|.++. +++.+||+.+|..|   .....|.++-|.      -|-|.|.+.+.|.+||..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            489999985 58899999999998   125688888875      4889999999999999764

>KOG0921|consensus

Probab=95.85  E-value=0.056  Score=60.18  Aligned_cols=14  Identities=29%  Similarity=0.541  Sum_probs=6.5

Q ss_pred             CCcceEEEEEecCH
Q psy1534         197 GKSRGFGTVEFDHP  210 (587)
Q Consensus       197 g~~~g~afV~f~~~  210 (587)
                      |+.++|+--.|++.
T Consensus       899 g~q~~~~g~kfsdh  912 (1282)
T KOG0921|consen  899 GTQRKFAGNKFSDH  912 (1282)
T ss_pred             cchhhccccccccc
Confidence            44444544444443

>KOG3152|consensus

Probab=95.81  E-value=0.0058  Score=57.83  Aligned_cols=64  Identities=28%  Similarity=0.431  Sum_probs=57.3

Q ss_pred             eEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC------------------CCeEEEEECCHHHHHHHHHHhCCCcccC
Q psy1534         518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK------------------GDIGLVRFDSEWTAKRAIDMMDRTRIDG  579 (587)
Q Consensus       518 ~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~------------------~g~g~v~f~~~~~a~~Ai~~l~g~~~~g  579 (587)
                      .|++++||.......|+.++..||+|-++-+-+.                  -.+|+|+|.+...|.+....||+..|+|
T Consensus        76 VvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Igg  155 (278)
T KOG3152|consen   76 VVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIGG  155 (278)
T ss_pred             EEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccCC
Confidence            8999999999999999999999999977766321                  0459999999999999999999999999


Q ss_pred             ce
Q psy1534         580 KI  581 (587)
Q Consensus       580 ~~  581 (587)
                      ++
T Consensus       156 kk  157 (278)
T KOG3152|consen  156 KK  157 (278)
T ss_pred             CC
Confidence            86

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.59  E-value=0.049  Score=42.72  Aligned_cols=57  Identities=25%  Similarity=0.340  Sum_probs=41.8

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhC
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH   93 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~   93 (587)
                      |...-||-=-+|.++...|| ++|+.||.| .|.-+-|      .-|||...+.+.|..|+..+.
T Consensus         6 P~RdHVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~d------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    6 PSRDHVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWIND------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             -SGCCEEEEE--TT--HHHHHHHCCCCCCE-EEEEECT------TEEEEEECCCHHHHHHHHHHT
T ss_pred             CCcceEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcC------CcEEEEeecHHHHHHHHHHhc
Confidence            34444554449999999999 999999998 5555555      579999999999999998876

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.46  E-value=0.087  Score=39.19  Aligned_cols=54  Identities=19%  Similarity=0.171  Sum_probs=44.1

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcC---CeeEEEeecCCCeEEEEECCHHHHHHHHHHh
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCG---DIKFAEIKGKGDIGLVRFDSEWTAKRAIDMM  572 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G---~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l  572 (587)
                      ..|+|+|+. +.+-+|++.+|..|-   ...+++-..+ ..+-|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD-tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD-TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC-CcEEEEECCHHHHHHHHHcC
Confidence            389999995 688899999999991   2445565555 67899999999999999875

>KOG2591|consensus

Probab=95.32  E-value=0.039  Score=57.83  Aligned_cols=70  Identities=17%  Similarity=0.237  Sum_probs=57.7

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHh--cCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEEEc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRL--AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN--QNLFERRITVRMD  235 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~--~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~a  235 (587)
                      |.|.|+-||..+-+|+++.+|+.  |-.+++|.+-.+.      -=||+|++..||+.|.+.|..  ++|.|++|..++.
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgKpImARIK  249 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMARIK  249 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhhh
Confidence            68899999999999999999986  6678888876643      248999999999999988853  4677888777664

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.30  E-value=0.058  Score=46.65  Aligned_cols=77  Identities=21%  Similarity=0.255  Sum_probs=59.8

Q ss_pred             ccCCCCCCCcEEEcCCCCCCCH-HHH----HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC
Q psy1534          25 IETGAPLEVPVVMDLIQGDASL-YQI----SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG   99 (587)
Q Consensus        25 ~~~~~~~~~~vfV~nlp~~~t~-~~l----~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g   99 (587)
                      +....|+..+|.|+=|..++.- +|+    ...+.||+|.+|.+.-      +-.|.|.|.+..+|-+|+.++.. ...|
T Consensus        79 k~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pg  151 (166)
T PF15023_consen   79 KNTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPG  151 (166)
T ss_pred             ccCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCC
Confidence            3455678889999887777632 233    5579999999998763      45799999999999999998654 6778


Q ss_pred             eEEEEEecc
Q psy1534         100 RKLVIKEAV  108 (587)
Q Consensus       100 r~i~V~~a~  108 (587)
                      ..+.+.|..
T Consensus       152 tm~qCsWqq  160 (166)
T PF15023_consen  152 TMFQCSWQQ  160 (166)
T ss_pred             ceEEeeccc
Confidence            888888765

>KOG2416|consensus

Probab=94.99  E-value=0.02  Score=60.45  Aligned_cols=80  Identities=18%  Similarity=0.184  Sum_probs=64.4

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHh-cCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CeEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRL-AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF---ERRI  230 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l  230 (587)
                      ....++.|||.||-.-+|.-.|+.++.. +|.|++.+|-+     -+..|||.|.+.++|...+.+|||..+-   .+.|
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk-----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK-----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHH-----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            3456899999999999999999999995 66676663322     2457999999999999999999998874   6778


Q ss_pred             EEEEccCCC
Q psy1534         231 TVRMDRVAD  239 (587)
Q Consensus       231 ~v~~a~~~~  239 (587)
                      .+.|.....
T Consensus       515 ~adf~~~de  523 (718)
T KOG2416|consen  515 IADFVRADE  523 (718)
T ss_pred             EeeecchhH
Confidence            887766543

>KOG4285|consensus

Probab=94.22  E-value=0.15  Score=49.66  Aligned_cols=71  Identities=15%  Similarity=0.119  Sum_probs=56.7

Q ss_pred             cEEEcCCCCCCCHHHHHhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC-eEEEEEecccc
Q psy1534          34 PVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG-RKLVIKEAVED  110 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g-r~i~V~~a~~~  110 (587)
                      =|=|=++|....--.|.+|++||+|.++...  .+|   .+-+|.|.+.-+|++||.. ||+.|.| ..|-|+.+..+
T Consensus       199 WVTVfGFppg~~s~vL~~F~~cG~Vvkhv~~--~ng---NwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  199 WVTVFGFPPGQVSIVLNLFSRCGEVVKHVTP--SNG---NWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             eEEEeccCccchhHHHHHHHhhCeeeeeecC--CCC---ceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCCH
Confidence            4667788888888888999999999886543  334   5899999999999999976 9999986 56677776633

>KOG2068|consensus

Probab=93.83  E-value=0.021  Score=56.59  Aligned_cols=79  Identities=11%  Similarity=0.152  Sum_probs=61.4

Q ss_pred             CCcEEEcCCCCCCCH-HHH---HhcccCCCeEEEEEeeCCC--CCcc--eEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          32 EVPVVMDLIQGDASL-YQI---SHLSTVGDVTYVEILNDDT--GKPR--GSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~-~~l---~~F~~~G~V~~v~i~~d~~--g~sk--G~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      ...+||-+|+..... ..|   +.|.+||.|..|.+.++++  ..+-  --++|+|...|+|..||...+|..+.++.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            356888888876643 444   6799999999998888652  1111  1379999999999999999999999999988


Q ss_pred             EEecccc
Q psy1534         104 IKEAVED  110 (587)
Q Consensus       104 V~~a~~~  110 (587)
                      ..+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            8777644

>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=93.82  E-value=0.34  Score=37.75  Aligned_cols=66  Identities=17%  Similarity=0.271  Sum_probs=42.9

Q ss_pred             eEEEe-CCCCCCChHHHHHHHhhcCCe-----eEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         518 TVVVK-NLPPTITWQELRDKFRNCGDI-----KFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       518 ~v~V~-~Lp~~~~~~~l~~~f~~~G~v-----~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      |+||. +=-+.+++.+|..++...+.|     -.++|..+  +.||+-... .|+.+++.|++..+.|++|+|+.
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~   73 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVER   73 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---EEEEE-TT--HHHHHHHHTT--SSS----EEE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEE
Confidence            55555 556788999999999998754     56666665  888887765 78999999999999999999975

; PDB: 2G0C_A 3MOJ_B.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=93.77  E-value=0.29  Score=38.49  Aligned_cols=55  Identities=15%  Similarity=0.238  Sum_probs=41.8

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCC
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDR  574 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g  574 (587)
                      ...+|. .|..+.-.||.++|++||.|.-.=|..  ..|||...+++.+..|++.++-
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~d--TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIND--TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEECT--TEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcC--CcEEEEeecHHHHHHHHHHhcc
Confidence            344455 999999999999999999986555544  5999999999999999998863

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=93.74  E-value=0.17  Score=46.89  Aligned_cols=57  Identities=25%  Similarity=0.195  Sum_probs=47.3

Q ss_pred             hHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhC--CCcccCceEEEEE
Q psy1534         530 WQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMD--RTRIDGKIIDVTF  586 (587)
Q Consensus       530 ~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~--g~~~~g~~i~v~~  586 (587)
                      .+.|+++|..++.++.....+.=+..+|.|.+.++|.+|...|+  +..|.|..++|.+
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf   67 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYF   67 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE-
T ss_pred             HHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEE
Confidence            57899999999998877777766889999999999999999999  9999999999875

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.59  E-value=0.32  Score=42.22  Aligned_cols=74  Identities=15%  Similarity=0.215  Sum_probs=56.1

Q ss_pred             CCCCcEEEEecCCCCCcH----HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         156 CPLINKVFVANLDYKVDE----KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te----~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      .++-.+|.|+=|..++..    ..+....+.||+|.+|.+.-      +--|.|.|.+..+|-+|+.+++. ...|..+.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEE
Confidence            456678888776665433    34556677899999998764      34699999999999999999875 56678888


Q ss_pred             EEEcc
Q psy1534         232 VRMDR  236 (587)
Q Consensus       232 v~~a~  236 (587)
                      +.|..
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            88743

>KOG2591|consensus

Probab=93.27  E-value=0.12  Score=54.26  Aligned_cols=71  Identities=23%  Similarity=0.390  Sum_probs=56.8

Q ss_pred             CCCCCCeEEEeCCCCCCChHHHHHHHhh--cCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCC--cccCceEE
Q psy1534         512 SNIERDTVVVKNLPPTITWQELRDKFRN--CGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT--RIDGKIID  583 (587)
Q Consensus       512 ~~~~~~~v~V~~Lp~~~~~~~l~~~f~~--~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~--~~~g~~i~  583 (587)
                      ....+|.|+++-||..+-.+++|.+|+.  +-+++.|+.-.+ .-=+|+|++..||+.|.+.|...  +|.|+.|.
T Consensus       171 p~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N-~nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  171 PNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN-DNWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec-CceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            3445678889999999999999999986  557888888655 46799999999999999887654  56666654

>KOG2416|consensus

Probab=93.25  E-value=0.058  Score=57.03  Aligned_cols=74  Identities=15%  Similarity=0.118  Sum_probs=61.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-Hhcc-cCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC---CeEEEEE
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLS-TVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK---GRKLVIK  105 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~-~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~---gr~i~V~  105 (587)
                      ..+-|||.||-.-.|+-+| ++.. ..|.|++.+|-+     -|-.|||.|.+.++|...+.+|||..+-   .+.|.+.
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk-----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK-----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHHHHHH-----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            4457999999999999999 6665 788888886533     2467999999999999999999998874   6888888


Q ss_pred             eccc
Q psy1534         106 EAVE  109 (587)
Q Consensus       106 ~a~~  109 (587)
                      |...
T Consensus       518 f~~~  521 (718)
T KOG2416|consen  518 FVRA  521 (718)
T ss_pred             ecch
Confidence            8773

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.02  E-value=0.23  Score=45.91  Aligned_cols=78  Identities=13%  Similarity=0.115  Sum_probs=49.1

Q ss_pred             CCCcEEEcCCCCCCCHHHH-Hhccc-CCCe---EEEEEeeC--CCCC-cceEEEEEECCHHHHHHHHHHhCCceeCC---
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLST-VGDV---TYVEILND--DTGK-PRGSAIVEFQSPDLVRKAVNKMHRFETKG---   99 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~-~G~V---~~v~i~~d--~~g~-skG~aFV~F~~~e~A~~Al~~l~g~~l~g---   99 (587)
                      ...+|.|++||+++|++++ +..+. ++.-   ..+.-...  .... .-.-|||.|.+.+++..-.+.++|+.|.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4469999999999999987 55555 6665   34431222  2222 22569999999999999999999988754   


Q ss_pred             --eEEEEEecc
Q psy1534         100 --RKLVIKEAV  108 (587)
Q Consensus       100 --r~i~V~~a~  108 (587)
                        .+..|+++.
T Consensus        86 ~~~~~~VE~Ap   96 (176)
T PF03467_consen   86 NEYPAVVEFAP   96 (176)
T ss_dssp             -EEEEEEEE-S
T ss_pred             CCcceeEEEcc
Confidence              344555555

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=92.64  E-value=1.1  Score=37.73  Aligned_cols=66  Identities=15%  Similarity=0.066  Sum_probs=49.1

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCC-eeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGK-VENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF  226 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  226 (587)
                      ..+.+...|..++-++|..+.+.+-. |..++|++|.. .++-.+.++|.+.++|.+-.+.+||+.+.
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            34444445555666677766666544 78889998764 24557899999999999999999999876

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2135|consensus

Probab=92.62  E-value=0.065  Score=55.26  Aligned_cols=71  Identities=15%  Similarity=0.273  Sum_probs=58.7

Q ss_pred             CCeEEEeCCCCCC-ChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEEC
Q psy1534         516 RDTVVVKNLPPTI-TWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF  587 (587)
Q Consensus       516 ~~~v~V~~Lp~~~-~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~  587 (587)
                      .+.+-+.-.|+.. |-.+|-.||.+||.|..|.|....-.|+|+|.+..+|..|-.- .+..|++|-|+|+|.
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~s-~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYAS-HGAVLNNRFIKLFWH  443 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhcc-ccceecCceeEEEEe
Confidence            3455566555544 5678999999999999999977667899999999999888664 899999999999984

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=92.33  E-value=0.23  Score=45.95  Aligned_cols=81  Identities=11%  Similarity=0.090  Sum_probs=51.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHh-cCCe---eEEEEeeCC--C-CCcceEEEEEecCHHHHHHHHHHhCCceeCC----
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRL-AGKV---ENVEIALDK--D-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE----  227 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~-~G~i---~~v~i~~~~--~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g----  227 (587)
                      ..+|.|++||+.+||+++.+.++. ++.-   ..+.-....  . -....-|||.|.+.+++..-+..++|+.+.+    
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            469999999999999999997776 5554   333312222  1 1223459999999999999999999988752    


Q ss_pred             -eEEEEEEccCCC
Q psy1534         228 -RRITVRMDRVAD  239 (587)
Q Consensus       228 -~~l~v~~a~~~~  239 (587)
                       .+..|++|-.+.
T Consensus        87 ~~~~~VE~Apyqk   99 (176)
T PF03467_consen   87 EYPAVVEFAPYQK   99 (176)
T ss_dssp             EEEEEEEE-SS--
T ss_pred             CcceeEEEcchhc
Confidence             356677776543

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>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=90.27  E-value=0.91  Score=42.17  Aligned_cols=63  Identities=16%  Similarity=0.167  Sum_probs=46.6

Q ss_pred             cHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCeEEEEEEccCCC
Q psy1534         172 DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN--NQNLFERRITVRMDRVAD  239 (587)
Q Consensus       172 te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~~a~~~~  239 (587)
                      ..+.|+++|..|+.+....+++.     -+-..|.|.+.++|.+|...|+  +..+.|..++|.++....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            45789999999999888877764     3458999999999999999999  999999999999985443

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.

>KOG3285|consensus

Probab=89.99  E-value=0.38  Score=43.11  Aligned_cols=44  Identities=41%  Similarity=0.819  Sum_probs=39.7

Q ss_pred             hHHHHHHhhhccccceeEEEEeccCccceeeeeceeeeeecCCC
Q psy1534         264 PLQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSD  307 (587)
Q Consensus       264 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  307 (587)
                      .+.++.+|+....++++++++++..++|++|+|+|.+..+....
T Consensus        67 ilsQ~~~WL~~~kiqklvlvI~~~~tgEvlErWqFnie~~~~~~  110 (203)
T KOG3285|consen   67 ILSQVHEWLSKGKIQKLVLVITSKHTGEVLERWQFNIETENTAS  110 (203)
T ss_pred             HHHHHHHHHHhCCcceEEEEEEecccccchhheeeeeeeecccc
Confidence            67889999999999999999999999999999999998776443

>KOG4574|consensus

Probab=89.79  E-value=0.29  Score=54.15  Aligned_cols=79  Identities=15%  Similarity=0.159  Sum_probs=64.8

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEEEccCC
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF--ERRITVRMDRVA  238 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~~a~~~  238 (587)
                      +.++.|.+-..+...|..+|++||.|.+++.+++-     -.|.|+|.+.+.|..|+++|+|+++.  |-+.+|.+++.-
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~-----N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL-----NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc-----cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            34445556667778899999999999999998874     37999999999999999999999864  889999998877


Q ss_pred             CCCCCC
Q psy1534         239 DRLDGP  244 (587)
Q Consensus       239 ~~~~~~  244 (587)
                      +..+.+
T Consensus       375 ~~~ep~  380 (1007)
T KOG4574|consen  375 PMYEPP  380 (1007)
T ss_pred             ccccCC
Confidence            654433

>KOG4574|consensus

Probab=89.26  E-value=0.19  Score=55.46  Aligned_cols=74  Identities=20%  Similarity=0.177  Sum_probs=62.5

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC--CeEEEEEe
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK--GRKLVIKE  106 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~--gr~i~V~~  106 (587)
                      |-..+.++.|.+-..+-..| .+|++||.|.+.+.+++     -..|.|+|.+.|.|..|+++|+|+++.  |-+.+|.+
T Consensus       296 plqp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~  370 (1007)
T KOG4574|consen  296 PLQPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSF  370 (1007)
T ss_pred             cCcchhhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEe
Confidence            34446677777778888888 78999999999999987     357999999999999999999997764  78888888


Q ss_pred             cc
Q psy1534         107 AV  108 (587)
Q Consensus       107 a~  108 (587)
                      ++
T Consensus       371 ak  372 (1007)
T KOG4574|consen  371 AK  372 (1007)
T ss_pred             cc
Confidence            87

>KOG2068|consensus

Probab=88.74  E-value=0.14  Score=50.94  Aligned_cols=79  Identities=16%  Similarity=0.212  Sum_probs=60.7

Q ss_pred             cEEEEecCCCCCcHHHHH---HHHHhcCCeeEEEEeeCCC--CCc--ceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         160 NKVFVANLDYKVDEKKLR---EVFRLAGKVENVEIALDKD--GKS--RGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~---~~F~~~G~i~~v~i~~~~~--g~~--~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      +.+||-+|+..+..+++.   +.|.+||.|..|.+.++..  ...  ..-++|+|...++|..||...+|..+.|+.+++
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            467888888876555543   5788999999998888762  111  112799999999999999999999999999777


Q ss_pred             EEccCC
Q psy1534         233 RMDRVA  238 (587)
Q Consensus       233 ~~a~~~  238 (587)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            665544

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=88.55  E-value=2.9  Score=33.63  Aligned_cols=80  Identities=16%  Similarity=0.252  Sum_probs=50.1

Q ss_pred             EEEEECCHHHHHHHHHHhCC--ceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhcc
Q psy1534          75 AIVEFQSPDLVRKAVNKMHR--FETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESL  152 (587)
Q Consensus        75 aFV~F~~~e~A~~Al~~l~g--~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (587)
                      |+|+|.+++-|++-++. ..  ..+.+..+.|....-....                     ..++          .   
T Consensus         1 AlITF~e~~VA~~i~~~-~~~~v~l~~~~~~V~v~P~~~~~---------------------~~k~----------q---   45 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKK-KKHPVPLEDCCVRVKVSPVTLGH---------------------LQKF----------Q---   45 (88)
T ss_pred             CEEEeCcHHHHHHHHhC-CEEEEEECCEEEEEEEEeEecCC---------------------ceEE----------E---
Confidence            68999999999999964 33  4456666666554411100                     0000          0   


Q ss_pred             CCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC
Q psy1534         153 GINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD  196 (587)
Q Consensus       153 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~  196 (587)
                      -......++|-|.|||..+++++|++.       .++.+-+.++
T Consensus        46 v~~~vs~rtVlvsgip~~l~ee~l~D~-------LeIhFqK~sn   82 (88)
T PF07292_consen   46 VFSGVSKRTVLVSGIPDVLDEEELRDK-------LEIHFQKPSN   82 (88)
T ss_pred             EEEcccCCEEEEeCCCCCCChhhheee-------EEEEEecCCC
Confidence            002234578999999999999999864       4565655544

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG4285|consensus

Probab=88.49  E-value=1.6  Score=42.78  Aligned_cols=65  Identities=25%  Similarity=0.410  Sum_probs=53.8

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCce
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKI  581 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~  581 (587)
                      .++=|.|.+.|.... .-|..+|.+||.|+..---.+...=.|.|.++-+|++||.+ ||+.|.|..
T Consensus       196 ~D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALsk-ng~ii~g~v  260 (350)
T KOG4285|consen  196 ADTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALSK-NGTIIDGDV  260 (350)
T ss_pred             ccceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhhh-cCeeeccce
Confidence            467899999987655 45778999999987554445557899999999999999998 999999875

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=88.29  E-value=2.5  Score=32.00  Aligned_cols=55  Identities=20%  Similarity=0.329  Sum_probs=43.6

Q ss_pred             CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       170 ~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      .++-++++..+..|. ...  |..|+    .|| ||.|.+.++|+++....+++.+....|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~--I~~d~----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDR--IRDDR----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cce--EEecC----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            578899999999995 333  44454    355 89999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=88.25  E-value=28  Score=34.38  Aligned_cols=189  Identities=13%  Similarity=0.240  Sum_probs=109.8

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC--------CCCcceEEEEEECCHHHHHH----HHHHhCC--ce
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD--------TGKPRGSAIVEFQSPDLVRK----AVNKMHR--FE   96 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~--------~g~skG~aFV~F~~~e~A~~----Al~~l~g--~~   96 (587)
                      .|.|...|+..+++...+ ..|-+||+|++|.++.+.        ..+..-...+.|-+.+.+-.    .++.|..  ..
T Consensus        15 TRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~~   94 (309)
T PF10567_consen   15 TRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKTK   94 (309)
T ss_pred             eHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHHh
Confidence            456888999999999887 889999999999999875        22334678999999988754    4444443  55


Q ss_pred             eCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHH
Q psy1534          97 TKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKL  176 (587)
Q Consensus        97 l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l  176 (587)
                      +....|.+.+..-+......              +......+ ..+ . ...+.-.-.....++.|.|. +...+.++++
T Consensus        95 L~S~~L~lsFV~l~y~~~~~--------------~~~~~~~~-~~~-~-~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl  156 (309)
T PF10567_consen   95 LKSESLTLSFVSLNYQKKTD--------------PNDEEADF-SDY-L-VASLQYNIINRGATRSLAIE-FKDPVDKDDL  156 (309)
T ss_pred             cCCcceeEEEEEEecccccc--------------ccccccch-hhH-H-hhhhhheeecCCcceEEEEE-ecCccchhHH
Confidence            77788888877621110000              00000000 000 0 00000011123345667775 3344433332


Q ss_pred             -HHHH---HhcC----CeeEEEEeeCCC---CCcceEEEEEecCHHHHHHHHHHhC--CceeC-CeEEEEEEccCC
Q psy1534         177 -REVF---RLAG----KVENVEIALDKD---GKSRGFGTVEFDHPVEAVQSISMLN--NQNLF-ERRITVRMDRVA  238 (587)
Q Consensus       177 -~~~F---~~~G----~i~~v~i~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~-g~~l~v~~a~~~  238 (587)
                       .+.+   ..-+    .+++|.|+.-..   .-++-||.++|-+..-|.+.++.+.  ..... .+...|.++...
T Consensus       157 ~~~kL~fL~~~~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs~~~~~  232 (309)
T PF10567_consen  157 IEKKLPFLKNSNNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVSVQPHA  232 (309)
T ss_pred             HHHhhhhhccCCCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEeccCcc
Confidence             2222   1112    367788776432   4567799999999999999888775  33333 455666665433

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG0804|consensus

Probab=87.16  E-value=2.2  Score=44.20  Aligned_cols=67  Identities=12%  Similarity=0.096  Sum_probs=58.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCC-eeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGK-VENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF  226 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  226 (587)
                      ++.|+|-.+|..++-.||..|+..+-. |.+++|++|... .+=..+|+|.+.++|..-.+.+||+.|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            788999999999999999999987654 899999997642 2345899999999999999999999876

>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=86.88  E-value=3.2  Score=32.22  Aligned_cols=58  Identities=14%  Similarity=0.219  Sum_probs=36.4

Q ss_pred             CCcHHHHHHHHHhcCC-----eeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         170 KVDEKKLREVFRLAGK-----VENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       170 ~~te~~l~~~F~~~G~-----i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .++..+|..++...+.     |-.|.|..+       |+||+-.. +.|.++++.|++..+.|++++|+.|
T Consensus        12 g~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   12 GLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             T--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             CCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            5788899888887655     456777653       89999876 4899999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG2135|consensus

Probab=85.98  E-value=0.48  Score=49.12  Aligned_cols=74  Identities=16%  Similarity=0.204  Sum_probs=58.3

Q ss_pred             cEEEEecCCCCC-cHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         160 NKVFVANLDYKV-DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       160 ~~l~V~nLp~~~-te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      +.|-+.-.|+.. +-++|...|.+||+|..|.+-...     --|.|+|.+..+|-+|. ..++..|.+|.|+|.|..+.
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~-----~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS-----LHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCch-----hhheeeeeccccccchh-ccccceecCceeEEEEecCC
Confidence            444455556553 458899999999999999886542     35899999999998886 45899999999999998774


Q ss_pred             C
Q psy1534         239 D  239 (587)
Q Consensus       239 ~  239 (587)
                      .
T Consensus       447 ~  447 (526)
T KOG2135|consen  447 P  447 (526)
T ss_pred             c
Confidence            4

>KOG2253|consensus

Probab=85.92  E-value=1.5  Score=47.59  Aligned_cols=68  Identities=19%  Similarity=0.196  Sum_probs=61.2

Q ss_pred             CCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEE
Q psy1534         514 IERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV  584 (587)
Q Consensus       514 ~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v  584 (587)
                      .+..+|||.|+...+..+-++.....+|.|..++...   +||++|..+....+|+..+.-..+++.++-+
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            3467999999999999999999999999998887755   9999999999999999999999998887644

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=84.45  E-value=7.9  Score=32.66  Aligned_cols=66  Identities=9%  Similarity=0.078  Sum_probs=47.2

Q ss_pred             CcEEEcC-CCCCCCHHHHHhc-ccCC-CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC
Q psy1534          33 VPVVMDL-IQGDASLYQISHL-STVG-DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG   99 (587)
Q Consensus        33 ~~vfV~n-lp~~~t~~~l~~F-~~~G-~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g   99 (587)
                      ..|.|=- .|+-++-++|-.| +.+- .|..++|++|.+. ++=-+.++|.+.++|+.-.+.+||+.|..
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3454444 4555566666433 4443 5788999998543 45678999999999999999999988864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2253|consensus

Probab=83.62  E-value=0.74  Score=49.85  Aligned_cols=73  Identities=22%  Similarity=0.387  Sum_probs=63.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      +.++..++||+|+...+..+-++.+...+|.|.++....        |+|+.|..+.-..+|+..++-..+.+..+.+..
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            345667999999999999999999999999998876654        999999999999999999988888888877766


Q ss_pred             c
Q psy1534         235 D  235 (587)
Q Consensus       235 a  235 (587)
                      .
T Consensus       108 d  108 (668)
T KOG2253|consen  108 D  108 (668)
T ss_pred             h
Confidence            4

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=80.19  E-value=7.8  Score=29.35  Aligned_cols=56  Identities=14%  Similarity=0.223  Sum_probs=44.6

Q ss_pred             CCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEE
Q psy1534         526 PTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV  584 (587)
Q Consensus       526 ~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v  584 (587)
                      ..++-+|+|..++.|   ...+|..++.-=+|.|.+..+|++..+..|+..+...++.+
T Consensus        10 ~~~~v~d~K~~Lr~y---~~~~I~~d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKY---RWDRIRDDRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcC---CcceEEecCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            356788999999999   44555555434478999999999999999999988777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	587
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		3e-20
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		2e-08
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		2e-08
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		3e-08
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		1e-06
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		4e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		8e-06
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		3e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		4e-05
1duj_A	187	Solution Structure Of The Spindle Assembly Checkpoi		5e-05
2v64_D	207	Crystallographic Structure Of The Conformational Di		5e-05
2vfx_A	206	Structure Of The Symmetric Mad2 Dimer Length = 206		6e-05
3gmh_A	207	Crystal Structure Of The Mad2 Dimer Length = 207		6e-05
2qyf_A	206	Crystal Structure Of The Mad2P31(COMET)MAD2-Binding		7e-05
1s2h_A	206	The Mad2 Spindle Checkpoint Protein Possesses Two D		7e-05
2v64_A	213	Crystallographic Structure Of The Conformational Di		7e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		7e-05
1klq_A	197	The Mad2 Spindle Checkpoint Protein Undergoes Simil		7e-05
1go4_A	205	Crystal Structure Of Mad1-Mad2 Reveals A Conserved		8e-05
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		8e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		8e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		1e-04
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		1e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-04
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-04
2o3d_A	113	Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (		2e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-04
3beg_B	115	Crystal Structure Of Sr Protein Kinase 1 Complexed		2e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-04
1x4c_A	108	Solution Structure Of Rrm Domain In Splicing Factor		3e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		3e-04
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		3e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		4e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		4e-04
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		4e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		4e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		7e-04
1wg4_A	98	Solution Structure Of Rrm Domain In Protein Bab3198		9e-04

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 49/81 (60%), Positives = 59/81 (72%)
Query: 158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
           L + VFVANLDYKV  KKL+EVF +AG V   +I  DKDGKSRG GTV F+  +EAVQ+I
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
Query: 218 SMLNNQNLFERRITVRMDRVA 238
           SM N Q LF+R + V+MD  A
Sbjct: 74  SMFNGQLLFDRPMHVKMDERA 94

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 42/71 (59%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           VFV NL+ +V E+ L E+F  AG +  V I  D++GK + FG V F HP     +I++LN
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 222 NQNLFERRITV 232
              L+ R I V
Sbjct: 79  GIRLYGRPINV 89

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/70 (42%), Positives = 45/70 (64%), Gaps = 4/70 (5%)
Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIK---GKGD-IGLVRFDSEWTAKRAIDMMDR 574
           + V+NLP   TW+ L+DKF  CG + +A+IK   GK    G+V+F+S   A+RA  MM+ 
Sbjct: 11  IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 575 TRIDGKIIDV 584
            ++ G+ IDV
Sbjct: 71  MKLSGREIDV 80

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/70 (42%), Positives = 45/70 (64%), Gaps = 4/70 (5%)
Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIK---GKGD-IGLVRFDSEWTAKRAIDMMDR 574
           + V+NLP   TW+ L+DKF  CG + +A+IK   GK    G+V+F+S   A+RA  MM+ 
Sbjct: 8   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 67
Query: 575 TRIDGKIIDV 584
            ++ G+ IDV
Sbjct: 68  MKLSGREIDV 77

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQS 216
           ++  + V  +   VDE +LR++F   G +E+V+I  D++ + SRG+G V+F     A Q+
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100
Query: 217 ISMLNNQNLFERRITVRM 234
           I+ LN  N+  +R+ V +
Sbjct: 101 IAGLNGFNILNKRLKVAL 118

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 51/84 (60%), Gaps = 2/84 (2%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           ++V NLD  +D+++LR+ F   G + + ++ ++  G+S+GFG V F  P EA ++++ +N
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 222 NQNLFERRITVRM-DRVADRLDGP 244
            + +  + + V +  R  +R  GP
Sbjct: 77  GRIVATKPLYVALAQRKEERQSGP 100

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 45/88 (51%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+F+  L+ + +EK L+ VF   G +  V +  D+  KSRGF  + F++P +A  +   +
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 221 NNQNLFERRITVRMDRVADRLDGPVRLP 248
           N ++L  + I V   +      G  R P
Sbjct: 69  NGKSLHGKAIKVEQAKKPSFQSGGRRRP 96

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 3/83 (3%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           ++V +L + + E  LR +F   GK++N+ +  D D G+S+G+G + F     A +++  L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 221 NNQNLFERRITVRMDRVADRLDG 243
           N   L  R   +R+  V +RLDG
Sbjct: 68  NGFELAGR--PMRVGHVTERLDG 88

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 48/95 (50%), Gaps = 8/95 (8%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISML 220
           ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I  +
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 221 NNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIG 255
           N   LF R I V + +       P+R+ E   S G
Sbjct: 75  NESELFGRTIRVNLAK-------PMRIKESGPSSG 102

>pdb|1DUJ|A Chain A, Solution Structure Of The Spindle Assembly Checkpoint Protein Human Mad2 Length = 187

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 6/66 (9%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKTDSTN 324
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ +      ++A +  S  
Sbjct: 61  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKD------DSAPREKSQK 114
Query: 325 AEKDKI 330
           A +D+I
Sbjct: 115 AIQDEI 120

>pdb|2V64|D Chain D, Crystallographic Structure Of The Conformational Dimer Of The Spindle Assembly Checkpoint Protein Mad2. Length = 207

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 32/51 (62%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVN 315
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK S E    ++ 
Sbjct: 77  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKGSGEKSQKAIQ 127

>pdb|2VFX|A Chain A, Structure Of The Symmetric Mad2 Dimer Length = 206

Iteration: 1
 Score = 46.2 bits (108), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 33/47 (70%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA 311
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A
Sbjct: 70  VEQLKDWLYKSSVQKLVVVISNIESGEVLERWQFDIESDKTAKDDSA 116

>pdb|3GMH|A Chain A, Crystal Structure Of The Mad2 Dimer Length = 207

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 33/47 (70%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA 311
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A
Sbjct: 71  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSA 117

>pdb|2QYF|A Chain A, Crystal Structure Of The Mad2P31(COMET)MAD2-Binding Peptide Ternary Complex Length = 206

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 33/47 (70%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA 311
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A
Sbjct: 70  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSA 116

>pdb|1S2H|A Chain A, The Mad2 Spindle Checkpoint Protein Possesses Two Distinct Natively Folded States Length = 206

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 33/47 (70%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA 311
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A
Sbjct: 70  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSA 116

>pdb|2V64|A Chain A, Crystallographic Structure Of The Conformational Dimer Of The Spindle Assembly Checkpoint Protein Mad2. Length = 213

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 33/47 (70%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA 311
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A
Sbjct: 77  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSA 123

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/100 (29%), Positives = 52/100 (52%), Gaps = 8/100 (8%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
           +  VFV N+ Y+  E++L+++F   G V +  +  D++ GK +G+G  E+     A+ ++
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 218 SMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMG 257
             LN +    R   +R+D  A   +      E LKS+G G
Sbjct: 68  RNLNGREFSGR--ALRVDNAASEKN-----KEELKSLGTG 100

>pdb|1KLQ|A Chain A, The Mad2 Spindle Checkpoint Protein Undergoes Similar Major Conformational Changes Upon Binding To Either Mad1 Or Cdc20 Length = 197

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 33/47 (70%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA 311
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A
Sbjct: 61  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSA 107

>pdb|1GO4|A Chain A, Crystal Structure Of Mad1-Mad2 Reveals A Conserved Mad2 Binding Motif In Mad1 And Cdc20. Length = 205

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 33/47 (70%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDA 311
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A
Sbjct: 69  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSA 115

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 152 LGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPV 211
           LG    + N VFV  +D ++DE ++R  F   G V+ V+I  D+ G S+G+G V F + V
Sbjct: 3   LGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 62
Query: 212 EAVQSI 217
           + VQ I
Sbjct: 63  D-VQKI 67

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           +  +F+ NLD  +D K L + F   G + + ++  D++G S+G+G V F+    A ++I 
Sbjct: 103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIE 161
Query: 219 -----MLNNQNLFERRITVRMDRVAD 239
                +LN++ +F  R   R +R A+
Sbjct: 162 KMNGMLLNDRKVFVGRFKSRKEREAE 187

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISML 220
           ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I  +
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 221 NNQNLFERRITVRM 234
           N   LF R I V +
Sbjct: 126 NESELFGRTIRVNL 139

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           +FVA ++Y   E KLR  F + G ++ + +   K  GK RG+  +E++H  +   +    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 221 NNQNLFERRITVRMDR 236
           + + +  RR+ V ++R
Sbjct: 165 DGKKIDGRRVLVDVER 180

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           +  +F+ NLD  +D K L + F   G + + ++  D++G S+G+G V F+    A ++I 
Sbjct: 98  VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIE 156
Query: 219 -----MLNNQNLFERRITVRMDRVAD 239
                +LN++ +F  R   R +R A+
Sbjct: 157 KMNGMLLNDRKVFVGRFKSRKEREAE 182

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
           N VFV  +D ++DE ++R  F   G V+ V+I  D+ G S+G+G V F + V+ VQ I
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD-VQKI 66

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           +  +F+ NLD  +D K L + F   G + + ++  D++G S+G+G V F+    A ++I 
Sbjct: 11  VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIE 69
Query: 219 -----MLNNQNLFERRITVRMDRVAD 239
                +LN++ +F  R   R +R A+
Sbjct: 70  KMNGMLLNDRKVFVGRFKSRKEREAE 95

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
           N VFV  +D ++DE ++R  F   G V+ V+I  D+ G S+G+G V F + V+ VQ I
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD-VQKI 66

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           +FVA ++Y   E KLR  F + G ++ + +   K  GK RG+  +E++H  +   +    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 221 NNQNLFERRITVRMDR 236
           + + +  RR+ V ++R
Sbjct: 165 DGKKIDGRRVLVDVER 180

>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2) Length = 113

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 499 RAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVR 558
           R G  S RS N+        VVV  LPP+ +WQ+L+D  R  GD+ +A++   G  G+V 
Sbjct: 6   RYGPPSRRSENR--------VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVE 56
Query: 559 FDSEWTAKRAIDMMDRTR 576
           F  +     A+  +D T+
Sbjct: 57  FVRKEDMTYAVRKLDNTK 74

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 50/86 (58%), Gaps = 2/86 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L +  +E+ L +VF   G++  V +  D++  +SRGFG V F++  +A  ++  
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 220 LNNQNLFERRITV-RMDRVADRLDGP 244
           +N +++  R+I V +  + +D   GP
Sbjct: 74  MNGKSVDGRQIRVDQAGKSSDNRSGP 99

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISML 220
           ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I  +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 221 NNQNLFERRITVRMDR 236
           N   LF R I V + +
Sbjct: 68  NESELFGRTIRVNLAK 83

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISML 220
           ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I  +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 221 NNQNLFERRITVRMDR 236
           N   LF R I V + +
Sbjct: 70  NESELFGRTIRVNLAK 85

>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its Substrate AsfSF2 Length = 115

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 499 RAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVR 558
           R G  S RS N+        VVV  LPP+ +WQ+L+D  R  GD+ +A++   G  G+V 
Sbjct: 7   RYGPPSRRSENR--------VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVE 57
Query: 559 FDSEWTAKRAIDMMDRTR 576
           F  +     A+  +D T+
Sbjct: 58  FVRKEDMTYAVRKLDNTK 75

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISML 220
           ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I  +
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 221 NNQNLFERRITVRM 234
           N   LF R I V +
Sbjct: 65  NESELFGRTIRVNL 78

>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2 Length = 108

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
           VVV  LPP+ +WQ+L+D  R  GD+ +A++   G  G+V F  +     A+  +D T+ 
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLDNTKF 75

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFD 208
           + K+FV  +    +E  LR+ F   GK+E +EI  D+  GK RGF  V FD
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFD 208
           + K+FV  +    +E  LR+ F   GK+E +EI  D+  GK RGF  V FD
Sbjct: 103 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 153

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 6/83 (7%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS--- 218
           +F+ NLD  +D K L + F   G + + ++  D++G S+G+G V F+    A ++I    
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMN 66
Query: 219 --MLNNQNLFERRITVRMDRVAD 239
             +LN++ +F  R   R +R A+
Sbjct: 67  GMLLNDRKVFVGRFKSRKEREAE 89

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFD 208
           + K+FV  +    +E  LR+ F   GK+E +EI  D+  GK RGF  V FD
Sbjct: 105 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 155

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 3/84 (3%)
Query: 506 RSMNQSSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-IGLVRFDSE 562
           +   + S  ERD  T++ KNLP  +T  EL++ F +  +I+     GK   I  + F +E
Sbjct: 81  KPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTE 140
Query: 563 WTAKRAIDMMDRTRIDGKIIDVTF 586
             A++  +    T IDG+ I + +
Sbjct: 141 ADAEKTFEEKQGTEIDGRSISLYY 164

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 2/85 (2%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISML 220
           V+V  LD KV E  L E+F  AG V N  +  D+  G+ +G+G VEF    +A  +I ++
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 221 NNQNLFERRITVRMDRVADR-LDGP 244
           +   L+ + I V      ++ L GP
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNLSGP 102

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFD 208
           + K+FV  +    +E  LR+ F   GK+E +EI  D+  GK RGF  V FD
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFD 208
           + K+FV  +    +E  LR+ F   GK+E +EI  D+  GK RGF  V FD
Sbjct: 97  VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 147

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/83 (26%), Positives = 48/83 (57%), Gaps = 3/83 (3%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           +++V +L + + E  LR +F   G++E++++ +D + G+S+G+G + F     A +++  
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 220 LNNQNLFERRITVRMDRVADRLD 242
           LN   L  R   +++  V +R D
Sbjct: 88  LNGFELAGR--PMKVGHVTERTD 108

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 38/64 (59%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           ++V NLD  + E  L++ F++ G + N++I +DK+ K+  +  VE+    +A  ++  LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 222 NQNL 225
            + +
Sbjct: 63  GKQI 66

>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986 Length = 98

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 19/58 (32%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           V+V  LPP+ +WQ+L+D  R  GD+ +A+++  G +G+V +  +   + A+  +D T+
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-MGMVEYLRKEDMEYALRKLDDTK 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	587
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-28
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-24
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-23
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-08
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-06
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	8e-22
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-17
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-21
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-08
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-11
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-07
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-06
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-21
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-20
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-08
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-08
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-20
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-10
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-09
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-20
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-06
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-06
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-20
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-06
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-20
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	8e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-06
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-06
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-19
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-08
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-18
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-18
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-07
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-18
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-18
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-06
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-06
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-17
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	6e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-17
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-17
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-09
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-17
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-08
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-08
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-17
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-06
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	9e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-05
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-16
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-08
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-05
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-16
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-07
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-16
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-08
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-16
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-05
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-16
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-16
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	7e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-16
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-15
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-05
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-15
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-07
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	7e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-15
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-05
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-15
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-15
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-06
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-07
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	7e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-06
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-08
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-08
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	9e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-07
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-14
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-07
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-14
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-13
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-11
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-08
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-07
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	9e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-07
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-13
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-13
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	9e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-04
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-12
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-06
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	6e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-04
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-04
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	8e-12
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-11
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-11
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-04
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-10
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-10
2div_A	99	TRNA selenocysteine associated protein; structural	5e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-08
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-10
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	5e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	5e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-10
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	9e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	9e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	9e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-09
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-09
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-09
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	8e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	7e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-08
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	8e-07
4aez_B	203	MAD2, mitotic spindle checkpoint component MAD2; c	1e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	6e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	8e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	7e-05
2vfx_A	206	Mitotic spindle assembly checkpoint protein MAD2A;	1e-05
3abd_A	227	Mitotic spindle assembly checkpoint protein MAD2B;	2e-05
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	9e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	8e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	7e-04

>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 =  108 bits (273), Expect = 1e-28
 Identities = 48/81 (59%), Positives = 58/81 (71%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + VFVANLDYKV  KKL+EVF +AG V   +I  DKDGKSRG GTV F+  +EAVQ+ISM
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75

Query: 220 LNNQNLFERRITVRMDRVADR 240
            N Q LF+R + V+MD  A  
Sbjct: 76  FNGQLLFDRPMHVKMDERALP 96

>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 = 67.3 bits (165), Expect = 5e-14
 Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 8/88 (9%)

Query: 504 SNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGL 556
           S+ S          + V V NL   + W++L++ F   G +  A+I      K +G IG 
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG-IGT 60

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
           V F+    A +AI M +   +  + + V
Sbjct: 61  VTFEQSIEAVQAISMFNGQLLFDRPMHV 88

>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 = 56.2 bits (136), Expect = 5e-10
 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 1/66 (1%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
           S  G V   +IL D  GK RG   V F+      +A++  +      R + +K   E   
Sbjct: 37  SMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD-ERAL 95

Query: 113 GRRNMG 118
            + +  
Sbjct: 96  PKGDFF 101

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

 Score = 94.6 bits (236), Expect = 8e-24
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++FV NL +    K L++ F   G V   +I ++ +GKS+G G V+F+ P  A ++  M
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 67

Query: 220 LNNQNLFERRITVRMDRVADR 240
           +N   L  R I VR+DR A  
Sbjct: 68  MNGMKLSGREIDVRIDRNASG 88

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

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 30/72 (41%), Positives = 45/72 (62%), Gaps = 6/72 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMM 572
            + V+NLP   TW+ L+DKF  CG + +A+I     K KG  G+V+F+S   A+RA  MM
Sbjct: 10  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKG-CGVVKFESPEVAERACRMM 68

Query: 573 DRTRIDGKIIDV 584
           +  ++ G+ IDV
Sbjct: 69  NGMKLSGREIDV 80

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

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 42  GDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
               L      +  G V Y +I   + GK +G  +V+F+SP++  +A   M+  +  GR+
Sbjct: 21  TWKMLKD--KFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGRE 77

Query: 102 LVIKEAVEDKGGRRN 116
           + ++    +  G  +
Sbjct: 78  IDVRID-RNASGPSS 91

>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 = 91.9 bits (229), Expect = 8e-23
 Identities = 30/73 (41%), Positives = 42/73 (57%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             VFV NL+ +V E+ L E+F  AG +  V I  D++GK + FG V F HP     +I++
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76

Query: 220 LNNQNLFERRITV 232
           LN   L+ R I V
Sbjct: 77  LNGIRLYGRPINV 89

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 52.2 bits (126), Expect = 7e-09
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +  LY++      G +T V I  D  GKP+    V F+ P+ V  A+  ++     GR +
Sbjct: 30  EEILYEL--FLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87

Query: 103 VIKEA 107
            +   
Sbjct: 88  NVSGP 92

>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 = 50.7 bits (122), Expect = 3e-08
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
           TV V NL   +  + L + F   G +    I      K K   G V F    +   AI +
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS-FGFVCFKHPESVSYAIAL 76

Query: 572 MDRTRIDGKIIDV 584
           ++  R+ G+ I+V
Sbjct: 77  LNGIRLYGRPINV 89

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

 Score = 94.7 bits (236), Expect = 2e-22
 Identities = 34/192 (17%), Positives = 80/192 (41%), Gaps = 36/192 (18%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           + ++ Q    +  G +  +++  D  T K +G A VE++ P+  + A+ +M+     GR 
Sbjct: 42  EDTIRQA--FAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRN 99

Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
           + +         +  +             L   +  F                     N+
Sbjct: 100 IKVGRPSNIGQAQPII-----------DQLAEEARAF---------------------NR 127

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           ++VA++   + +  ++ VF   GK+++  +A D   GK +G+G +E++    +  ++S +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

Query: 221 NNQNLFERRITV 232
           N  +L  + + V
Sbjct: 188 NLFDLGGQYLRV 199

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

 Score = 76.2 bits (188), Expect = 5e-16
 Identities = 20/77 (25%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQ 215
            ++++V+V ++ Y++ E  +R+ F   G +++++++ D    K +GF  VE++ P  A  
Sbjct: 26  AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 85

Query: 216 SISMLNNQNLFERRITV 232
           ++  +N+  L  R I V
Sbjct: 86  ALEQMNSVMLGGRNIKV 102

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

 Score = 55.8 bits (135), Expect = 5e-09
 Identities = 22/106 (20%), Positives = 41/106 (38%), Gaps = 15/106 (14%)

Query: 496 GNPRAGLDSNRSMNQSSNIERD-------TVVVKNLPPTITWQELRDKFRNCGDIKFAEI 548
           G+  A +   + M + S  +R         V V ++   +    +R  F   G IK  ++
Sbjct: 1   GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60

Query: 549 -------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
                  K KG    V ++    A+ A++ M+   + G+ I V   
Sbjct: 61  SWDSVTMKHKG-FAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP 105

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

 Score = 48.5 bits (116), Expect = 1e-06
 Identities = 15/98 (15%), Positives = 37/98 (37%), Gaps = 8/98 (8%)

Query: 494 GYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI----- 548
           G  +                   + + V ++   ++  +++  F   G IK A +     
Sbjct: 103 GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT 162

Query: 549 --KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
             K KG  G + ++   +++ A+  M+   + G+ + V
Sbjct: 163 TGKHKG-YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

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

 Score = 44.6 bits (106), Expect = 3e-05
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
              G +    +  D  TGK +G   +E++     + AV+ M+ F+  G+ L + +AV 
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 89.6 bits (223), Expect = 8e-22
 Identities = 19/75 (25%), Positives = 41/75 (54%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+ V+NLD+ V +  ++E+F   G ++   +  D+ G+S G   V F+   +A++++  
Sbjct: 30  GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 89

Query: 220 LNNQNLFERRITVRM 234
            N   L  R + +++
Sbjct: 90  YNGVPLDGRPMNIQL 104

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 58.1 bits (141), Expect = 9e-11
 Identities = 15/93 (16%), Positives = 38/93 (40%), Gaps = 12/93 (12%)

Query: 500 AGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGD 553
           +G      +     +     +V NL   ++  ++++ F   G +K A +      +  G 
Sbjct: 18  SGFGGGAGVETGGKL-----LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG- 71

Query: 554 IGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
              V F+ +  A +A+   +   +DG+ +++  
Sbjct: 72  TADVHFERKADALKAMKQYNGVPLDGRPMNIQL 104

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 12/56 (21%), Positives = 24/56 (42%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
           +  G +    +  D +G+  G+A V F+      KA+ + +     GR + I+   
Sbjct: 51  AEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 = 91.1 bits (227), Expect = 1e-21
 Identities = 30/190 (15%), Positives = 68/190 (35%), Gaps = 48/190 (25%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
            A L     +S +     + +++  TG  R    V+F+S + + KA+ ++   +  G ++
Sbjct: 27  VAELKVA--ISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEI 83

Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
            +++       +                                               +
Sbjct: 84  KLEKPKGRDSKKVRAA-----------------------------------------RTL 102

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
              NL + + E +L+EVF  A ++  V     +DGKS+G   +EF    +A +++     
Sbjct: 103 LAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQG 158

Query: 223 QNLFERRITV 232
             +  R +++
Sbjct: 159 AEIDGRSVSL 168

>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 = 77.6 bits (192), Expect = 7e-17
 Identities = 12/77 (15%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +F+ NL+      +L+          ++ +   + G +R FG V+F+   +  +++ +
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALEL 73

Query: 220 LNNQNLFERRITVRMDR 236
                +F   I +   +
Sbjct: 74  -TGLKVFGNEIKLEKPK 89

>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 = 60.3 bits (147), Expect = 7e-11
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG--KGDIGLVRFDSEWTAKRAIDMMDR 574
            T++ KNL   IT  EL++ F +  +I+     G  KG I  + F SE  A++ ++    
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG-IAYIEFKSEADAEKNLEEKQG 158

Query: 575 TRIDGKIIDVTF 586
             IDG+ + + +
Sbjct: 159 AEIDGRSVSLYY 170

>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 = 54.1 bits (131), Expect = 1e-08
 Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 8/73 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
            + + NL P  +  EL+             +        +   G V F+S    ++A++ 
Sbjct: 15  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK-FGYVDFESAEDLEKALE- 72

Query: 572 MDRTRIDGKIIDV 584
           +   ++ G  I +
Sbjct: 73  LTGLKVFGNEIKL 85

>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 = 48.0 bits (115), Expect = 1e-06
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
               ++  V       GK +G A +EF+S     K + +    E  GR + +    E KG
Sbjct: 121 EDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE-KG 175

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 91.1 bits (226), Expect = 2e-21
 Identities = 28/136 (20%), Positives = 53/136 (38%), Gaps = 2/136 (1%)

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
           G RRN        R+  A                       G       K+ V+NLD+ V
Sbjct: 41  GPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGV 100

Query: 172 DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT 231
            +  ++E+F   G ++   +  D+ G+S G   V F+   +A++++       L  R + 
Sbjct: 101 SDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD 160

Query: 232 VRMDRVADRLDGPVRL 247
           +++  VA ++D     
Sbjct: 161 IQL--VASQIDLEHHH 174

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 59.5 bits (144), Expect = 1e-10
 Identities = 19/133 (14%), Positives = 43/133 (32%), Gaps = 12/133 (9%)

Query: 460 SRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTV 519
           +R             GG          +       +    +G      +   + +     
Sbjct: 37  NRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKL----- 91

Query: 520 VVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           +V NL   ++  ++++ F   G +K A +      +  G    V F+    A +A+    
Sbjct: 92  LVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG-TADVHFERRADALKAMKQYK 150

Query: 574 RTRIDGKIIDVTF 586
              +DG+ +D+  
Sbjct: 151 GVPLDGRPMDIQL 163

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 53.7 bits (129), Expect = 1e-08
 Identities = 12/65 (18%), Positives = 24/65 (36%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
           +  G +    +  D +G+  G+A V F+      KA+ +       GR + I+       
Sbjct: 110 AEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169

Query: 113 GRRNM 117
              + 
Sbjct: 170 LEHHH 174

>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 = 93.9 bits (234), Expect = 2e-21
 Identities = 31/182 (17%), Positives = 59/182 (32%), Gaps = 51/182 (28%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
            E+      K +G+A V   + +    A+N  H+   + R+L ++    D          
Sbjct: 46  YELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD---------- 95

Query: 121 GGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVF 180
                                                    + VANL   + +++  E+ 
Sbjct: 96  ---------------------------------------ALLCVANLPPSLTQQQFEELV 116

Query: 181 RLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV-RMDRVA 238
           R  G +E   +    + G+S+G+G  E+     A ++ S L  + L  R + V   D   
Sbjct: 117 RPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ 176

Query: 239 DR 240
             
Sbjct: 177 LT 178

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 92.0 bits (229), Expect = 8e-21
 Identities = 27/183 (14%), Positives = 53/183 (28%), Gaps = 42/183 (22%)

Query: 53  STVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
              G +    ++  + TG+ +G    E+   D   +A + +       R L +     D 
Sbjct: 117 RPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT--DA 174

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
           G                ALL +                            + V  L    
Sbjct: 175 GQLT------------PALLHSR--------------------------CLCVDRLPPGF 196

Query: 172 -DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRI 230
            D   L             ++A  +DG+ +GF  +E++    A ++    +  +L    +
Sbjct: 197 NDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL 256

Query: 231 TVR 233
            V 
Sbjct: 257 RVS 259

>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 = 67.3 bits (165), Expect = 1e-12
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+ +  L   V  +++ ++        + E+      K +G   V   +  +A  +I+ 
Sbjct: 23  RKILIRGLPGDVTNQEVHDLL------SDYELKYCFVDKYKGTAFVTLLNGEQAEAAINA 76

Query: 220 LNNQNLFERRITVRMDRVADRL 241
            +   L ER ++V++      L
Sbjct: 77  FHQSRLRERELSVQLQPTDALL 98

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 60.8 bits (148), Expect = 3e-10
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            + V NLPP++T Q+  +  R  G ++   +       + KG  G   +  + +A RA  
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG-YGFAEYMKKDSAARAKS 155

Query: 571 MMDRTRIDGKIIDVTF 586
            +    +  + + V +
Sbjct: 156 DLLGKPLGPRTLYVHW 171

>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 = 58.1 bits (141), Expect = 2e-09
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 1/83 (1%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
                 +     R  ++++ LP  +T QE+ D   +         K KG    V   +  
Sbjct: 10  KRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKG-TAFVTLLNGE 68

Query: 564 TAKRAIDMMDRTRIDGKIIDVTF 586
            A+ AI+   ++R+  + + V  
Sbjct: 69  QAEAAINAFHQSRLRERELSVQL 91

>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 = 57.3 bits (139), Expect = 3e-09
 Identities = 14/90 (15%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTIT-WQELRDKFRNCGDIKFAEI------KGKGDIGL 556
           ++      + +    + V  LPP       L           F ++      + KG   +
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKG-FAV 230

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           + +++   A+ A    D   + G  + V+F
Sbjct: 231 LEYETAEMAEEAQQQADGLSLGGSHLRVSF 260

>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 = 90.5 bits (225), Expect = 4e-21
 Identities = 31/196 (15%), Positives = 70/196 (35%), Gaps = 29/196 (14%)

Query: 43  DASLYQI-SHLSTVGDVTYVE---ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK 98
           + ++    +    +G +T      +L     + +  A +EF+S D   +A+        +
Sbjct: 18  EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQ 76

Query: 99  GRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPL 158
           G+ L I+    D      M                           S             
Sbjct: 77  GQSLKIRRP-HDYQPLPGMSENPS---------VYVPGVVSTVVPDSA------------ 114

Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
            +K+F+  L   +++ +++E+    G ++   +  D   G S+G+   E+       Q+I
Sbjct: 115 -HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173

Query: 218 SMLNNQNLFERRITVR 233
           + LN   L ++++ V+
Sbjct: 174 AGLNGMQLGDKKLLVQ 189

>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 = 62.0 bits (151), Expect = 3e-11
 Identities = 11/80 (13%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD------KDGKSRGFGTVEFDHPVEA 213
            +++V N+ + + E+ + + F    ++  +  A        +  + + F  +EF    E 
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 214 VQSISMLNNQNLFERRITVR 233
            Q+++  +      + + +R
Sbjct: 65  TQAMAF-DGIIFQGQSLKIR 83

>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 = 49.6 bits (119), Expect = 4e-07
 Identities = 13/68 (19%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           D  + ++  L++ G +    ++ D  TG  +G A  E+   ++  +A+  ++  +   +K
Sbjct: 128 DDQVKEL--LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 102 LVIKEAVE 109
           L+++ A  
Sbjct: 186 LLVQRASV 193

>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 = 46.9 bits (112), Expect = 4e-06
 Identities = 14/103 (13%), Positives = 34/103 (33%), Gaps = 14/103 (13%)

Query: 497 NPRAGLDSNRSMNQSSNIER------DTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-- 548
            P  G+  N S+     +          + +  LP  +   ++++   + G +K   +  
Sbjct: 89  QPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 148

Query: 549 -----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
                  KG      +       +AI  ++  ++  K + V  
Sbjct: 149 DSATGLSKG-YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190

>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 = 88.8 bits (221), Expect = 7e-21
 Identities = 36/195 (18%), Positives = 74/195 (37%), Gaps = 49/195 (25%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
                 +    ++G++   +++ D  TG+  G   V +  P    KA+N ++    + + 
Sbjct: 16  QEEFRSL--FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 73

Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
           + +  A                        + +S+   +                     
Sbjct: 74  IKVSYA------------------------RPSSASIRDA-------------------N 90

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           ++V+ L   + +K+L ++F   G++    I +D+  G SRG G + FD  +EA ++I  L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 221 NNQNL--FERRITVR 233
           N Q        ITV+
Sbjct: 151 NGQKPSGATEPITVK 165

>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 = 73.0 bits (180), Expect = 3e-15
 Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            + V  L   + +++ R +F   G++E+ ++  DK  G+S G+G V +  P +A ++I+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRL 247
           LN   L  + I V   R +        L
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRDANL 91

>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 = 51.0 bits (123), Expect = 8e-08
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V  LP  +T +E R  F + G+I+  ++       +  G  G V +     A++AI+ ++
Sbjct: 7   VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG-YGFVNYIDPKDAEKAINTLN 65

Query: 574 RTRIDGKIIDVTF 586
             R+  K I V++
Sbjct: 66  GLRLQTKTIKVSY 78

>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 = 49.5 bits (119), Expect = 3e-07
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 505 NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLV 557
           + +   S++I    + V  LP T+T +EL   F   G I  + I         +G +G +
Sbjct: 77  SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG-VGFI 135

Query: 558 RFDSEWTAKRAIDMMDRTRIDG 579
           RFD    A+ AI  ++  +  G
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSG 157

>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 = 87.6 bits (218), Expect = 2e-20
 Identities = 40/195 (20%), Positives = 69/195 (35%), Gaps = 49/195 (25%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           D  LY +     +G +    I+ D  TG   G A V+F S    ++A+  ++    + ++
Sbjct: 17  DRELYAL--FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74

Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
           L +  A    GG                                                
Sbjct: 75  LKVSYA--RPGGESIKDT-----------------------------------------N 91

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           ++V NL   + + +L  +F   G +    I  DK  G+ RG   V ++   EA ++IS L
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 221 NNQNL--FERRITVR 233
           NN       + ++VR
Sbjct: 152 NNVIPEGGSQPLSVR 166

>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 = 76.1 bits (188), Expect = 2e-16
 Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            + V  L   + +++L  +FR  G +    I  D   G S G+  V+F   +++ ++I +
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 220 LNNQNLFERRITV-RMDRVADRLDG 243
           LN   +  +R+ V       + +  
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKD 89

>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 = 52.6 bits (127), Expect = 3e-08
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 8/82 (9%)

Query: 505 NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLV 557
           + +     +I+   + V NLP TIT  +L   F   G I    I       + +G +  V
Sbjct: 78  SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG-VAFV 136

Query: 558 RFDSEWTAKRAIDMMDRTRIDG 579
           R++    A+ AI  ++    +G
Sbjct: 137 RYNKREEAQEAISALNNVIPEG 158

>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 = 52.2 bits (126), Expect = 4e-08
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            ++V  LP  +T +EL   FR  G I    I          G    V F SE  ++RAI 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYG-YAFVDFTSEMDSQRAIK 63

Query: 571 MMDRTRIDGKIIDVTF 586
           +++   +  K + V++
Sbjct: 64  VLNGITVRNKRLKVSY 79

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 86.3 bits (214), Expect = 2e-20
 Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+ V+NLD+ V +  ++E+F   G ++   +  D+ G+S G   V F+   +A++++  
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95

Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRL 247
                L  R + +++  VA ++D     
Sbjct: 96  YKGVPLDGRPMDIQL--VASQIDLEHHH 121

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 56.2 bits (136), Expect = 7e-10
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           V NL   ++  ++++ F   G +K A +      +  G    V F+    A +A+     
Sbjct: 40  VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG-TADVHFERRADALKAMKQYKG 98

Query: 575 TRIDGKIIDVTF 586
             +DG+ +D+  
Sbjct: 99  VPLDGRPMDIQL 110

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 54.3 bits (131), Expect = 3e-09
 Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 1/63 (1%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
           +  G +    +  D +G+  G+A V F+      KA+ +       GR + I+     + 
Sbjct: 57  AEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV-ASQI 115

Query: 113 GRR 115
              
Sbjct: 116 DLE 118

>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 = 86.8 bits (216), Expect = 4e-20
 Identities = 32/191 (16%), Positives = 63/191 (32%), Gaps = 44/191 (23%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +  L Q       G +  ++I+ D   K    A VE+        A+  ++  + +   +
Sbjct: 14  EDILKQY--FQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIV 71

Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
            I  A + +    +                                             +
Sbjct: 72  KINWAFQSQQSSSDDTF-----------------------------------------NL 90

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLN 221
           FV +L+  VD++ LR  F+      +  +  D   G SRG+G V F    +A  ++  + 
Sbjct: 91  FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 150

Query: 222 NQNLFERRITV 232
            Q+L  R + +
Sbjct: 151 GQDLNGRPLRI 161

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 74.9 bits (185), Expect = 6e-16
 Identities = 18/71 (25%), Positives = 40/71 (56%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           ++V NLD  + E  L++ F++ G + N++I +DK+ K+  +  VE+    +A  ++  LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 222 NQNLFERRITV 232
            + +    + +
Sbjct: 63  GKQIENNIVKI 73

>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 = 47.5 bits (114), Expect = 1e-06
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 7/75 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
            + V NL   IT   L+  F+  G I   +I      K       V +     A  A+  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN-YAFVEYHQSHDANIALQT 60

Query: 572 MDRTRIDGKIIDVTF 586
           ++  +I+  I+ + +
Sbjct: 61  LNGKQIENNIVKINW 75

>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 = 47.5 bits (114), Expect = 1e-06
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V +L   +  + LR+ F++        +         +G  G V F S+  A+ A+D M 
Sbjct: 92  VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG-YGFVSFTSQDDAQNAMDSMQ 150

Query: 574 RTRIDGKIIDVTF 586
              ++G+ + + +
Sbjct: 151 GQDLNGRPLRINW 163

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

 Score = 84.8 bits (210), Expect = 4e-20
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
            +V  A L+  V E  L+++ R  G+VE VEI L     K  G   V F     A +++ 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 219 MLNNQNLFERRITVRMDR 236
            L+  ++    I  ++D 
Sbjct: 67  NLHLTSVMGNIIHAQLDI 84

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

 Score = 62.8 bits (153), Expect = 2e-12
 Identities = 19/76 (25%), Positives = 28/76 (36%), Gaps = 8/76 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            V    L   +    L+D  R  G+++  EI       K  G +  V F S   AK  + 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG-LARVLFTSTRGAKETVK 66

Query: 571 MMDRTRIDGKIIDVTF 586
            +  T + G II    
Sbjct: 67  NLHLTSVMGNIIHAQL 82

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

 Score = 50.1 bits (120), Expect = 6e-08
 Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 51  HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
                G+V  VEIL    T K  G A V F S    ++ V  +H     G  +  +  ++
Sbjct: 26  MCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQ--LD 83

Query: 110 DKGGRRN 116
            KG +R 
Sbjct: 84  IKGQQRM 90

>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 = 89.3 bits (222), Expect = 6e-20
 Identities = 34/184 (18%), Positives = 65/184 (35%), Gaps = 41/184 (22%)

Query: 53  STVGDVTY-VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
             +  V   + + +      R  A ++  S +  R  V K++  + +G  LV K +  + 
Sbjct: 139 QDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS--NP 196

Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
             +          R  SA L+                            ++ + NL  ++
Sbjct: 197 LEKS--------KRTDSATLEGR--------------------------EIMIRNLSTEL 222

Query: 172 -DEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFER 228
            DE  LRE F   G +E + I   +     +     + F++   A +++ M N   L  R
Sbjct: 223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNR 281

Query: 229 RITV 232
            I+V
Sbjct: 282 EISV 285

>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 = 87.7 bits (218), Expect = 3e-19
 Identities = 21/182 (11%), Positives = 52/182 (28%), Gaps = 53/182 (29%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
              G + +V++  D   K    A +EF   D    A+ K H+      ++++    E   
Sbjct: 63  KHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTHKVV-GQNEIIVSHLTE--- 117

Query: 113 GRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVD 172
                                                            +++ N      
Sbjct: 118 -----------------------------------------------CTLWMTNFPPSYT 130

Query: 173 EKKLREVFRLAGKVE-NVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT 231
           ++ +R++ +    V  ++ +   +   SR F  ++     +A   +  LN   +    + 
Sbjct: 131 QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV 190

Query: 232 VR 233
            +
Sbjct: 191 TK 192

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

 Score = 73.9 bits (182), Expect = 1e-14
 Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V V NL    ++ K+ + F+  G + +V++A     K+  F  +EF     A+ +I+  +
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-KKNFRFARIEFARYDGALAAITKTH 102

Query: 222 NQNLFERRITV 232
              + +  I V
Sbjct: 103 KV-VGQNEIIV 112

>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 = 61.5 bits (150), Expect = 1e-10
 Identities = 11/77 (14%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKR 567
              T+ + N PP+ T + +RD  ++   +  +           +     +   S+  A+ 
Sbjct: 116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR-FAYIDVTSKEDARY 174

Query: 568 AIDMMDRTRIDGKIIDV 584
            ++ ++  +I+G  +  
Sbjct: 175 CVEKLNGLKIEGYTLVT 191

>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 = 57.7 bits (140), Expect = 3e-09
 Identities = 23/99 (23%), Positives = 41/99 (41%), Gaps = 9/99 (9%)

Query: 496 GNPRAGLDSNRSMNQSSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIK-----FAEI 548
           G+P A   +++  N++    R+  TV+VKNLP +    ++   F++CG I       +  
Sbjct: 19  GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK 78

Query: 549 KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
           K       + F     A  AI    +  +    I V+  
Sbjct: 79  KNFR-FARIEFARYDGALAAITKTHK-VVGQNEIIVSHL 115

>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 = 46.9 bits (112), Expect = 9e-06
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 11/87 (12%)

Query: 509 NQSSNIERDTVVVKNLPPTIT-WQELRDKFRNCGDIKFAEI--------KGKGDIGLVRF 559
             S+ +E   ++++NL   +     LR+ F   G I+   I                + F
Sbjct: 203 TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC-CAFMVF 261

Query: 560 DSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           +++ +A+RA+  M+R+ +  + I V+ 
Sbjct: 262 ENKDSAERALQ-MNRSLLGNREISVSL 287

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 86.0 bits (214), Expect = 8e-20
 Identities = 41/186 (22%), Positives = 69/186 (37%), Gaps = 48/186 (25%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
            +    G VT ++I+ D  TG+ RG   + F+ P  V + V   H     G+ +  K A+
Sbjct: 22  EYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHIL--DGKVIDPKRAI 79

Query: 109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLD 168
                 +                                             K+FV  + 
Sbjct: 80  PRDEQDKT-------------------------------------------GKIFVGGIG 96

Query: 169 YKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE 227
             V  K+  E F   G + + ++ LDKD G+SRGFG V +D   +AV  +      +  +
Sbjct: 97  PDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA-DAVDRVCQNKFIDFKD 155

Query: 228 RRITVR 233
           R+I ++
Sbjct: 156 RKIEIK 161

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 62.9 bits (154), Expect = 8e-12
 Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP--VEAVQS 216
           K+F+  L++   E  LRE F   G V +++I  D   G+SRGFG + F+ P  V+ V  
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 46.8 bits (112), Expect = 3e-06
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 51  HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
             S  G +   +++ D DTG+ RG   V + S D V +   +    + K RK+ IK A 
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAE 164

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 43.7 bits (104), Expect = 3e-05
 Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 9/90 (10%)

Query: 502 LDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDI 554
           +D  R++ +    +   + V  + P +  +E  + F   G I  A++       + +G  
Sbjct: 73  IDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRG-F 131

Query: 555 GLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
           G V +DS     R            + I++
Sbjct: 132 GFVTYDSADAVDRVCQ-NKFIDFKDRKIEI 160

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 40.2 bits (95), Expect = 5e-04
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 10/74 (13%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            + +  L    T   LR+ F   G +   +I       + +G  G + F+   +      
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRG-FGFLSFEKPSSVDEV-- 61

Query: 571 MMDRTRIDGKIIDV 584
           +  +  +DGK+ID 
Sbjct: 62  VKTQHILDGKVIDP 75

>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 = 85.4 bits (212), Expect = 2e-19
 Identities = 32/187 (17%), Positives = 54/187 (28%), Gaps = 45/187 (24%)

Query: 53  STVGDVTYVEILNDDTGKP---RGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
              G V  + +L D +  P   +G   V F +     +A N +H  +         +   
Sbjct: 25  EQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKP 84

Query: 110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
               + N                                            K+F+  +  
Sbjct: 85  ADSEKNNAVED---------------------------------------RKLFIGMISK 105

Query: 170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE-- 227
           K  E  +R +F   G++E   I    DG SRG   V F     A  +I  ++     E  
Sbjct: 106 KCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC 165

Query: 228 -RRITVR 233
              + V+
Sbjct: 166 SSPMVVK 172

>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 = 72.3 bits (178), Expect = 6e-15
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 3/83 (3%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG---KSRGFGTVEFDHPVEAVQSI 217
           K+FV  +     EK LRE+F   G V  + +  D+     +S+G   V F     A+++ 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 218 SMLNNQNLFERRITVRMDRVADR 240
           + L+N  +          + AD 
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADS 87

>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 = 47.2 bits (113), Expect = 2e-06
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 7/63 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           +  +    T  ++R  F + G I+   I        +G    V F +   A+ AI  M +
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRG-CAFVTFTTRAMAQTAIKAMHQ 158

Query: 575 TRI 577
            + 
Sbjct: 159 AQT 161

>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 = 45.3 bits (108), Expect = 1e-05
 Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH---RFETKGRKLVIKEA 107
           G +    IL    G  RG A V F +  + + A+  MH     E     +V+K A
Sbjct: 120 GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>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 = 43.4 bits (103), Expect = 4e-05
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 10/76 (13%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI---------KGKGDIGLVRFDSEWTAKRA 568
            + V  +P T + ++LR+ F   G +    +         + KG    V F +   A  A
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG-CCFVTFYTRKAALEA 63

Query: 569 IDMMDRTRIDGKIIDV 584
            + +   ++   +   
Sbjct: 64  QNALHNMKVLPGMHHP 79

>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 = 82.8 bits (205), Expect = 2e-19
 Identities = 23/73 (31%), Positives = 41/73 (56%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+F+  L+ + +EK L+ VF   G +  V +  D+  KSRGF  + F++P +A  +   
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67

Query: 220 LNNQNLFERRITV 232
           +N ++L  + I V
Sbjct: 68  MNGKSLHGKAIKV 80

>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 = 52.7 bits (127), Expect = 1e-08
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 7/70 (10%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           +  L      + L+  F   G I    +      K +G    + F++   AK A   M+ 
Sbjct: 12  IGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG-FAFITFENPADAKNAAKDMNG 70

Query: 575 TRIDGKIIDV 584
             + GK I V
Sbjct: 71  KSLHGKAIKV 80

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 16/73 (21%), Positives = 32/73 (43%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           G ++ V ++ D T K RG A + F++P   + A   M+     G+ + +++A +      
Sbjct: 32  GPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSG 91

Query: 116 NMGGGGGVDRDLS 128
                    R+ S
Sbjct: 92  GRRRPPASSRNRS 104

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 81.9 bits (203), Expect = 3e-19
 Identities = 17/73 (23%), Positives = 43/73 (58%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +K+F++ L +   +++L E+ +  G V+++ +  ++ GK +G   VE+++  +A Q++  
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77

Query: 220 LNNQNLFERRITV 232
           ++   + E  I V
Sbjct: 78  MDGMTIKENIIKV 90

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 55.4 bits (134), Expect = 6e-10
 Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 7/93 (7%)

Query: 500 AGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGD 553
               S+     S+++E+  + +  LP + T +EL +  +  G +K   +      K KG 
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG- 59

Query: 554 IGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           +  V +++E  A +A+  MD   I   II V  
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKVAI 92

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 14/55 (25%), Positives = 26/55 (47%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
              G V  + ++ +  GKP+G A VE+++     +AV KM     K   + +  +
Sbjct: 39  KAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS 93

>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 = 79.9 bits (198), Expect = 1e-18
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I 
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 219 MLNNQNLFERRITV 232
            +N   LF R I V
Sbjct: 68  NMNESELFGRTIRV 81

>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 = 46.4 bits (111), Expect = 8e-07
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            + V  L   +  + L   F   GDI   +I       K +G    V F+    A  AID
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG-FAFVEFELAEDAAAAID 67

Query: 571 MMDRTRIDGKIIDV 584
            M+ + + G+ I V
Sbjct: 68  NMNESELFGRTIRV 81

>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 = 45.2 bits (108), Expect = 2e-06
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           GD+T ++I  D +T K RG A VEF+  +    A++ M+  E  GR + +  A
Sbjct: 32  GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 79.8 bits (197), Expect = 2e-18
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
           S  S    S    + VVV  LPP+ +WQ+L+D  R  GD+ +A++   G  G+V F  + 
Sbjct: 3   SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKE 61

Query: 564 TAKRAIDMMDRTRIDGKIIDVTF 586
               A+  +D T+      +  +
Sbjct: 62  DMTYAVRKLDNTKFRSHEGETAY 84

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 63.3 bits (154), Expect = 1e-12
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 8/85 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N+V V+ L      + L++  R AG V   ++         G G VEF    +   ++  
Sbjct: 16  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRK 69

Query: 220 LNNQNLFERRITVRMDRVADRLDGP 244
           L+N             RV  ++DGP
Sbjct: 70  LDNTKFRSHEGETAYIRV--KVDGP 92

>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 = 49.4 bits (118), Expect = 1e-07
 Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 51  HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED 110
           H+   GDV Y ++  D TG      +VEF   + +  AV K+   + +  +         
Sbjct: 35  HMREAGDVCYADVYRDGTG------VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 88

Query: 111 KGGRRNMGGGGG 122
             G R+   G  
Sbjct: 89  VDGPRSPSYGRS 100

>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 = 79.6 bits (197), Expect = 2e-18
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            V+V  LD KV E  L E+F  AG V N  +  D+  G+ +G+G VEF    +A  +I +
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76

Query: 220 LNNQNLFERRITV 232
           ++   L+ + I V
Sbjct: 77  MDMIKLYGKPIRV 89

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           +  L+++      G V    +  D  TG+ +G   VEF S +    A+  M   +  G+ 
Sbjct: 29  EPLLWEL--FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP 86

Query: 102 LVIKEAVEDKGGRRNMGGG 120
           + + +A            G
Sbjct: 87  IRVNKASAHNKNLSGPSSG 105

>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 = 9e-06
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 8/74 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
           TV V  L   ++   L + F   G +    +       + +G  G V F SE  A  AI 
Sbjct: 17  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG-YGFVEFLSEEDADYAIK 75

Query: 571 MMDRTRIDGKIIDV 584
           +MD  ++ GK I V
Sbjct: 76  IMDMIKLYGKPIRV 89

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 82.0 bits (203), Expect = 4e-18
 Identities = 45/187 (24%), Positives = 71/187 (37%), Gaps = 43/187 (22%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVN-KMHRFETKGRKLVIKEA 107
           SH    G +T   ++ D +T + RG   V + + + V  A+N + H+ +  GR +  K A
Sbjct: 32  SHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVD--GRVVEPKRA 89

Query: 108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANL 167
           V     R +    G                                     + K+FV  +
Sbjct: 90  V----SREDSQRPGAHLT---------------------------------VKKIFVGGI 112

Query: 168 DYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLF 226
               +E  LR+ F   GK+E +EI  D+  GK RGF  V FD   ++V  I +     + 
Sbjct: 113 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVIQKYHTVN 171

Query: 227 ERRITVR 233
                VR
Sbjct: 172 GHNCEVR 178

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 60.4 bits (147), Expect = 1e-10
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEA 213
           K+F+  L ++  ++ LR  F   G + +  +  D +  +SRGFG V +    E 
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 47.7 bits (114), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
            +    G +  +EI+ D  +GK RG A V F   D V K V         G    +++A+
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKAL 181

Query: 109 EDKGGRRNMGGGGGVDR 125
                ++ M       R
Sbjct: 182 S----KQEMASASSSQR 194

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 80.2 bits (198), Expect = 4e-18
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I 
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123

Query: 219 MLNNQNLFERRITV 232
            +N   LF R I V
Sbjct: 124 NMNESELFGRTIRV 137

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 49.0 bits (117), Expect = 3e-07
 Identities = 23/105 (21%), Positives = 39/105 (37%), Gaps = 9/105 (8%)

Query: 487 QASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFA 546
             +  +    +   G   +     S+  +R  + V  L   +  + L   F   GDI   
Sbjct: 35  AYTCVNCTERHVDGGSGGSGGSGGSATTKR-VLYVGGLAEEVDDKVLHAAFIPFGDITDI 93

Query: 547 EI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
           +I       K +G    V F+    A  AID M+ + + G+ I V
Sbjct: 94  QIPLDYETEKHRG-FAFVEFELAEDAAAAIDNMNESELFGRTIRV 137

>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 = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           GD+T ++I  D +T K RG A VEF+  +    A++ M+  E  GR + +  A
Sbjct: 88  GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 83.2 bits (206), Expect = 5e-18
 Identities = 31/187 (16%), Positives = 52/187 (27%), Gaps = 56/187 (29%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +    ++      G+ + V I  D     RG   +  +S  L   A  ++     K R L
Sbjct: 36  EEDFKRL--FERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPL 88

Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
            I+ A                                                      +
Sbjct: 89  RIRFATHGA-------------------------------------------------AL 99

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
            V NL   V  + L + F   G VE   + +D  G++ G G VEF     A +++    +
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGD 159

Query: 223 QNLFERR 229
                  
Sbjct: 160 GAFLLTT 166

>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 = 67.4 bits (165), Expect = 1e-12
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++FV NL   + E+  + +F   G+   V I      + RGFG +  +    A  + + 
Sbjct: 23  CRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-----NRDRGFGFIRLESRTLAEIAKAE 77

Query: 220 LNNQNLFERRITVR 233
           L+   L  R + +R
Sbjct: 78  LDGTILKSRPLRIR 91

>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 = 55.1 bits (133), Expect = 1e-08
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMD 573
           +R  + V NLP  IT ++ +  F   G+     I + +G  G +R +S   A+ A   +D
Sbjct: 21  QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG-FGFIRLESRTLAEIAKAELD 79

Query: 574 RTRIDGKIIDVTF 586
            T +  + + + F
Sbjct: 80  GTILKSRPLRIRF 92

>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 = 48.1 bits (115), Expect = 3e-06
 Identities = 27/160 (16%), Positives = 47/160 (29%), Gaps = 20/160 (12%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +  L Q    S  G V    ++ DD G+  G   VEF +    RKA+ +           
Sbjct: 110 NELLEQA--FSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT 167

Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK- 161
                VE      +  G       L   L   + ++       P+F +         ++ 
Sbjct: 168 PRPVIVEPMEQFDDEDG-------LPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRW 220

Query: 162 ----VFVANLDYKVD------EKKLREVFRLAGKVENVEI 191
                       +VD      ++KL      A     + +
Sbjct: 221 KALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLML 260

>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 = 45.1 bits (107), Expect = 3e-05
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           VKNL P ++ + L   F   G ++ A +      +  G  G V F ++  A++A++   
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG-KGFVEFAAKPPARKALERCG 158

>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 = 80.7 bits (200), Expect = 6e-18
 Identities = 28/196 (14%), Positives = 69/196 (35%), Gaps = 49/196 (25%)

Query: 43  DASLYQI-SHLSTVGDVTYVE---ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK 98
           + ++    +    +G +T      +L     + +  A +EF+S D   +A+        +
Sbjct: 18  EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQ 76

Query: 99  GRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPL 158
           G+ L I+   + +                                               
Sbjct: 77  GQSLKIRRPHDYQPLPGA------------------------------------------ 94

Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
            +K+F+  L   +++ +++E+    G ++   +  D   G S+G+   E+       Q+I
Sbjct: 95  -HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153

Query: 218 SMLNNQNLFERRITVR 233
           + LN   L ++++ V+
Sbjct: 154 AGLNGMQLGDKKLLVQ 169

>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 = 61.9 bits (151), Expect = 2e-11
 Identities = 14/93 (15%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD------KDGKSRGFGTVEFDHPVEAV 214
           +++V N+ + + E+ + + F    ++  +  A        +  + + F  +EF    E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 215 QSISMLNNQNLFERRITVRMDRVADRLDGPVRL 247
           Q+++  +      + + +R       L G  +L
Sbjct: 66  QAMAF-DGIIFQGQSLKIRRPHDYQPLPGAHKL 97

>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 = 50.3 bits (121), Expect = 2e-07
 Identities = 12/90 (13%), Positives = 30/90 (33%), Gaps = 8/90 (8%)

Query: 502 LDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDI 554
           L   R  +         + +  LP  +   ++++   + G +K   +         KG  
Sbjct: 80  LKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG-Y 138

Query: 555 GLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
               +       +AI  ++  ++  K + V
Sbjct: 139 AFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 46.5 bits (111), Expect = 4e-06
 Identities = 13/66 (19%), Positives = 34/66 (51%), Gaps = 3/66 (4%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           D  + ++  L++ G +    ++ D  TG  +G A  E+   ++  +A+  ++  +   +K
Sbjct: 108 DDQVKEL--LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 165

Query: 102 LVIKEA 107
           L+++ A
Sbjct: 166 LLVQRA 171

>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 = 77.2 bits (191), Expect = 1e-17
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             + V  L     E+ LREVF   G + +V I  D+   +SRGF  V F++  +A ++  
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 219 MLNNQNLFERRITV 232
             N   L  RRI V
Sbjct: 76  RANGMELDGRRIRV 89

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 8/91 (8%)

Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIG 555
            S  S N+++      + V  L    T ++LR+ F   G I    I       + +G   
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG-FA 60

Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
            V F++   AK A +  +   +DG+ I V+ 
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSG 91

>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 = 46.8 bits (112), Expect = 6e-07
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           G +  V I+ D  + + RG A V F++ D  ++A  + +  E  GR++ +   
Sbjct: 40  GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>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 = 76.9 bits (190), Expect = 2e-17
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           + V+V+NL + +    L  +F   GKV  V I  DKD  KS+G   + F     A     
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 219 MLNNQNLFERRITV 232
            +NN+ LF R I  
Sbjct: 77  AINNKQLFGRVIKA 90

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.3 bits (121), Expect = 4e-08
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
           S  G V  V I+ D DT K +G A + F   D  +     ++  +  GR +    A+
Sbjct: 38  SKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI 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 = 43.0 bits (102), Expect = 1e-05
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
           TV V NLP ++T  +L   F   G +    I       K KG +  + F  + +A+    
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG-VAFILFLDKDSAQNCTR 76

Query: 571 MMDRTRIDGKIIDV 584
            ++  ++ G++I  
Sbjct: 77  AINNKQLFGRVIKA 90

>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 = 77.7 bits (192), Expect = 2e-17
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 5/88 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            ++++NL   +DE++L  + +  G+V +  I  D  G SRG G    +   +    I   
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 221 NNQNLFERRITV-----RMDRVADRLDG 243
           N + +             + + +    G
Sbjct: 87  NGKFIKTPPGVSAPTEPLLCKFSGPSSG 114

>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 = 55.3 bits (134), Expect = 1e-09
 Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 7/70 (10%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           + NLP ++  QEL +  +  G +    I        +G +G  R +S    +  I   + 
Sbjct: 30  ISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG-VGFARMESTEKCEAVIGHFNG 88

Query: 575 TRIDGKIIDV 584
             I       
Sbjct: 89  KFIKTPPGVS 98

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 2/65 (3%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           +  L  +  L   G V    IL D +G  RG      +S +     +   +    K    
Sbjct: 39  EQELENM--LKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG 96

Query: 103 VIKEA 107
           V    
Sbjct: 97  VSAPT 101

>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 = 76.5 bits (189), Expect = 3e-17
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I 
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

Query: 219 MLNNQNLFERRITV 232
            +N   LF R I V
Sbjct: 73  NMNESELFGRTIRV 86

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.9 bits (120), Expect = 6e-08
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           GD+T ++I  D +T K RG A VEF+  +    A++ M+  E  GR + +  A   +   
Sbjct: 37  GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR--I 94

Query: 115 RNMGGGGG 122
           +  G   G
Sbjct: 95  KESGPSSG 102

>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 = 45.7 bits (109), Expect = 2e-06
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            + V  L   +  + L   F   GDI   +I       K +G    V F+    A  AID
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG-FAFVEFELAEDAAAAID 72

Query: 571 MMDRTRIDGKIIDV 584
            M+ + + G+ I V
Sbjct: 73  NMNESELFGRTIRV 86

>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 = 76.0 bits (188), Expect = 3e-17
 Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSI 217
            KV +  L   V +  + E+F   GK++ +++ +++     S+G+  VEF++P EA +++
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 218 SMLNNQNLFERRITV 232
             ++   +  + IT 
Sbjct: 65  KHMDGGQIDGQEITA 79

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 49.5 bits (119), Expect = 6e-08
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 9/77 (11%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI--------KGKGDIGLVRFDSEWTAKRAI 569
            V +  L   +T   + + F   G IK  ++          KG    V F++   A++A+
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG-YAYVEFENPDEAEKAL 64

Query: 570 DMMDRTRIDGKIIDVTF 586
             MD  +IDG+ I  T 
Sbjct: 65  KHMDGGQIDGQEITATA 81

>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 = 47.5 bits (114), Expect = 3e-07
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 53  STVGDVTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           ST G +  +++  +       +G A VEF++PD   KA+  M   +  G+++     
Sbjct: 26  STYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV 82

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 75.6 bits (187), Expect = 3e-17
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            ++V N+DY    ++L   F   G V  V I  DK  G  +GF  +EF    E+V++   
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66

Query: 220 LNNQNLFERRITVRMDR 236
           L+      R+I V   R
Sbjct: 67  LDESLFRGRQIKVIPKR 83

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
           +H    G V  V IL D  +G P+G A +EF   + VR ++  +     +GR++ +    
Sbjct: 25  AHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR 83

Query: 109 EDKGG 113
            ++ G
Sbjct: 84  TNRPG 88

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 41.3 bits (98), Expect = 5e-05
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 11/81 (13%)

Query: 514 IERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWT 564
           +E D  ++ V N+    T +EL   F  CG +    I         KG    + F  + +
Sbjct: 2   MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG-FAYIEFSDKES 60

Query: 565 AKRAIDMMDRTRIDGKIIDVT 585
            + ++  +D +   G+ I V 
Sbjct: 61  VRTSLA-LDESLFRGRQIKVI 80

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 75.7 bits (187), Expect = 4e-17
 Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 3/92 (3%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           + ++V +L + + E  LR +F   GK++N+ +  D D G+S+G+G + F     A +++ 
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 219 MLNNQNLFERRITVRMDRVADRLDGPVRLPEG 250
            LN   L  R + V    V +RLDG      G
Sbjct: 66  QLNGFELAGRPMRV--GHVTERLDGGSGPSSG 95

>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 = 51.4 bits (124), Expect = 2e-08
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
              G +  + ++ D DTG+ +G   + F   +  R+A+ +++ FE  GR + +     ++
Sbjct: 27  EPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV-TER 85

Query: 112 GGRRNMGGGG 121
               +    G
Sbjct: 86  LDGGSGPSSG 95

>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 = 41.0 bits (97), Expect = 8e-05
 Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 8/71 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V +L   IT   LR  F   G I    +       + KG  G + F     A+RA++ ++
Sbjct: 10  VGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKG-YGFITFSDSECARRALEQLN 68

Query: 574 RTRIDGKIIDV 584
              + G+ + V
Sbjct: 69  GFELAGRPMRV 79

>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 = 79.4 bits (195), Expect = 4e-17
 Identities = 25/189 (13%), Positives = 65/189 (34%), Gaps = 13/189 (6%)

Query: 45  SLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
            ++ +      G+V  V+ +        G+A+VE      V +A+  ++     G+K+ +
Sbjct: 21  RVFNV--FCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNV 74

Query: 105 KEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFV 164
             + +         G            ++ +++F      +   +          N +  
Sbjct: 75  CVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRI------QHPSNVLHF 128

Query: 165 ANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQ 223
            N   +V E+   E+    G      + +     +    G +E+D   +A++++  LN+ 
Sbjct: 129 FNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHY 188

Query: 224 NLFERRITV 232
            +       
Sbjct: 189 QMKNPNGPY 197

>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 = 56.3 bits (135), Expect = 3e-09
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 162 VFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           + V  LD  K++  ++  VF L G VE V+    K     G   VE        ++I+ L
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHL 62

Query: 221 NNQNLFERRITVRMDR 236
           NN  +F +++ V + +
Sbjct: 63  NNNFMFGQKMNVCVSK 78

>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 = 52.8 bits (126), Expect = 4e-08
 Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIK------GKGDIGLVRFDSEWTAKRAIDM 571
            +   N P  +T +   +     G  +   +K       +   GL+ +DS+  A   +  
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184

Query: 572 MDRTRIDGKIIDVTF 586
           ++  ++        +
Sbjct: 185 LNHYQMKNPNGPYPY 199

>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 = 52.4 bits (125), Expect = 7e-08
 Identities = 12/71 (16%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 518 TVVVKNLPP-TITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
            ++V  L    +    + + F   G+++  +  K K    +V     +   RAI  ++  
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65

Query: 576 RIDGKIIDVTF 586
            + G+ ++V  
Sbjct: 66  FMFGQKMNVCV 76

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 75.8 bits (187), Expect = 7e-17
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            VF   L  ++  + L + F   GKV +V I  D++  +S+G   VEF    ++V     
Sbjct: 27  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI-QSVPLAIG 85

Query: 220 LNNQNLFERRITV 232
           L  Q L    I V
Sbjct: 86  LTGQRLLGVPIIV 98

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 55.0 bits (133), Expect = 1e-09
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
              S VG V  V I++D ++ + +G A VEF     V  A+  +      G  ++++ + 
Sbjct: 44  DFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ 102

Query: 109 EDKGGRRNMGGG 120
            +K        G
Sbjct: 103 AEKNRLSGPSSG 114

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 24/91 (26%), Positives = 34/91 (37%), Gaps = 11/91 (12%)

Query: 504 SNRSMNQSSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDI 554
               ++  S  ERD  TV    L   I  ++L D F   G ++   I       + KG I
Sbjct: 11  VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG-I 69

Query: 555 GLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
             V F    +   AI  +   R+ G  I V 
Sbjct: 70  AYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQ 99

>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 = 75.3 bits (186), Expect = 8e-17
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            + V NL Y+     LR VF   G+V +V I  +      RGF  V F    +A  + + 
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 220 LNNQNLFERRITV 232
           ++   L  R + V
Sbjct: 75  MDGAELDGRELRV 87

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 19/69 (27%), Positives = 25/69 (36%), Gaps = 1/69 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
              G V  V I  +  T  PRG A V F      + A   M   E  GR+L ++ A   +
Sbjct: 35  EKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR 94

Query: 112 GGRRNMGGG 120
                   G
Sbjct: 95  RDLSGPSSG 103

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 22/101 (21%), Positives = 33/101 (32%), Gaps = 19/101 (18%)

Query: 493 GGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI---- 548
           G  G+    +D   +           + V NL    +   LR  F   G +    I    
Sbjct: 1   GSSGSSGPDVDGMIT-----------LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP 49

Query: 549 ---KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
                +G    VRF     A+ A   MD   +DG+ + V  
Sbjct: 50  HTKAPRG-FAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV 89

>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 = 78.5 bits (194), Expect = 9e-17
 Identities = 44/191 (23%), Positives = 76/191 (39%), Gaps = 45/191 (23%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           +A LY+    S  G +  + +  D  T +  G A V FQ P    +A++ M+    KG+ 
Sbjct: 29  EAMLYEK--FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 86

Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
           + I  +  D   R+                    S  GN                     
Sbjct: 87  VRIMWSQRDPSLRK--------------------SGVGN--------------------- 105

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +F+ NLD  +D K L + F   G + + ++  D +  S+G+G V F+    A ++I  +N
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMN 164

Query: 222 NQNLFERRITV 232
              L +R++ V
Sbjct: 165 GMLLNDRKVFV 175

>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 = 63.8 bits (156), Expect = 8e-12
 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
           ++V +L   V E  L E F  AG + ++ +  D    +S G+  V F  P +A +++  +
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 221 NNQNLFERRITV 232
           N   +  + + +
Sbjct: 78  NFDVIKGKPVRI 89

>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 = 55.7 bits (135), Expect = 4e-09
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFD 560
           +            + +KNL  +I  + L D F   G+I   ++       KG  G V F+
Sbjct: 93  QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG-YGFVHFE 151

Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTFF 587
           ++  A+RAI+ M+   ++ + + V  F
Sbjct: 152 TQEAAERAIEKMNGMLLNDRKVFVGRF 178

>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 = 43.8 bits (104), Expect = 4e-05
 Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 507 SMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVR 558
           SMN S+       + V +L P +T   L +KF   G I    +       +  G    V 
Sbjct: 5   SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG-YAYVN 63

Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
           F     A+RA+D M+   I GK + +
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRI 89

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 75.0 bits (185), Expect = 1e-16
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N VFV  +D ++DE ++R  F   G V+ V+I  D+ G S+G+G V F +    VQ I +
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND-VDVQKI-V 67

Query: 220 LNNQNLFERRITVR 233
            +  N   +++ + 
Sbjct: 68  ESQINFHGKKLKLG 81

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
           G V  V+I+ D TG  +G   V F +   V+K V     F   G+KL +  A+ 
Sbjct: 34  GSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQINF--HGKKLKLGPAIR 85

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 9/70 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           V  +   +   E+R  F   G +K  +I        KG  G V F ++   ++ ++    
Sbjct: 14  VGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG-YGFVSFYNDVDVQKIVESQ-- 70

Query: 575 TRIDGKIIDV 584
               GK + +
Sbjct: 71  INFHGKKLKL 80

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 74.1 bits (183), Expect = 1e-16
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             +FV +L+  VD++ LR  F+      +  +  D   G SRG+G V F    +A  ++ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 219 MLNNQNLFERRITV 232
            +  Q+L  R + +
Sbjct: 62  SMQGQDLNGRPLRI 75

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 8/71 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V +L   +  + LR+ F++        +         +G  G V F S+  A+ A+D M 
Sbjct: 6   VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG-YGFVSFTSQDDAQNAMDSMQ 64

Query: 574 RTRIDGKIIDV 584
              ++G+ + +
Sbjct: 65  GQDLNGRPLRI 75

>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 = 41.7 bits (99), Expect = 3e-05
 Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 3/66 (4%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           D +L                ++ D  TG  RG   V F S D  + A++ M   +  GR 
Sbjct: 15  DETLRNA--FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 72

Query: 102 LVIKEA 107
           L I  A
Sbjct: 73  LRINWA 78

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 75.0 bits (185), Expect = 1e-16
 Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 143 GLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGF 202
           GL P+       N     ++ V+N+ ++  +  LR++F   GK+ +VEI  ++ G S+GF
Sbjct: 13  GLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGF 71

Query: 203 GTVEFDHPVEAVQSISMLNNQNLFERRITV 232
           G V F++  +A ++   L+   +  R+I V
Sbjct: 72  GFVTFENSADADRAREKLHGTVVEGRKIEV 101

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.2 bits (123), Expect = 3e-08
 Identities = 27/106 (25%), Positives = 41/106 (38%), Gaps = 11/106 (10%)

Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDI 543
           GS            PR    +  + +Q   +      V N+P      +LR  F   G I
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMNTENKSQPKRL-----HVSNIPFRFRDPDLRQMFGQFGKI 56

Query: 544 KFAEI-----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
              EI       KG  G V F++   A RA + +  T ++G+ I+V
Sbjct: 57  LDVEIIFNERGSKG-FGFVTFENSADADRAREKLHGTVVEGRKIEV 101

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           G +  VEI+ +     +G   V F++     +A  K+H    +GRK+ +  A
Sbjct: 54  GKILDVEIIFN-ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 75.5 bits (186), Expect = 1e-16
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            V+V N+DY    + L   F   G +  + I  DK  G  +G+  +EF     +V +   
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSVDAAVA 96

Query: 220 LNNQNLFERRITVRMDR 236
           ++      R I V   R
Sbjct: 97  MDETVFRGRTIKVLPKR 113

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 52.8 bits (127), Expect = 1e-08
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
           +H S+ G +  + IL D  +G P+G A +EF   + V  AV  M     +GR + +    
Sbjct: 55  AHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR 113

Query: 109 EDKGGRRN 116
            +  G  +
Sbjct: 114 TNMPGISS 121

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 41.2 bits (97), Expect = 9e-05
 Identities = 25/97 (25%), Positives = 36/97 (37%), Gaps = 9/97 (9%)

Query: 496 GNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------- 548
           G    G     S  +   I++ +V V N+    T Q+L   F +CG I    I       
Sbjct: 16  GAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSG 75

Query: 549 KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
             KG    + F    +   A+  MD T   G+ I V 
Sbjct: 76  HPKG-YAYIEFAERNSVDAAVA-MDETVFRGRTIKVL 110

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 74.2 bits (183), Expect = 2e-16
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+FV  L+ +  E+ +  +F+  G ++   +    DG S+G   V+F    EA  +I  
Sbjct: 16  RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75

Query: 220 LNNQNLFE---RRITVR 233
           L+           + V+
Sbjct: 76  LHGSQTMPGASSSLVVK 92

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 3/66 (4%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH---RFETKGRKLVIKEAVEDKG 112
           G +    +L    G  +G A V+F S    + A++ +H           LV+K A  DK 
Sbjct: 40  GVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE 99

Query: 113 GRRNMG 118
              + G
Sbjct: 100 SGPSSG 105

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLV 557
           S  S ++S       + V  L    + +++   F+  G I    +        KG    V
Sbjct: 3   SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG-CAFV 61

Query: 558 RFDSEWTAKRAIDMMDRTRI 577
           +F S   A+ AI  +  ++ 
Sbjct: 62  KFSSHTEAQAAIHALHGSQT 81

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 73.8 bits (182), Expect = 2e-16
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
            ++FV NL Y   E+ L ++F   G +  +   +D    K +GF  V F  P  AV++ +
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 219 MLNNQNLFERRITV 232
            ++ Q    R + V
Sbjct: 69  EVDGQVFQGRMLHV 82

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
              S  G ++ +    D  T KP+G A V F  P+   KA  ++     +GR L +  + 
Sbjct: 27  KLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST 86

Query: 109 EDKGGRRNMGGGG 121
             K   ++    G
Sbjct: 87  IKKEASQSGPSSG 99

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 8/73 (10%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V+NL  T + ++L   F   G +            K KG    V F     A +A   +D
Sbjct: 13  VRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG-FAFVTFMFPEHAVKAYAEVD 71

Query: 574 RTRIDGKIIDVTF 586
                G+++ V  
Sbjct: 72  GQVFQGRMLHVLP 84

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 73.4 bits (181), Expect = 3e-16
 Identities = 17/87 (19%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            V++ ++ Y   E+++ ++    G V N+++  D   G+S+G+  +EF     +  ++  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 220 LNNQNLFERRITVRMDRVADRLDGPVR 246
           LN   L  R +       ++     V 
Sbjct: 64  LNGYQLGSRFLKC--GYSSNSDISGVS 88

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           S VG V  ++++ D  TG+ +G A +EF+  +    AV  ++ ++   R L    +    
Sbjct: 24  SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 83

Query: 112 GGRRNM 117
               ++
Sbjct: 84  ISGVSL 89

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 10/74 (13%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            V + ++P   T +++ D   N G +   ++       + KG    + F    ++  A+ 
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG-YAFIEFRDLESSASAVR 62

Query: 571 MMDRTRIDGKIIDV 584
            ++  ++  + +  
Sbjct: 63  NLNGYQLGSRFLKC 76

>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 = 74.2 bits (183), Expect = 3e-16
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +F+ NLD  +D K L + F   G + + ++  D+   S+G+G V F+    A ++I  
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEK 64

Query: 220 LNNQNLFERRITV 232
           +N   L +R++ V
Sbjct: 65  MNGMLLNDRKVFV 77

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 53.8 bits (130), Expect = 4e-09
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMMD 573
           + +KNL  +I  + L D F   G+I   ++       KG  G V F+++  A+RAI+ M+
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG-YGFVHFETQEAAERAIEKMN 66

Query: 574 RTRIDGKIIDVTFF 587
              ++ + + V  F
Sbjct: 67  GMLLNDRKVFVGRF 80

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 74.1 bits (182), Expect = 3e-16
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
            VVV  LPP+ +WQ+L+D  R  GD+ +A++   G  G+V F  +     A+  +D T+ 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT-GVVEFVRKEDMTYAVRKLDNTKF 76

Query: 578 DGKIIDVTF 586
                +  +
Sbjct: 77  RSHEGETAY 85

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 61.8 bits (150), Expect = 5e-12
 Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 8/91 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N+V V+ L      + L++  R AG V   ++         G G VEF    +   ++  
Sbjct: 17  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRK 70

Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRLPEG 250
           L+N             RV  ++DGP     G
Sbjct: 71  LDNTKFRSHEGETAYIRV--KVDGPRSPSYG 99

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 51.4 bits (123), Expect = 3e-08
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 51  HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED 110
           H+   GDV Y ++  D TG      +VEF   + +  AV K+   + +  +         
Sbjct: 36  HMREAGDVCYADVYRDGTG------VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 89

Query: 111 KGGRRNMGGGGGVDR 125
             G R+   G    R
Sbjct: 90  VDGPRSPSYGRSRSR 104

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 74.3 bits (183), Expect = 3e-16
 Identities = 25/98 (25%), Positives = 51/98 (52%), Gaps = 3/98 (3%)

Query: 140 NTYGLSPQFLESLG--INCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD- 196
            + GL+ Q + + G     P    +F+ +L  +  ++ L ++F   G V + ++ +DK  
Sbjct: 4   GSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63

Query: 197 GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM 234
             S+ FG V +D+PV A  +I  +N   +  +R+ V++
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 101

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 21/102 (20%), Positives = 38/102 (37%), Gaps = 9/102 (8%)

Query: 493 GGYGNPRAGLDSNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI--- 548
           G  G+      S  +            + + +LP     Q+L   F   G++  A++   
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 549 ----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
                 K   G V +D+  +A+ AI  M+  +I  K + V  
Sbjct: 61  KQTNLSKC-FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 101

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 45.0 bits (107), Expect = 4e-06
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 4/81 (4%)

Query: 42  GDASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
           GD  L Q       G+V   ++  D  T   +    V + +P   + A+  M+ F+   +
Sbjct: 38  GDQDLLQ--MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK 95

Query: 101 KLVIKEAVEDKGGRRNMGGGG 121
           +L ++     K   ++    G
Sbjct: 96  RLKVQLK-RSKNDSKSGPSSG 115

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 73.4 bits (181), Expect = 3e-16
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
            K+FV  L +  +E+ L +VF   G++  V +  D++  +SRGFG V F++  +A  ++ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 219 MLNNQNLFERRITV 232
            +N +++  R+I V
Sbjct: 73  AMNGKSVDGRQIRV 86

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           G ++ V ++ D +T + RG   V F++ D  + A+  M+     GR++ + +A +    R
Sbjct: 37  GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96

Query: 115 RNMGGG 120
                G
Sbjct: 97  SGPSSG 102

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 8/71 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V  L      Q L   F   G I    +       + +G  G V F++   AK A+  M+
Sbjct: 17  VGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG-FGFVTFENIDDAKDAMMAMN 75

Query: 574 RTRIDGKIIDV 584
              +DG+ I V
Sbjct: 76  GKSVDGRQIRV 86

>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 = 75.2 bits (185), Expect = 3e-16
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             ++V NL +   E+++ E+F  +G ++ + + LDK    + GF  VE+    +A  ++ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 219 MLNNQNLFERRITVRMDR 236
            +N   L +R I    D 
Sbjct: 100 YINGTRLDDRIIRTDWDA 117

>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 = 48.3 bits (115), Expect = 6e-07
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 3/81 (3%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           +  +Y+    S  GD+  + +  D       G   VE+ S      A+  ++      R 
Sbjct: 53  EEQIYE--LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 110

Query: 102 LVIKEAVEDKGGRRNMGGGGG 122
           +        K GR+   G  G
Sbjct: 111 IRTDWDAGFKEGRQYGRGRSG 131

>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 = 47.1 bits (112), Expect = 2e-06
 Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 12/112 (10%)

Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIER----DTVVVKNLPPTITWQELRDKFRN 539
           G    +++S  Y       D +   +     +      T+ V NL    T +++ + F  
Sbjct: 3   GGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSK 62

Query: 540 CGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
            GDIK   +          G    V + S   A+ A+  ++ TR+D +II  
Sbjct: 63  SGDIKKIIMGLDKMKKTACG-FCFVEYYSRADAENAMRYINGTRLDDRIIRT 113

>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 = 73.4 bits (181), Expect = 3e-16
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             + V NL     E  L+E+FR  G +  + +A DK  G+S+GF  + F    +A ++I+
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 219 MLNNQNLFERRITV 232
            ++        + V
Sbjct: 76  GVSGFGYDHLILNV 89

>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 = 50.7 bits (122), Expect = 3e-08
 Identities = 21/88 (23%), Positives = 32/88 (36%), Gaps = 8/88 (9%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
           S  S       +  T+ V NL       +L++ FR  G I    +       + KG    
Sbjct: 3   SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG-FAF 61

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
           + F     A RAI  +     D  I++V
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNV 89

>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 = 44.5 bits (106), Expect = 5e-06
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 5/68 (7%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           G ++ + +  D  TG+ +G A + F   +   +A+  +  F      L ++ A       
Sbjct: 40  GSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP----S 95

Query: 115 RNMGGGGG 122
            N G   G
Sbjct: 96  TNSGPSSG 103

>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 = 73.1 bits (180), Expect = 4e-16
 Identities = 24/90 (26%), Positives = 46/90 (51%), Gaps = 5/90 (5%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK----SRGFGTVEFDHPVEAVQ 215
           + +F+ NL++   E+ L+ VF   G +++  I+  K+      S GFG VE+  P +A +
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 216 SISMLNNQNLFERRITVRM-DRVADRLDGP 244
           ++  L    +   ++ VR+ +R      GP
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPASGP 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 = 53.0 bits (128), Expect = 5e-09
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 9/73 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI---------GLVRFDSEWTAKRAIDM 571
           +KNL  + T + L+  F   G IK   I  K +          G V +     A++A+  
Sbjct: 10  IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 69

Query: 572 MDRTRIDGKIIDV 584
           +    +DG  ++V
Sbjct: 70  LQGHTVDGHKLEV 82

>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 = 42.6 bits (101), Expect = 2e-05
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 5/73 (6%)

Query: 53  STVGDVTYVEILND-DTGKP---RGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
           S VG +    I    +        G   VE++ P+  +KA+ ++      G KL ++ + 
Sbjct: 27  SKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS- 85

Query: 109 EDKGGRRNMGGGG 121
           E      +    G
Sbjct: 86  ERATKPASGPSSG 98

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 73.1 bits (180), Expect = 5e-16
 Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 3/92 (3%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             VFV N+ Y+  E++L+++F   G V +  +  D++ GK +G+G  E+     A+ ++ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 219 MLNNQNLFERRITVRMDRVADRLDGPVRLPEG 250
            LN +    R + V  D  A   +       G
Sbjct: 69  NLNGREFSGRALRV--DNAASEKNKEELKSLG 98

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           S VG V    ++ D +TGKP+G    E+Q  +    A+  ++  E  GR L +  A  +K
Sbjct: 30  SEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK 89

Query: 112 GGRRNMGGGGG 122
                   G G
Sbjct: 90  NKEELKSLGTG 100

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 72.2 bits (178), Expect = 6e-16
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
           +  ++V NL Y    ++++E+F   GKV NV++  D++  K +GFG VE        ++I
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAI 59

Query: 218 SMLNNQNLFERRITVR 233
           + L+N +   R I V 
Sbjct: 60  AKLDNTDFMGRTIRVT 75

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           S  G V  V+++ D +T KP+G   VE Q    V +A+ K+   +  GR + + EA   K
Sbjct: 23  SQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKK 81

Query: 112 GGRRN 116
               +
Sbjct: 82  SLEHH 86

>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 = 73.6 bits (181), Expect = 6e-16
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             + V  L     E+ LREVF   G + +V I  D+   +SRGF  V F++  +A ++  
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 219 MLNNQNLFERRITV 232
             N   L  RRI V
Sbjct: 107 RANGMELDGRRIRV 120

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 49.0 bits (117), Expect = 3e-07
 Identities = 27/120 (22%), Positives = 46/120 (38%), Gaps = 8/120 (6%)

Query: 474 SGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQEL 533
           S  +     G   + S  +   G  + G  S    N+++      + V  L    T ++L
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDL 63

Query: 534 RDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           R+ F   G I    I       + +G    V F++   AK A +  +   +DG+ I V F
Sbjct: 64  REVFSKYGPIADVSIVYDQQSRRSRG-FAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122

>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 = 44.7 bits (106), Expect = 7e-06
 Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           G +  V I+ D  + + RG A V F++ D  ++A  + +  E  GR++ +  ++  +
Sbjct: 71  GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127

>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 = 73.2 bits (180), Expect = 6e-16
 Identities = 21/105 (20%), Positives = 46/105 (43%), Gaps = 4/105 (3%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +++ NL YK+  +++ ++F   G +  + +      ++RG   V ++   +A  ++  L+
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNAVDHLS 68

Query: 222 NQNLFERRITV--RMDRVADRLDGPVRLPEGLKSIGMGLGANGAP 264
             N+  R + V       A +     +  E LK +    G N  P
Sbjct: 69  GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 113

>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 = 54.3 bits (131), Expect = 3e-09
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD---IGLVRFDSEWTAKRAIDMMD 573
             + ++NLP  IT +E+ D F   G I+   +    +      V ++  + AK A+D + 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68

Query: 574 RTRIDGKIIDVTF 586
              +  + + V +
Sbjct: 69  GFNVSNRYLVVLY 81

>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 = 46.2 bits (110), Expect = 1e-06
 Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
              G +  + + N  T + RG+A V ++     + AV+ +  F    R LV+     ++ 
Sbjct: 30  GKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRA 87

Query: 113 GRRN 116
            ++ 
Sbjct: 88  FQKM 91

>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 = 72.7 bits (179), Expect = 7e-16
 Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++ V+N+ ++  +  LR++F   GK+ +VEI  ++ G S+GFG V F++  +A ++   
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 74

Query: 220 LNNQNLFERRITV 232
           L+   +  R+I V
Sbjct: 75  LHGTVVEGRKIEV 87

>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 = 50.0 bits (120), Expect = 6e-08
 Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVR 558
           S  S N  S      + V N+P      +LR  F   G I   EI       KG  G V 
Sbjct: 3   SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG-FGFVT 61

Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
           F++   A RA + +  T ++G+ I+V
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEV 87

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
              G +  VEI+ +     +G   V F++     +A  K+H    +GRK+ +  A   + 
Sbjct: 37  GQFGKILDVEIIFN-ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA-TARV 94

Query: 113 GRRNMGGGG 121
              +    G
Sbjct: 95  MTNSGPSSG 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 72.7 bits (179), Expect = 7e-16
 Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             +FV  +  +  E+ + + F   G+++N+ + LD+  G  +G+  VE++   EA  ++ 
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 219 MLNNQNLFERRITV 232
            LN Q+L  + I+V
Sbjct: 84  GLNGQDLMGQPISV 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 9/95 (9%)

Query: 499 RAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGK 551
               D +    Q S +E   + V  +    T +++ DKF   G+IK   +         K
Sbjct: 7   SVEQDGDEPGPQRS-VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65

Query: 552 GDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           G   LV +++   A+ A++ ++   + G+ I V +
Sbjct: 66  G-YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 9/56 (16%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           +  G++  + +  D  TG  +G  +VE+++    + A+  ++  +  G+ + +   
Sbjct: 45  AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 100

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 73.6 bits (181), Expect = 7e-16
 Identities = 26/100 (26%), Positives = 40/100 (40%), Gaps = 1/100 (1%)

Query: 134 NSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIAL 193
            S   G   G           +   +  + V NL Y+     LR VF   G+V +V I  
Sbjct: 22  ASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81

Query: 194 DKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV 232
           D+   +SRGF  V F    +A  ++  ++   L  R + V
Sbjct: 82  DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 48.6 bits (116), Expect = 4e-07
 Identities = 22/102 (21%), Positives = 35/102 (34%), Gaps = 8/102 (7%)

Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI--- 548
           S   G        +            ++ V NL    +   LR  F   G +    I   
Sbjct: 23  SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82

Query: 549 ----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
               + +G    VRF  +  A+ A+D MD   +DG+ + V  
Sbjct: 83  RYTKESRG-FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 47.4 bits (113), Expect = 9e-07
 Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
           G V  V I  D  T + RG A V F        A++ M      GR+L ++ A   +   
Sbjct: 72  GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131

Query: 115 RN 116
            +
Sbjct: 132 SH 133

>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 = 72.3 bits (178), Expect = 1e-15
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            +FV ++  +  E +++E F   G+++N+ + LD+  G S+G+  VE++   +A+ +   
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 220 LNNQNLFERRITV 232
           LN   +  + I V
Sbjct: 88  LNGAEIMGQTIQV 100

>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 = 46.9 bits (112), Expect = 8e-07
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
              G++  + +  D  TG  +G A+VE+++      A   ++  E  G+ + +      K
Sbjct: 48  CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC-FVK 106

Query: 112 GGRR 115
           G +R
Sbjct: 107 GPKR 110

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 8/91 (8%)

Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIG 555
           D         ++E   + V ++       E+++KF + G+IK   +         KG   
Sbjct: 13  DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG-YA 71

Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           LV +++   A  A + ++   I G+ I V +
Sbjct: 72  LVEYETHKQALAAKEALNGAEIMGQTIQVDW 102

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 4/74 (5%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             +FV  L     E+ L+E F          I  D++ G S+GFG V+F+   +A  +  
Sbjct: 16  KTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72

Query: 219 MLNNQNLFERRITV 232
            + +  +   ++T+
Sbjct: 73  AMEDGEIDGNKVTL 86

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 44.9 bits (107), Expect = 4e-06
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
                  I+ D +TG  +G   V+F S +  + A   M   E  G K+ +  A + KG  
Sbjct: 37  DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA-KPKGEG 95

Query: 115 RNMGGGG 121
            +    G
Sbjct: 96  GSGPSSG 102

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 25/90 (27%), Positives = 37/90 (41%), Gaps = 11/90 (12%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
           S  S   + +    T+ VK L    T + L++ F        A I         KG  G 
Sbjct: 3   SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKG-FGF 58

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           V F+SE  AK A + M+   IDG  + + +
Sbjct: 59  VDFNSEEDAKAAKEAMEDGEIDGNKVTLDW 88

>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 = 71.4 bits (176), Expect = 1e-15
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            +++  L     ++ L ++ +  GK+ + +  LDK   K +G+G V+FD P  A ++++ 
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 220 LNNQNLFERRITVR 233
           L    +  +     
Sbjct: 67  LKASGVQAQMAKQS 80

>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 = 46.4 bits (111), Expect = 7e-07
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 8/71 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           ++ L P  T Q+L    +  G I   +        K KG  G V FDS   A++A+  + 
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG-YGFVDFDSPSAAQKAVTALK 68

Query: 574 RTRIDGKIIDV 584
            + +  ++   
Sbjct: 69  ASGVQAQMAKQ 79

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 56  GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
           G +   + + D  T K +G   V+F SP   +KAV  +     + +  
Sbjct: 30  GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 72.4 bits (178), Expect = 1e-15
 Identities = 26/117 (22%), Positives = 49/117 (41%), Gaps = 1/117 (0%)

Query: 121 GGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVF 180
            G+ +  SA   + S         +        I  P    +F+ +L  +  +  L   F
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61

Query: 181 RLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR 236
              G V + ++ +DK    S+ FG V FD+P  A  +I  +N   +  +R+ V++ +
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           + +LP   T  +L   F   G++  A++         K   G V FD+  +A+ AI  M+
Sbjct: 45  IYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC-FGFVSFDNPDSAQVAIKAMN 103

Query: 574 RTRIDGKIIDVTF 586
             ++  K + V  
Sbjct: 104 GFQVGTKRLKVQL 116

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 46.6 bits (111), Expect = 1e-06
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 3/67 (4%)

Query: 42  GDASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
            D  L         G+V   ++  D  T   +    V F +PD  + A+  M+ F+   +
Sbjct: 53  TDTDLAS--TFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK 110

Query: 101 KLVIKEA 107
           +L ++  
Sbjct: 111 RLKVQLK 117

>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 = 72.0 bits (177), Expect = 1e-15
 Identities = 20/73 (27%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           +++V +L + + E  LR +F   G++E++++ +D + G+S+G+G + F     A +++  
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 220 LNNQNLFERRITV 232
           LN   L  R + V
Sbjct: 88  LNGFELAGRPMKV 100

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 48.1 bits (115), Expect = 3e-07
 Identities = 12/56 (21%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
              G +  ++++ D +TG+ +G   + F   +  +KA+ +++ FE  GR + +   
Sbjct: 48  EPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V +L   IT   LR  F   G I+  ++       + KG  G + F     AK+A++ ++
Sbjct: 31  VGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG-YGFITFSDSECAKKALEQLN 89

Query: 574 RTRIDGKIIDV 584
              + G+ + V
Sbjct: 90  GFELAGRPMKV 100

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 73.0 bits (179), Expect = 2e-15
 Identities = 28/134 (20%), Positives = 50/134 (37%), Gaps = 3/134 (2%)

Query: 100 RKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLI 159
           +     EAV+     +        +        ++++K       S      + +     
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGM-- 70

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             + V NL Y+     LR VF   G+V +V I  D+   +SRGF  V F    +A  ++ 
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

Query: 219 MLNNQNLFERRITV 232
            ++   L  R + V
Sbjct: 131 AMDGAVLDGRELRV 144

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 46.0 bits (109), Expect = 5e-06
 Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 11/100 (11%)

Query: 497 NPRAGLDSNRSMNQSSNIERD---TVVVKNLPPTITWQELRDKFRNCGDIKFAEI----- 548
             +    +  S +   +++ +   ++ V NL    +   LR  F   G +    I     
Sbjct: 48  ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 107

Query: 549 --KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
             + +G    VRF  +  A+ A+D MD   +DG+ + V  
Sbjct: 108 TKESRG-FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 45.2 bits (107), Expect = 7e-06
 Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 1/60 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
              G V  V I  D  T + RG A V F        A++ M      GR+L ++ A   +
Sbjct: 92  EKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 151

>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 = 71.1 bits (175), Expect = 2e-15
 Identities = 21/74 (28%), Positives = 46/74 (62%), Gaps = 1/74 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            ++V NLD  +D+++LR+ F   G + + ++ ++  G+S+GFG V F  P EA ++++ +
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75

Query: 221 NNQNLFERRITVRM 234
           N + +  + + V +
Sbjct: 76  NGRIVATKPLYVAL 89

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
           VKNL   I  + LR  F   G I  A++     + KG  G V F S   A +A+  M+  
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKG-FGFVCFSSPEEATKAVTEMNGR 78

Query: 576 RIDGKIIDV 584
            +  K + V
Sbjct: 79  IVATKPLYV 87

>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 = 42.2 bits (100), Expect = 3e-05
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 67  DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGG 121
           + G+ +G   V F SP+   KAV +M+      + L +  A + K  R++    G
Sbjct: 50  EGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA-QRKEERQSGPSSG 103

>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 = 73.8 bits (181), Expect = 3e-15
 Identities = 33/187 (17%), Positives = 74/187 (39%), Gaps = 17/187 (9%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
             SL+ +      GDV  V+IL +     + +A+V+    +  + A++ ++  +  G+ +
Sbjct: 18  PQSLFIL--FGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPI 71

Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
            I  +      +          ++   L ++  +   + +       ++     P    +
Sbjct: 72  RITLS------KHQNVQLPREGQEDQGLTKDYGNSPLHRF--KKPGSKNFQNIFPPSATL 123

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
            ++N+   V E+ L+ +F   G V        KD   R    ++     EAVQ++  L+N
Sbjct: 124 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHN 180

Query: 223 QNLFERR 229
            +L E  
Sbjct: 181 HDLGENH 187

>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 = 57.2 bits (138), Expect = 1e-09
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 162 VFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           + V+NL+  +V  + L  +F + G V+ V+I  +K    +    V+     +A  ++S L
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 61

Query: 221 NNQNLFERRITVRM 234
           N   L  + I + +
Sbjct: 62  NGHKLHGKPIRITL 75

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

 Score = 53.7 bits (129), Expect = 2e-08
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 518 TVVVKNLPP-TITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
            ++V NL P  +T Q L   F   GD++  +I   K +  LV+      A+ A+  ++  
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64

Query: 576 RIDGKIIDVTF 586
           ++ GK I +T 
Sbjct: 65  KLHGKPIRITL 75

>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 = 51.8 bits (124), Expect = 8e-08
 Identities = 19/123 (15%), Positives = 49/123 (39%), Gaps = 7/123 (5%)

Query: 467 YGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPP 526
               +      E     G  +    S  +   + G  + +++   S     T+ + N+PP
Sbjct: 75  LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA----TLHLSNIPP 130

Query: 527 TITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI-DGKIID 583
           +++ ++L+  F + G +   F   +    + L++  S   A +A+  +    + +   + 
Sbjct: 131 SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR 190

Query: 584 VTF 586
           V+F
Sbjct: 191 VSF 193

>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 = 72.6 bits (178), Expect = 4e-15
 Identities = 25/140 (17%), Positives = 59/140 (42%), Gaps = 8/140 (5%)

Query: 94  RFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLG 153
             +  G + +++   + K  +    G     R+     +   ++  +     PQ      
Sbjct: 14  EVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQ------ 67

Query: 154 INCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVE 212
                   +FV ++  +  E +++E F   G+++N+ + LD+  G S+G+  VE++   +
Sbjct: 68  -RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 126

Query: 213 AVQSISMLNNQNLFERRITV 232
           A+ +   LN   +  + I V
Sbjct: 127 ALAAKEALNGAEIMGQTIQV 146

>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 = 48.3 bits (115), Expect = 9e-07
 Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 8/111 (7%)

Query: 483 GGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGD 542
           G           Y   R   D         ++E   + V ++       E+++KF + G+
Sbjct: 39  GSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGE 98

Query: 543 IKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           IK   +         KG   LV +++   A  A + ++   I G+ I V +
Sbjct: 99  IKNIHLNLDRRTGFSKG-YALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148

>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 = 44.8 bits (106), Expect = 1e-05
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
              G++  + +  D  TG  +G A+VE+++      A   ++  E  G+ + +      K
Sbjct: 94  CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC-FVK 152

Query: 112 GGRRNMGGGG 121
           G +R      
Sbjct: 153 GPKRVKKSEK 162

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 71.7 bits (176), Expect = 4e-15
 Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 153 GINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPV 211
                ++  + V  +   VDE +LR++F   G +E+V+I  D++  +SRG+G V+F    
Sbjct: 36  NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95

Query: 212 EAVQSISMLNNQNLFERRITV 232
            A Q+I+ LN  N+  +R+ V
Sbjct: 96  SAQQAIAGLNGFNILNKRLKV 116

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 47.8 bits (114), Expect = 6e-07
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 42  GDASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
            +  L Q+      G +  V+I+ D +T + RG   V+FQS    ++A+  ++ F    +
Sbjct: 55  DEVQLRQL--FERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK 112

Query: 101 KLVIKEAVEDKGGRRNMGGGGG 122
           +L +  A      R  + G  G
Sbjct: 113 RLKVALA-ASGHQRPGIAGAVG 133

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 25/117 (21%), Positives = 45/117 (38%), Gaps = 13/117 (11%)

Query: 477 NEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDK 536
           ++ D  G + Q                 N   +   N+     +V  +P T+   +LR  
Sbjct: 8   SQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNL-----MVNYIPTTVDEVQLRQL 62

Query: 537 FRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           F   G I+  +I       + +G  G V+F S  +A++AI  ++   I  K + V  
Sbjct: 63  FERYGPIESVKIVCDRETRQSRG-YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118

>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 = 71.2 bits (175), Expect = 4e-15
 Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             +FV  +  +  E+ + + F   G+++N+ + LD+  G  +G+  VE++   EA  ++ 
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 219 MLNNQNLFERRITV 232
            LN Q+L  + I+V
Sbjct: 83  GLNGQDLMGQPISV 96

>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 = 47.0 bits (112), Expect = 1e-06
 Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 9/97 (9%)

Query: 497 NPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------K 549
                 D +    Q S +E   + V  +    T +++ DKF   G+IK   +        
Sbjct: 4   YDSVEQDGDEPGPQRS-VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62

Query: 550 GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
            KG   LV +++   A+ A++ ++   + G+ I V +
Sbjct: 63  LKG-YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98

>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 = 45.1 bits (107), Expect = 5e-06
 Identities = 12/74 (16%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           +  G++  + +  D  TG  +G  +VE+++    + A+  ++  +  G+ + +       
Sbjct: 44  AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 103

Query: 112 GGRRNMGGGGGVDR 125
             +    GG    R
Sbjct: 104 PPKGKRRGGRRRSR 117

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 69.5 bits (171), Expect = 5e-15
 Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAG--KVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
            +++ NL +   ++ L E     G   +  ++   ++  G+S+GF  V       + + +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 218 SMLNNQNLFERRITV 232
            +L  + L  +   V
Sbjct: 63  DLLPKRELHGQNPVV 77

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 48.3 bits (116), Expect = 2e-07
 Identities = 11/63 (17%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 55  VGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
           V D+  ++   +   G+ +G A+V   S    +K ++ + + E  G+  V+  +      
Sbjct: 27  VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS-NKLEH 85

Query: 114 RRN 116
             +
Sbjct: 86  HHH 88

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIK-------G--KGDIGLVRFDSEWTAKRAIDM 571
           + NL    T ++L +   + G     EIK       G  KG   LV   SE ++K+ +D+
Sbjct: 6   IGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG-FALVGVGSEASSKKLMDL 64

Query: 572 MDRTRIDGKIIDVTF 586
           + +  + G+   VT 
Sbjct: 65  LPKRELHGQNPVVTP 79

>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 = 69.6 bits (171), Expect = 6e-15
 Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             + ++NL Y   E+ L+EVF  A     +++  +++GKS+G+  +EF    +A ++++ 
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 220 LNNQNLFERRITV 232
            N + +  R I +
Sbjct: 73  CNKREIEGRAIRL 85

>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 = 50.0 bits (120), Expect = 6e-08
 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 4/86 (4%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI---KGKGDIGLVRFD 560
           S  S N + + E  T+V+ NL  + T + L++ F     IK  +    K KG    + F 
Sbjct: 3   SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKG-YAFIEFA 61

Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTF 586
           S   AK A++  ++  I+G+ I +  
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLEL 87

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
           +++  +  GK +G A +EF S +  ++A+N  ++ E +GR + ++     +G   +    
Sbjct: 42  IKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ-GPRGSPNSGPSS 100

Query: 121 G 121
           G
Sbjct: 101 G 101

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 70.0 bits (172), Expect = 6e-15
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  +   +DEK L+ +F   GK+  + +  D+  G  +G   + +     A+++ S 
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 220 LNNQNLFE---RRITVR 233
           L+ Q       R I V+
Sbjct: 75  LHEQKTLPGMNRPIQVK 91

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 4/59 (6%)

Query: 53  STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMH---RFETKGRKLVIKEA 107
              G +  + +L D  TG  +G A + +   +   KA + +H         R + +K A
Sbjct: 35  EEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPA 93

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 69.2 bits (170), Expect = 9e-15
 Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
             + V N+ + V   ++ + F     +   V +  ++ G   G   V F+   EA  ++ 
Sbjct: 16  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 219 MLNNQNLFERRITV 232
            LN++ +  R++ +
Sbjct: 76  DLNDRPIGSRKVKL 89

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 52.3 bits (126), Expect = 7e-09
 Identities = 14/53 (26%), Positives = 23/53 (43%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
           V +  ++ G P G A+V F+S D    AV  ++      RK+ +        G
Sbjct: 46  VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 9/86 (10%)

Query: 509 NQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFD 560
             SS     T++ V+N+P T++  E+ D F     I  +            G+  +V F+
Sbjct: 7   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE-AMVAFE 65

Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTF 586
           S   A  A+  ++   I  + + +  
Sbjct: 66  SRDEATAAVIDLNDRPIGSRKVKLVL 91

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 68.9 bits (169), Expect = 1e-14
 Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 4/88 (4%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           KV+V NL     + +L   F   G +  V IA +      GF  VEF+ P +A  ++  L
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 221 NNQNLFERRITVRMDRVADRLDGPVRLP 248
           + + +   R+ V +     R     R P
Sbjct: 58  DGKVICGSRVRVELSTGMPRRSRFDRPP 85

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 1/67 (1%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-IGLVRFDSEWTAKRAIDMMDRTRIDG 579
           V NL       EL   F   G ++   I         V F+    A+ A+  +D   I G
Sbjct: 5   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 64

Query: 580 KIIDVTF 586
             + V  
Sbjct: 65  SRVRVEL 71

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 7/70 (10%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           G +  V I  +    P G A VEF+ P     AV  +      G ++ ++ +    G  R
Sbjct: 25  GPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS---TGMPR 77

Query: 116 NMGGGGGVDR 125
                    R
Sbjct: 78  RSRFDRPPAR 87

>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 = 72.3 bits (177), Expect = 1e-14
 Identities = 34/187 (18%), Positives = 73/187 (39%), Gaps = 17/187 (9%)

Query: 43  DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
             SL+ +      GDV  V+IL       + +A+V+    +  + A++ ++  +  G+ +
Sbjct: 49  PQSLFIL--FGVYGDVQRVKILF----NKKENALVQMADGNQAQLAMSHLNGHKLHGKPI 102

Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
            I  +          G      ++   L ++  +   + +       ++     P    +
Sbjct: 103 RITLSKHQNVQLPREG------QEDQGLTKDYGNSPLHRF--KKPGSKNFQNIFPPSATL 154

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
            ++N+   V E+ L+ +F   G V        KD   R    ++     EAVQ++  L+N
Sbjct: 155 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHN 211

Query: 223 QNLFERR 229
            +L E  
Sbjct: 212 HDLGENH 218

>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 = 60.0 bits (145), Expect = 2e-10
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 2/106 (1%)

Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPP-TITWQELRDKFRNCGD 542
           GS            PR       ++   +      ++V NL P  +T Q L   F   GD
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61

Query: 543 IKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
           ++  +I   K +  LV+      A+ A+  ++  ++ GK I +T  
Sbjct: 62  VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS 107

>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 = 54.2 bits (130), Expect = 2e-08
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 162 VFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           + V+NL+  +V  + L  +F + G V+ V+I  +K    +    V+     +A  ++S L
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 92

Query: 221 NNQNLFERRITVRM 234
           N   L  + I + +
Sbjct: 93  NGHKLHGKPIRITL 106

>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 = 51.2 bits (122), Expect = 2e-07
 Identities = 19/131 (14%), Positives = 51/131 (38%), Gaps = 7/131 (5%)

Query: 459 YSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDT 518
           + +         +      E     G  +    S  +   + G  + +++   S     T
Sbjct: 98  HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA----T 153

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           + + N+PP+++ ++L+  F + G +   F   +    + L++  S   A +A+  +    
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 213

Query: 577 I-DGKIIDVTF 586
           + +   + V+F
Sbjct: 214 LGENHHLRVSF 224

>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 = 68.9 bits (169), Expect = 2e-14
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            +++V NL   +  K + +VF   G + ++++          F  VEF+ P +A  ++  
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK--NRRGGPPFAFVEFEDPRDAEDAVYG 80

Query: 220 LNNQNLFERRITVRMDR 236
            +  +    R+ V   R
Sbjct: 81  RDGYDYDGYRLRVEFPR 97

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.3 bits (144), Expect = 4e-11
 Identities = 27/107 (25%), Positives = 42/107 (39%), Gaps = 16/107 (14%)

Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDI 543
           GS  +S  SGG        +++             + V NLPP I  +++ D F   G I
Sbjct: 1   GSSGSSGMSGGGVIRGPAGNNDC-----------RIYVGNLPPDIRTKDIEDVFYKYGAI 49

Query: 544 KFAEIK----GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           +  ++K    G      V F+    A+ A+   D    DG  + V F
Sbjct: 50  RDIDLKNRRGGPP-FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 95

>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 = 43.8 bits (104), Expect = 8e-06
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 5/67 (7%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           G +  +++ N         A VEF+ P     AV     ++  G +L ++     + GR 
Sbjct: 47  GAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP---RSGRG 101

Query: 116 NMGGGGG 122
              G   
Sbjct: 102 TGSGPSS 108

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 68.5 bits (168), Expect = 2e-14
 Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
             + V N+ + V   ++ + F     +   V +  ++ G   G   V F+   EA  ++ 
Sbjct: 16  TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 219 MLNNQNLFERRITV 232
            LN++ +  R++ +
Sbjct: 76  DLNDRPIGSRKVKL 89

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 51.9 bits (125), Expect = 9e-09
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 509 NQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFD 560
             SS     TV+ V+N+P T++  E+ D F     I  +            G+  +V F+
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE-AMVAFE 65

Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTF 586
           S   A  A+  ++   I  + + ++ 
Sbjct: 66  SRDEATAAVIDLNDRPIGSRKVKLSG 91

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 13/44 (29%), Positives = 22/44 (50%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
           V +  ++ G P G A+V F+S D    AV  ++      RK+ +
Sbjct: 46  VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL 89

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 68.9 bits (169), Expect = 2e-14
 Identities = 19/76 (25%), Positives = 46/76 (60%), Gaps = 3/76 (3%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSI 217
           +K+ V N+ ++ +++++RE+F   G+++ V +       G  RGFG V+F    +A ++ 
Sbjct: 16  SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75

Query: 218 -SMLNNQNLFERRITV 232
            ++ ++ +L+ RR+ +
Sbjct: 76  NALCHSTHLYGRRLVL 91

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 10/92 (10%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI--------KGKGDIG 555
           S  S           ++V+N+P     +E+R+ F   G++K   +          +G  G
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG-FG 61

Query: 556 LVRFDSEWTAKRAID-MMDRTRIDGKIIDVTF 586
            V F ++  AK+A + +   T + G+ + + +
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVLEW 93

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 53  STVGDVTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIKEAVE 109
           ST G++  V +      TG  RG   V+F +    +KA N + H     GR+LV++ A  
Sbjct: 37  STFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

Query: 110 DKGGRRNMGGGGG 122
           +       G   G
Sbjct: 97  EV--TVQSGPSSG 107

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 68.9 bits (169), Expect = 2e-14
 Identities = 15/74 (20%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             +++ NL  +V E+ L  +F    + +   I      G+ RG   + F +   A Q++ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 219 MLNNQNLFERRITV 232
           ++N   L+ + + +
Sbjct: 86  LVNGYKLYGKILVI 99

>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 = 46.9 bits (112), Expect = 1e-06
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
           +  L  +   +   +     I     TG+ RG A + F + ++  +A++ ++ ++  G+ 
Sbjct: 39  ERDLVSL--FARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI 96

Query: 102 LVIKEAVEDK 111
           LVI+     K
Sbjct: 97  LVIEFGKNKK 106

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           +KNL P +T ++L   F    + K   I       + +G    + F ++  A +A+ +++
Sbjct: 30  LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG-QAFITFPNKEIAWQALHLVN 88

Query: 574 RTRIDGKIIDVTF 586
             ++ GKI+ + F
Sbjct: 89  GYKLYGKILVIEF 101

>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 = 67.6 bits (166), Expect = 2e-14
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            VFV +L  ++    +   F   G++ +  +  D   GKS+G+G V F +  +A  +I  
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 220 LNNQNLFERRITVRM 234
           +  Q L  R+I    
Sbjct: 68  MGGQWLGGRQIRTNW 82

>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 = 22/71 (30%), Positives = 30/71 (42%), Gaps = 8/71 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V +L P IT   +   F   G I  A +       K KG  G V F ++W A+ AI  M 
Sbjct: 11  VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG-YGFVSFFNKWDAENAIQQMG 69

Query: 574 RTRIDGKIIDV 584
              + G+ I  
Sbjct: 70  GQWLGGRQIRT 80

>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 = 41.4 bits (98), Expect = 5e-05
 Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 3/69 (4%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
            A++      +  G ++   ++ D  TGK +G   V F +      A+ +M      GR+
Sbjct: 20  TAAIAAA--FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ 77

Query: 102 LVIKEAVED 110
           +    A   
Sbjct: 78  IRTNWATRK 86

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 67.6 bits (166), Expect = 3e-14
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+FV N+      ++LR +F   G+V   ++        + +  V  +   +A  +I+ L
Sbjct: 11  KIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQL 63

Query: 221 NNQNLFERRITVRMDRVADRLDGP 244
           N + +  +RI V +     +  GP
Sbjct: 64  NGKEVKGKRINVELSTKGQKKSGP 87

>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 = 52.2 bits (126), Expect = 7e-09
 Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
           V N+    T QELR  F   G +   ++    D   V  + E  AK AI  ++   + GK
Sbjct: 14  VGNVSAACTSQELRSLFERRGRVIECDV--VKDYAFVHMEKEADAKAAIAQLNGKEVKGK 71

Query: 581 IIDVTF 586
            I+V  
Sbjct: 72  RINVEL 77

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 11/67 (16%), Positives = 29/67 (43%), Gaps = 10/67 (14%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           G V   +++       +  A V  +     + A+ +++  E KG+++ ++ +     G++
Sbjct: 34  GRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS---TKGQK 83

Query: 116 NMGGGGG 122
             G   G
Sbjct: 84  KSGPSSG 90

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 69.6 bits (170), Expect = 3e-14
 Identities = 19/123 (15%), Positives = 46/123 (37%), Gaps = 6/123 (4%)

Query: 120 GGGVDRDLSALLQNNSSKFGNT---YGLSPQFLESLGINCPLINKVFVANLDYKVDEKKL 176
            G  +    ++      +   +      +P  L +          V+V +  +   +++L
Sbjct: 13  LGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQL 72

Query: 177 REVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR 233
            +V R  G  + VE+   ++   G+S+G+  V         + + +L  + L   ++ VR
Sbjct: 73  IQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR 132

Query: 234 MDR 236
              
Sbjct: 133 PAT 135

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.1 bits (122), Expect = 7e-08
 Identities = 20/121 (16%), Positives = 39/121 (32%), Gaps = 10/121 (8%)

Query: 475 GGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELR 534
           G   + +        ++      P     +           R  V V +     T Q+L 
Sbjct: 14  GTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLI 73

Query: 535 DKFRNCGDIKFAEIK---------GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
              R+ G     E+K          KG    V   SE +  + ++++    ++G+ +DV 
Sbjct: 74  QVIRSIGVYDVVELKFAENRANGQSKG-YAEVVVASENSVHKLLELLPGKVLNGEKVDVR 132

Query: 586 F 586
            
Sbjct: 133 P 133

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 49.1 bits (117), Expect = 3e-07
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 1/72 (1%)

Query: 55  VGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
           V DV  ++   +   G+ +G A V   S + V K +  +      G K+ ++ A      
Sbjct: 81  VYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140

Query: 114 RRNMGGGGGVDR 125
           +           
Sbjct: 141 QFEAQARKRECV 152

>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 = 67.7 bits (166), Expect = 3e-14
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +   NL + + E +L+EVF  A ++  V     +DGKS+G   +EF    +A +++  
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 220 LNNQNLFERRITV 232
                +  R +++
Sbjct: 73  KQGAEIDGRSVSL 85

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT 575
           T++ KNL   IT  EL++ F +  +I+    + K KG I  + F SE  A++ ++     
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG-IAYIEFKSEADAEKNLEEKQGA 76

Query: 576 RIDGKIIDVTF 586
            IDG+ + + +
Sbjct: 77  EIDGRSVSLYY 87

>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 = 46.5 bits (111), Expect = 7e-07
 Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 60  YVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
            +EI      GK +G A +EF+S     K + +    E  GR + +     +KGG R
Sbjct: 40  ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT-GEKGGTR 95

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 67.5 bits (165), Expect = 4e-14
 Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 6/98 (6%)

Query: 493 GGYGNPR---AGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCG-DIKFAEI 548
           G   +     +GL    S       +R  + +KNLP   +WQ+L+D  R    +  F+ +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61

Query: 549 KGKGD--IGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
             +     G + F SE     A++ ++     G +I V
Sbjct: 62  NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 66.8 bits (163), Expect = 9e-14
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 2/77 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++ + NL      + L+++ R          +        G G +EF      V+++  
Sbjct: 29  YRITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDGTGALEFPSEEILVEALER 86

Query: 220 LNNQNLFERRITVRMDR 236
           LNN       ITV  D 
Sbjct: 87  LNNIEFRGSVITVERDD 103

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 11/63 (17%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
               + T+  +   +T    G+  +EF S +++ +A+ +++  E +G  + ++       
Sbjct: 51  ENSLETTFSSV---NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPP 107

Query: 113 GRR 115
            RR
Sbjct: 108 IRR 110

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 67.8 bits (166), Expect = 5e-14
 Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN--------VEIALDKD-GKSRGFGTVEFDHP 210
           + ++V  L+  V    L + F+  G V+         + I LDK+ GK +G  TV ++ P
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 211 VEAVQSISMLNNQNLFERRITVRMDR 236
             A  ++   + ++    ++ V + R
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLAR 101

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 56.6 bits (137), Expect = 3e-10
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 14/82 (17%)

Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI--------------GLVRFDSE 562
             + V+ L  ++T  +L D F+ CG +K  +  G+  I                V ++  
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 563 WTAKRAIDMMDRTRIDGKIIDV 584
            TAK A++  D     G  + V
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKV 97

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 63  ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGG 122
            L+ +TGKP+G A V ++ P   + AV      + +G KL +  A +      N G   G
Sbjct: 56  YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP--PMNSGPSSG 113

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 66.9 bits (164), Expect = 7e-14
 Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            +F+ NL+      +L+          ++ +   + G +R FG V+F+   +  +++ + 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALEL- 77

Query: 221 NNQNLFERRITVR 233
               +F   I + 
Sbjct: 78  TGLKVFGNEIKLE 90

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 8/73 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
            + + NL P  +  EL+             +        +   G V F+S    ++A++ 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK-FGYVDFESAEDLEKALE- 76

Query: 572 MDRTRIDGKIIDV 584
           +   ++ G  I +
Sbjct: 77  LTGLKVFGNEIKL 89

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 11/59 (18%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
                + +++  TG  R    V+F+S + + KA+ ++   +  G ++ +++     G R
Sbjct: 42  FAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTR 99

>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 = 66.1 bits (162), Expect = 1e-13
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKV-ENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
            +F+ NLD ++DEK L + F   G + +  +I  D D G S+G+  + F     +  +I 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 219 MLNNQNLFERRITV 232
            +N Q L  R ITV
Sbjct: 67  AMNGQYLCNRPITV 80

>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 = 43.0 bits (102), Expect = 2e-05
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDI-KFAEI-------KGKGDIGLVRFDSEWTAKRAIDMM 572
           + NL P I  + L D F   G I +  +I         KG    + F S   +  AI+ M
Sbjct: 10  IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKG-YAFINFASFDASDAAIEAM 68

Query: 573 DRTRIDGKIIDVTFF 587
           +   +  + I V++ 
Sbjct: 69  NGQYLCNRPITVSYA 83

>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 = 66.2 bits (162), Expect = 1e-13
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            VFV +L  ++  + ++  F   G++ +  +  D   GKS+G+G V F +  +A  +I  
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 220 LNNQNLFERRITVRM 234
           +  Q L  R+I    
Sbjct: 77  MGGQWLGGRQIRTNW 91

>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 = 7e-06
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 8/71 (11%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V +L P IT ++++  F   G I  A +       K KG  G V F ++W A+ AI  M 
Sbjct: 20  VGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG-YGFVSFFNKWDAENAIQQMG 78

Query: 574 RTRIDGKIIDV 584
              + G+ I  
Sbjct: 79  GQWLGGRQIRT 89

>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 = 42.3 bits (100), Expect = 4e-05
 Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 3/81 (3%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
              +      +  G ++   ++ D  TGK +G   V F +      A+ +M      GR+
Sbjct: 29  TEDIKAA--FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ 86

Query: 102 LVIKEAVEDKGGRRNMGGGGG 122
           +    A       ++      
Sbjct: 87  IRTNWATRKPPAPKSTYESNT 107

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +++FV NL   + E+++R++F   GK   V I      K +GFG +  +    A  +   
Sbjct: 16  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-----KDKGFGFIRLETRTLAEIAKVE 70

Query: 220 LNNQNLFERRITVRM 234
           L+N  L  +++ VR 
Sbjct: 71  LDNMPLRGKQLRVRF 85

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDS 561
            S  S  + +  +R  + V NLPP IT +E+R  F   G      I K KG  G +R ++
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-FGFIRLET 60

Query: 562 EWTAKRAIDMMDRTRIDGKIIDVTF 586
              A+ A   +D   + GK + V F
Sbjct: 61  RTLAEIAKVELDNMPLRGKQLRVRF 85

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 69.4 bits (169), Expect = 2e-13
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQS 216
             +++ NL +   ++ L E     G  + +EI   ++   G+S+GF  V       + + 
Sbjct: 69  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128

Query: 217 ISMLNNQNLFERRITVR 233
           + +L  + L  +   V 
Sbjct: 129 MDLLPKRELHGQNPVVT 145

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 54.0 bits (129), Expect = 2e-08
 Identities = 25/134 (18%), Positives = 49/134 (36%), Gaps = 12/134 (8%)

Query: 462 NASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVV 521
           +  ++Y +    S  N           ++      +   G   N     +   +R  + +
Sbjct: 16  DQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTG--KRIALYI 73

Query: 522 KNLPPTITWQELRDKFRNCGDIKFAEIK---------GKGDIGLVRFDSEWTAKRAIDMM 572
            NL    T ++L +   + G     EIK          KG   LV   SE ++K+ +D++
Sbjct: 74  GNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG-FALVGVGSEASSKKLMDLL 132

Query: 573 DRTRIDGKIIDVTF 586
            +  + G+   VT 
Sbjct: 133 PKRELHGQNPVVTP 146

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 47.0 bits (111), Expect = 5e-06
 Identities = 15/94 (15%), Positives = 34/94 (36%), Gaps = 1/94 (1%)

Query: 55  VGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
           V D+  ++   +   G+ +G A+V   S    +K ++ + + E  G+  V+    +    
Sbjct: 94  VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLS 153

Query: 114 RRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQ 147
           +  M           +         G++    PQ
Sbjct: 154 QFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 64.9 bits (159), Expect = 3e-13
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           NK+FV  + +   E +LRE F+  G V  V +  D +  + RGFG + F+   ++V    
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE-QSVDQAV 69

Query: 219 MLNNQNLFERRITVR 233
            ++  ++  +++ V+
Sbjct: 70  NMHFHDIMGKKVEVK 84

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
            +    G VT V ++ D +  +PRG   + F+    V +AVN MH  +  G+K+ +K A 
Sbjct: 29  EYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAE 87

Query: 109 EDKGGRRNMGGGG 121
             +  + +    G
Sbjct: 88  P-RDSKSSGPSSG 99

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 9/71 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V  +P      ELR+ F+  G +    +       + +G  G + F+ E +  +A++ M 
Sbjct: 15  VGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRG-FGFITFEDEQSVDQAVN-MH 72

Query: 574 RTRIDGKIIDV 584
              I GK ++V
Sbjct: 73  FHDIMGKKVEV 83

>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 = 66.1 bits (161), Expect = 4e-13
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
           +CPL  KV+V NL    ++ +L   F   G + +V +A +      GF  VEF+ P +A 
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAA 124

Query: 215 QSISMLNNQNLFERRITVRMDR 236
            ++  L+ + L   R+ V +  
Sbjct: 125 DAVRELDGRTLCGCRVRVELSN 146

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 50.6 bits (121), Expect = 9e-08
 Identities = 17/90 (18%), Positives = 28/90 (31%), Gaps = 1/90 (1%)

Query: 498 PRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-IGL 556
                  +  M++ S      V V NL       EL   F   G ++   +         
Sbjct: 55  TEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAF 114

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           V F+    A  A+  +D   + G  + V  
Sbjct: 115 VEFEDPRDAADAVRELDGRTLCGCRVRVEL 144

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 64.3 bits (157), Expect = 4e-13
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGK--VENVEIALDKD-GKSRGFGTVEFDHPVEAVQS 216
           + + + N+        +           V N+ +  DK   ++RGF  V+    ++A Q 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 217 ISMLNNQNLFE----RRITV 232
           + +L + +       + I V
Sbjct: 70  LQILQSLHPPLKIDGKTIGV 89

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 49.2 bits (118), Expect = 8e-08
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 14/92 (15%)

Query: 508 MNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIK---------GKGDIGLVR 558
           M    +   DT++++N+ P      +         +    I+          +G    V+
Sbjct: 1   MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG-FAFVQ 59

Query: 559 FDSEWTAKRAIDMMD----RTRIDGKIIDVTF 586
             S   A + + ++       +IDGK I V F
Sbjct: 60  LSSAMDASQLLQILQSLHPPLKIDGKTIGVDF 91

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 64.2 bits (157), Expect = 5e-13
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKV--------ENVEIALDKD-GKSRGFGTVEFDHP 210
           N +FV  L   V  + + + F+  G +          + +  D++ GK +G  TV FD P
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 211 VEAVQSISMLNNQNLFERRITV 232
             A  +I   + +      I V
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKV 95

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 16/97 (16%)

Query: 505 NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG-------------- 550
               +  S+ + +T+ V+ L   +T + + D F+  G IK  +  G              
Sbjct: 2   GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61

Query: 551 -KGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
            KG+   V FD   +AK AID  D     G  I V+F
Sbjct: 62  LKGE-ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 12/45 (26%), Positives = 20/45 (44%)

Query: 63  ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
             + +TGK +G A V F  P   + A++     E  G  + +  A
Sbjct: 54  YTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 64.7 bits (158), Expect = 5e-13
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            VF+ NL +  +E+ L EV +  G ++ V + L  D   S+G    +F     A + ++ 
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 220 LNNQNLFE------RRITV 232
            + +          R++ V
Sbjct: 77  ASLEAEGGGLKLDGRQLKV 95

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 9/74 (12%)

Query: 43  DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHR------F 95
           + +L +   L   GD+ YV ++   DT   +G A  +F + +  +K +            
Sbjct: 29  EEALGE--VLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL 86

Query: 96  ETKGRKLVIKEAVE 109
           +  GR+L +  AV 
Sbjct: 87  KLDGRQLKVDLAVT 100

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 14/96 (14%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
           S  S   S   E  TV ++NL      + L +  +  GD+K+  +         KG    
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG-CAF 61

Query: 557 VRFDSEWTAKRAIDMMDRTR------IDGKIIDVTF 586
            +F ++  A++ +             +DG+ + V  
Sbjct: 62  AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 64.7 bits (158), Expect = 5e-13
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN--------VEIALDKD-GKSRGFGTVEFDHP 210
           N +FV  L   V  + + + F+  G ++         + +  D++ GK +G  TV FD P
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 211 VEAVQSISMLNNQNLFERRITVRM 234
             A  +I   + +      I V  
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSF 91

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.6 bits (137), Expect = 4e-10
 Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 14/91 (15%)

Query: 510 QSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI--------------G 555
           +  N + +T+ V+ L   +T + + D F+  G IK  +  G+  I               
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
            V FD   +AK AID  D     G  I V+F
Sbjct: 61  TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 91

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 47.8 bits (114), Expect = 5e-07
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 63  ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE-DKGGRRNMGGGG 121
             + +TGK +G A V F  P   + A++     E  G  + +  A       R    G G
Sbjct: 48  YTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRG 107

Query: 122 GVDR 125
           G++ 
Sbjct: 108 GLEH 111

>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 = 63.8 bits (156), Expect = 5e-13
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 7/75 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+ V N+      ++LR  F   G V   +I        + +  V  +   +AV++I  
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRG 63

Query: 220 LNNQNLFERRITVRM 234
           L+N     +R+ V++
Sbjct: 64  LDNTEFQGKRMHVQL 78

>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 = 46.8 bits (112), Expect = 5e-07
 Identities = 23/64 (35%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
           V N+ PT T QELR KF   G +   +I    D   V  +    A  AI  +D T   GK
Sbjct: 15  VGNISPTCTNQELRAKFEEYGPVIECDI--VKDYAFVHMERAEDAVEAIRGLDNTEFQGK 72

Query: 581 IIDV 584
            + V
Sbjct: 73  RMHV 76

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 64.2 bits (157), Expect = 5e-13
 Identities = 18/84 (21%), Positives = 35/84 (41%)

Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSE 562
            S  S ++ +      + V+NL  + + + +  +F N        +K   D   V F + 
Sbjct: 2   SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 61

Query: 563 WTAKRAIDMMDRTRIDGKIIDVTF 586
             A  A+  ++   +DG  I+VT 
Sbjct: 62  EDAVEAMKALNGKVLDGSPIEVTL 85

>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 = 61.9 bits (151), Expect = 3e-12
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            ++V NL     E+ + + F          +      K R +  V F +  +AV+++  L
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKAL 71

Query: 221 NNQNLFERRITV 232
           N + L    I V
Sbjct: 72  NGKVLDGSPIEV 83

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 63.8 bits (156), Expect = 7e-13
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+F+ NL  +  E+++R +F   GKV   +I        + +G V  +    A  +I  L
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62

Query: 221 NNQNLFERRITVRMDR 236
           ++  L    I V   +
Sbjct: 63  HHYKLHGVNINVEASK 78

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 51.8 bits (125), Expect = 9e-09
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
           + NLP   T QE+R  F   G +   +I  K   G V  + +  A+ AI  +   ++ G 
Sbjct: 13  IGNLPREATEQEIRSLFEQYGKVLECDII-KN-YGFVHIEDKTAAEDAIRNLHHYKLHGV 70

Query: 581 IIDV 584
            I+V
Sbjct: 71  NINV 74

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 8/65 (12%), Positives = 20/65 (30%), Gaps = 7/65 (10%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           G V   +I+       +    V  +       A+  +H ++  G  + ++ +        
Sbjct: 33  GKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASS 85

Query: 116 NMGGG 120
               G
Sbjct: 86  GPSSG 90

>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 = 64.8 bits (158), Expect = 8e-13
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN------VEIALDKDGKSRGFGTVEFDHPVEA 213
            +++V NL   V EK L+ +F       +       +I L K+G+ +G   +   +   A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 214 VQSISMLNNQNLFERRITV 232
            +++   N   LF + + V
Sbjct: 106 AKALKEANGYVLFGKPMVV 124

>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 = 46.7 bits (111), Expect = 2e-06
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 11/77 (14%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-----------GLVRFDSEWTAKRAI 569
           VKNL   +  ++L+  F    D      +   DI             +   +E  A +A+
Sbjct: 50  VKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109

Query: 570 DMMDRTRIDGKIIDVTF 586
              +   + GK + V F
Sbjct: 110 KEANGYVLFGKPMVVQF 126

>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 = 46.0 bits (109), Expect = 3e-06
 Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 7/71 (9%)

Query: 52  LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA---- 107
            S+       +I     G+ +G A +   +     KA+ + + +   G+ +V++ A    
Sbjct: 72  FSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSAR 131

Query: 108 ---VEDKGGRR 115
                 +G R+
Sbjct: 132 PKQDPKEGKRK 142

>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 = 63.2 bits (154), Expect = 9e-13
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 511 SSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAID 570
           SS      ++VKNLP     QE+ D  ++   +K+  +        V   +   A+ AI 
Sbjct: 2   SSG--SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 571 MMDRTRIDGKIIDVTF 586
           M  +    GK + V  
Sbjct: 59  MFHQYSFRGKDLIVQL 74

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 58.6 bits (142), Expect = 4e-11
 Identities = 11/86 (12%), Positives = 35/86 (40%), Gaps = 7/86 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + + V NL    + +++ ++ +    ++   +      +++    V   +  +A  +I M
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQM 59

Query: 220 LNNQNLFERRITVRMDRVADRL-DGP 244
            +  +   + + V++      L  GP
Sbjct: 60  FHQYSFRGKDLIVQLQPTDALLCSGP 85

>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 = 37.8 bits (88), Expect = 9e-04
 Identities = 7/45 (15%), Positives = 21/45 (46%)

Query: 67  DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
              + + +A V   + +  + A+   H++  +G+ L+++    D 
Sbjct: 35  YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA 79

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 63.6 bits (155), Expect = 1e-12
 Identities = 18/95 (18%), Positives = 39/95 (41%), Gaps = 2/95 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
               + N+ + + +  + +        EN V + +D +G+  G   V+F +  +A +S  
Sbjct: 16  VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 75

Query: 219 MLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKS 253
           + + + L  R   V +  + D  +     P   KS
Sbjct: 76  L-HRKKLNGREAFVHVVTLEDMREIEKNPPAQGKS 109

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 50.1 bits (120), Expect = 6e-08
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 9/88 (10%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
           S  S     N  +    + N+P +IT  ++          + A         +G G   L
Sbjct: 3   SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ-AL 61

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
           V+F +E  A+++   + R +++G+   V
Sbjct: 62  VQFKNEDDARKSER-LHRKKLNGREAFV 88

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           V +L D+ G+  G A+V+F++ D  RK+  ++HR +  GR+  +     + 
Sbjct: 46  VHVLVDNNGQGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLED 95

>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 = 63.3 bits (154), Expect = 1e-12
 Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 2/76 (2%)

Query: 511 SSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRA 568
           S +  R    ++ KNLP      E+++ F   G +    +   G   +V F     A++A
Sbjct: 3   SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKA 62

Query: 569 IDMMDRTRIDGKIIDV 584
              +  ++     + +
Sbjct: 63  FRHLAYSKFHHVPLYL 78

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 51.0 bits (122), Expect = 3e-08
 Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 5/71 (7%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           +   NL       +++E F   G +  V +      +      VEF  P+EA ++   L 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLA 67

Query: 222 NQNLFERRITV 232
                   + +
Sbjct: 68  YSKFHHVPLYL 78

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 62.1 bits (152), Expect = 2e-12
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L     E+K+RE F   G+VE++E+ +D    K RGF  + F    E V+ I  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE-EPVKKIME 59

Query: 220 LNNQNLFERRITVR 233
               N+   +  ++
Sbjct: 60  KKYHNVGLSKCEIK 73

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 44.8 bits (107), Expect = 2e-06
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 51  HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAV-NKMHRFETKGRKLVIKEA 107
           +    G+V  +E+  D  T K RG   + F+  + V+K +  K H       K  IK A
Sbjct: 19  YFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH--NVGLSKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 40.6 bits (96), Expect = 6e-05
 Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V  L P    +++R+ F   G+++  E+       K +G    + F  E   K+ ++   
Sbjct: 4   VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG-FCFITFKEEEPVKKIMEKKY 62

Query: 574 RTRIDGKIIDV 584
              +     ++
Sbjct: 63  HN-VGLSKCEI 72

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + V +    + V EK + E      K   + I  +  G   G+  V+F +  E  Q++  
Sbjct: 11  HTVKLRGAPFNVTEKNVMEFLA-PLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC 69

Query: 220 LNNQNLFERRITV 232
            N + +  R I V
Sbjct: 70  -NREYMGGRYIEV 81

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 509 NQSSNIERDTVVVKNLPPTITWQELRDKFRNCG--DIKF---AEIKGKGDIGLVRFDSEW 563
           + SS     TV ++  P  +T + + +         I+    A     G    V F +E 
Sbjct: 3   SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGY-IFVDFSNEE 61

Query: 564 TAKRAIDMMDRTRIDGKIIDV 584
             K+A+   +R  + G+ I+V
Sbjct: 62  EVKQALK-CNREYMGGRYIEV 81

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSIS 218
             F+ NL Y V E+ ++E FR    +  V +  +     + +GFG  EF+  ++++ S  
Sbjct: 21  TAFLGNLPYDVTEESIKEFFR-GLNISAVRLPREPSNPERLKGFGYAEFED-LDSLLSAL 78

Query: 219 MLNNQNLFERRITV 232
            LN ++L  RRI V
Sbjct: 79  SLNEESLGNRRIRV 92

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 8/58 (13%), Positives = 27/58 (46%), Gaps = 3/58 (5%)

Query: 56  GDVTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
            +++ V +  +  +  + +G    EF+  D +  A++ ++      R++ +  A + +
Sbjct: 43  LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQ 99

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 63.7 bits (155), Expect = 2e-12
 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + V +  L YK  E  +   F        V I +  DG+  G   VEF    EAV ++S 
Sbjct: 47  HCVHMRGLPYKATENDIYNFFS-PLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK 105

Query: 220 LNNQNLFERRITVRMDRVAD 239
            +  N+  R I + ++    
Sbjct: 106 -DRANMQHRYIELFLNSTTG 124

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.9 bits (127), Expect = 1e-08
 Identities = 21/125 (16%), Positives = 42/125 (33%), Gaps = 19/125 (15%)

Query: 465 NMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNL 524
           + + +S     G+ M            +   G  + G  S  S     +     V ++ L
Sbjct: 7   HHHHSSGLVPRGSHM------------ASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGL 54

Query: 525 PPTITWQELRDKFRNCGDIKFAEIKG-----KGDIGLVRFDSEWTAKRAIDMMDRTRIDG 579
           P   T  ++ + F     ++     G      G+   V F +   A  A+   DR  +  
Sbjct: 55  PYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGE-ADVEFATHEEAVAAMS-KDRANMQH 112

Query: 580 KIIDV 584
           + I++
Sbjct: 113 RYIEL 117

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI-----KEAVEDKGGRR 115
           V I     G+  G A VEF + +    A+    R   + R + +       A       +
Sbjct: 75  VHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQ 133

Query: 116 NMGGGG 121
            M G G
Sbjct: 134 VMQGMG 139

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 13/72 (18%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            ++V NL   V E  + ++F   G  ++ ++  +       +  VEF    +A  +++ +
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAM 75

Query: 221 NNQNLFERRITV 232
           N + +  + + V
Sbjct: 76  NGRKILGKEVKV 87

>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 = 45.7 bits (109), Expect = 2e-06
 Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 6/72 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMM 572
           T+ V NL   +T   +   F   G  K  ++             V F     A  A+  M
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAM 75

Query: 573 DRTRIDGKIIDV 584
           +  +I GK + V
Sbjct: 76  NGRKILGKEVKV 87

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
              +V NL +   +  +  +F+    + +V +  DKD  K +GF  VEFD  V++++   
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFK-DLSIRSVRLVRDKDTDKFKGFCYVEFDE-VDSLKEAL 73

Query: 219 MLNNQNLFERRITV 232
             +   L +R + V
Sbjct: 74  TYDGALLGDRSLRV 87

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 58  VTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRN 116
           +  V ++ D DT K +G   VEF   D +++A+          R L +  A   K  +  
Sbjct: 41  IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQDKSG 99

Query: 117 MGGG 120
              G
Sbjct: 100 PSSG 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++FV      V E +L E+F   G ++ V+I         GF  VEF+    A ++I  
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEE 84

Query: 220 LNNQNLFERRITV 232
           ++ ++   + + V
Sbjct: 85  VHGKSFANQPLEV 97

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 56.9 bits (138), Expect = 3e-10
 Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 5/103 (4%)

Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDI 543
           GS            PR     +R   + SN     + V+  P  +   EL + F   G +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMHHRQEGELSNT---RLFVRPFPLDVQESELNEIFGPFGPM 58

Query: 544 KFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           K  +I   G    V F+   +A +AI+ +       + ++V +
Sbjct: 59  KEVKIL-NG-FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 60.9 bits (149), Expect = 4e-12
 Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L      + ++  F   GKV++  +  DK   + RGFG V F+   + V+ +  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE-DIVEKVCE 59

Query: 220 LNNQNLFERRITVR 233
           ++   +  + +  +
Sbjct: 60  IHFHEINNKMVECK 73

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.5 bits (96), Expect = 6e-05
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
            +    G V    ++ D  T + RG   V F+S D+V K   ++H  E   + +  K+A
Sbjct: 18  HYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 37.8 bits (89), Expect = 5e-04
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 9/71 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
           V  L    T ++++  F   G +  A +       + +G  G V F+SE   ++  ++  
Sbjct: 4   VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRG-FGFVTFESEDIVEKVCEIHF 62

Query: 574 RTRIDGKIIDV 584
              I+ K+++ 
Sbjct: 63  HE-INNKMVEC 72

>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 = 61.5 bits (150), Expect = 4e-12
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           NK+++ NL   V    LR++F         ++         G+  V++     A+++I  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIET 63

Query: 220 LNNQ-NLFERRITVR 233
           L+ +  L  + + V 
Sbjct: 64  LSGKVELHGKIMEVD 78

>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 = 48.4 bits (116), Expect = 2e-07
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMD-RTR 576
            + + NL P +T  +LR  F +       ++  K     V +  +  A RAI+ +  +  
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 69

Query: 577 IDGKIIDV 584
           + GKI++V
Sbjct: 70  LHGKIMEV 77

>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 = 39.9 bits (94), Expect = 2e-04
 Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 3/64 (4%)

Query: 60  YVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH-RFETKGRKLVIKEAVEDKGGRRNMG 118
               L        G A V++   +   +A+  +  + E  G+ + +  +V  K   R+ G
Sbjct: 32  RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK--LRSSG 89

Query: 119 GGGG 122
              G
Sbjct: 90  PSSG 93

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.7 bits (150), Expect = 5e-12
 Identities = 12/75 (16%), Positives = 25/75 (33%), Gaps = 1/75 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             V++           ++E     G+V N+++        +G   V FD    A + +  
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 71

Query: 220 LNNQNLFERRITVRM 234
              Q   E  + +  
Sbjct: 72  -PGQKYKETDLLILF 85

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
             L   G V  +++        +GS  V F S +  +K V +    + K   L+I    +
Sbjct: 30  EWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKDD 88

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.0 bits (112), Expect = 7e-07
 Identities = 11/72 (15%), Positives = 29/72 (40%), Gaps = 6/72 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-----IGLVRFDSEWTAKRAIDMM 572
           +V +K  P   T  ++++   + G +   +++            V FDS  +AK+ ++  
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72

Query: 573 DRTRIDGKIIDV 584
            +       + +
Sbjct: 73  GQK-YKETDLLI 83

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSIS 218
             F+ NL Y V E+ ++E FR    +  V +  +     + +GFG  EF+  ++++ S  
Sbjct: 17  TAFLGNLPYDVTEESIKEFFR-GLNISAVRLPREPSNPERLKGFGYAEFED-LDSLLSAL 74

Query: 219 MLNNQNLFERRITVR 233
            LN ++L  +RI V 
Sbjct: 75  SLNEESLGNKRIRVD 89

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 41.9 bits (99), Expect = 5e-05
 Identities = 8/65 (12%), Positives = 27/65 (41%), Gaps = 3/65 (4%)

Query: 58  VTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           ++ V +  +  +  + +G    EF+  D +  A++ ++      +++ +  A + +    
Sbjct: 41  ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDS 99

Query: 116 NMGGG 120
               G
Sbjct: 100 GPSSG 104

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 60.9 bits (148), Expect = 7e-12
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSIS 218
               + +    V +K L  +F  AGKV N+E  +D+  GK++GF  VE     +A + I 
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 219 MLNNQNLFERRITVRMDRVAD 239
             + +   + +  + +  + D
Sbjct: 73  SFHGKR-LDLKHRLFLYTMKD 92

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 41.3 bits (97), Expect = 7e-05
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 52  LSTVGDVTYVEI-LNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
            S  G V  +E  +++ TGK +G   VE  S +  +K +   H      +
Sbjct: 33  FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 8/68 (11%)

Query: 520 VVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMM 572
           V+ +    +  + L   F   G +   E        K KG    V   S   AK+ I   
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKG-FLFVECGSMNDAKKIIKSF 74

Query: 573 DRTRIDGK 580
              R+D K
Sbjct: 75  HGKRLDLK 82

>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 = 60.7 bits (148), Expect = 7e-12
 Identities = 14/90 (15%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLA----GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQ 215
           + +++ NL+ K+ + +L++         G++  ++I + +  K RG   V F     A  
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATN 66

Query: 216 SISMLNNQNLFERRITV-----RMDRVADR 240
           ++  +     +++ + +       D +A  
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96

>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 = 41.4 bits (98), Expect = 5e-05
 Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 7/76 (9%)

Query: 518 TVVVKNLPPTITWQELRDK----FRNCGDIKFAEIKGKGDI---GLVRFDSEWTAKRAID 570
           T+ + NL   I   EL+      F   G I    +     +     V F    +A  A+ 
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 69

Query: 571 MMDRTRIDGKIIDVTF 586
            M       K + + +
Sbjct: 70  SMQGFPFYDKPMRIQY 85

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 41.4 bits (98), Expect = 6e-05
 Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           S  G +  + +    + K RG A V F+       A+  M  F    + + I+ A
Sbjct: 34  SRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 61.8 bits (150), Expect = 8e-12
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
             V++  L ++ + K + + F+    VE+ + IA   +GK+ G G VEF +  +   ++ 
Sbjct: 26  FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 85

Query: 219 MLNNQNLFERRITV 232
             + Q +  R I V
Sbjct: 86  R-HKQYMGNRFIQV 98

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 45.2 bits (107), Expect = 4e-06
 Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 9/86 (10%)

Query: 506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVR 558
           RS ++S +     V +K LP     + + D F+    ++ +         K  G+ G V 
Sbjct: 15  RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE-GFVE 73

Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
           F +E   K A+    +  +  + I V
Sbjct: 74  FRNEADYKAALC-RHKQYMGNRFIQV 98

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI-----KEAVEDKGGRR 115
           + I     GK  G   VEF++    + A+   H+     R + +     K  +E     R
Sbjct: 56  IYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIR 114

Query: 116 NMGGGG 121
                G
Sbjct: 115 KRLQSG 120

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 60.5 bits (147), Expect = 1e-11
 Identities = 17/86 (19%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 160 NKVFVANL------DYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
           + + V N+        +  +  + ++F   GK+ N     + DGK++G+  +E+  P  A
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHA 74

Query: 214 VQSISMLNNQNLFERRITVRMDRVAD 239
           V ++   +     +++ T R++   D
Sbjct: 75  VDAVKNADGYK-LDKQHTFRVNLFTD 99

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 13/82 (15%)

Query: 518 TVVVKNLPPTITWQE------LRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAK 566
            +VV N+P     +       +   F   G I          K KG    + + S   A 
Sbjct: 17  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKG-YIFLEYASPAHAV 75

Query: 567 RAIDMMDRTRIDGK-IIDVTFF 587
            A+   D  ++D +    V  F
Sbjct: 76  DAVKNADGYKLDKQHTFRVNLF 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 52  LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
            S  G +T      ++ GK +G   +E+ SP     AV     ++   +
Sbjct: 42  FSKFGKITNDFY-PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 60.5 bits (147), Expect = 1e-11
 Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V V  + +   E  +R+ F    +V+ V +  D  G++ G G V+F  P +  +++   N
Sbjct: 19  VSVHGMPFSAMENDVRDFFH-GLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKR-N 76

Query: 222 NQNLFERRITV 232
              + +R + V
Sbjct: 77  RMLMIQRYVEV 87

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 7/90 (7%)

Query: 501 GLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCG--DIKF---AEIKGKGDIG 555
           G   +       N +   V V  +P +    ++RD F       +        +  G+ G
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGN-G 59

Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
           LV+F S      A+   +R  +  + ++V+
Sbjct: 60  LVKFLSPQDTFEALK-RNRMLMIQRYVEVS 88

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 44.0 bits (104), Expect = 8e-06
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 57  DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK----G 112
            V  V +L D  G+  G+ +V+F SP    +A+ K +R     R + +  A E +    G
Sbjct: 41  RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAAG 99

Query: 113 GRRNMGGGGG 122
           G    G   G
Sbjct: 100 GHITSGPSSG 109

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 60.1 bits (146), Expect = 2e-11
 Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 2/79 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V +  L Y+  E  +   F        V I +  DG+  G   VEF    +AV +++  +
Sbjct: 18  VHMRGLPYRATENDIYNFFS-PLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK-D 75

Query: 222 NQNLFERRITVRMDRVADR 240
             N+  R + + ++  A  
Sbjct: 76  KANMQHRYVELFLNSTAGT 94

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 13/86 (15%), Positives = 31/86 (36%), Gaps = 7/86 (8%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGD-----IKFAEIKGKGDIGLVR 558
           S  S +   +     V ++ LP   T  ++ + F              + +  G+   V 
Sbjct: 3   SGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGE-ADVE 61

Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
           F +   A  A+   D+  +  + +++
Sbjct: 62  FATHEDAVAAMA-KDKANMQHRYVEL 86

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 3/62 (4%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
           V I     G+  G A VEF + +    A+    +   + R   ++  +    G    G  
Sbjct: 44  VHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRY--VELFLNSTAGTSGSGPS 100

Query: 121 GG 122
            G
Sbjct: 101 SG 102

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 59.4 bits (144), Expect = 2e-11
 Identities = 15/87 (17%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI---KGKGDIGLVRFD 560
           S  S +         + ++N+PP + W+ L       G ++  E      +  +  V + 
Sbjct: 3   SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYS 62

Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTFF 587
           S+  A++A+D ++  +++   + V + 
Sbjct: 63  SKDQARQALDKLNGFQLENFTLKVAYI 89

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 57.5 bits (139), Expect = 1e-10
 Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            K+ + N+   +  + L  +    G VE+ E              V +    +A Q++  
Sbjct: 16  RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV--NTDSETAVVNVTYSSKDQARQALDK 73

Query: 220 LNNQNLFERRITV 232
           LN   L    + V
Sbjct: 74  LNGFQLENFTLKV 86

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
              G V   E +N D         V + S D  R+A++K++ F+ +   L +
Sbjct: 37  VQYGVVESCEQVNTD--SETAVVNVTYSSKDQARQALDKLNGFQLENFTLKV 86

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 59.9 bits (145), Expect = 3e-11
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
             V +  L +   ++++ + F     V N + + +D +GK  G   V+F     A +++ 
Sbjct: 43  GFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102

Query: 219 MLNNQNLFERRITV 232
             + + +  R I V
Sbjct: 103 K-HKERIGHRYIEV 115

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 39.5 bits (92), Expect = 5e-04
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 49  ISHLSTVGDVTY-VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           +   S +  V   + +  D  GK  G A V+F S +L  KA+   H+     R + + ++
Sbjct: 60  VQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKS 118

>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 = 65.6 bits (159), Expect = 3e-11
 Identities = 57/378 (15%), Positives = 117/378 (30%), Gaps = 97/378 (25%)

Query: 16  HQDFPM------FQRIETGAPLEVPVVMDLIQGDASLYQISHL--STVGDVTYVEIL--- 64
           H DF        ++ I       + V  D    +     +  +  S +       I+   
Sbjct: 6   HMDFETGEHQYQYKDI-------LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSK 58

Query: 65  NDDTGKPRGSAIVEFQSPDLVRKAVNKMH-----------RFETKGRKLVIKEAVEDKGG 113
           +  +G  R    +  +  ++V+K V ++            + E +   ++ +  +E    
Sbjct: 59  DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ--- 115

Query: 114 RRNMGGGG------GVDR-----DL-SALLQNNSSKFGNTYG--------LSPQFLESLG 153
           R  +           V R      L  ALL+   +K     G        ++     S  
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175

Query: 154 INCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
           + C +  K+F  NL      + + E       ++ +   +D +  SR   +      + +
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLE------MLQKLLYQIDPNWTSRSDHSSNIKLRIHS 229

Query: 214 VQS-ISMLNNQNLFER---------------------RI--TVRMDRVADRLDGPVRLPE 249
           +Q+ +  L     +E                      +I  T R  +V D L        
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289

Query: 250 GLKSIGMGLGANGAPLQDVANWLLQEKVQKLS--------LIIS--NRNTKEVLERWDF- 298
            L    M L  +      +  + L  + Q L           +S    + ++ L  WD  
Sbjct: 290 SLDHHSMTLTPDEV-KSLLLKY-LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW 347

Query: 299 -KLQYDKSSDENDAASVN 315
             +  DK +   + +S+N
Sbjct: 348 KHVNCDKLTTIIE-SSLN 364

>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 = 59.2 bits (144), Expect = 3e-11
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +FV NL   V E+ L + F   GK+E V+         + +  + FD    AV+++  
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHFDERDGAVKAMEE 64

Query: 220 LNNQNLFERRITV 232
           +N ++L    I +
Sbjct: 65  MNGKDLEGENIEI 77

>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 = 55.4 bits (134), Expect = 6e-10
 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 509 NQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKR 567
           + SS + +  V+ V+NL  T+T + L   F   G ++   +K   D   + FD    A +
Sbjct: 3   SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLE--RVKKLKDYAFIHFDERDGAVK 60

Query: 568 AIDMMDRTRIDGKIIDVTF 586
           A++ M+   ++G+ I++ F
Sbjct: 61  AMEEMNGKDLEGENIEIVF 79

>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 = 58.5 bits (142), Expect = 5e-11
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAG-KVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
            +++ +L+  +DE  +   F   G  V +V+I  ++  G   G+  VEF     A + + 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 219 MLNNQNLFERRITVRM 234
            +N + L       R 
Sbjct: 71  KINGKPLPGATPAKRF 86

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.1 bits (141), Expect = 6e-11
 Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            VFV+     VD  +L E F   G V +V +  DKD     F  VE      A +++   
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVM--DKD--KGVFAIVEMGDV-GAREAVLSQ 64

Query: 221 NNQNLFERRITVRMDRVADRLDGPVRLPEG 250
           +  +L   R+ VR     +      + P+G
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQSPASKSPKG 94

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.0 bits (120), Expect = 5e-08
 Identities = 12/68 (17%), Positives = 24/68 (35%), Gaps = 2/68 (2%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
           +V V   P  +   +L + F   G +    + K KG   +V        +  +    +  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHS 68

Query: 577 IDGKIIDV 584
           + G  + V
Sbjct: 69  LGGHRLRV 76

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

 Score = 58.1 bits (141), Expect = 8e-11
 Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 5/71 (7%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
            ++ N+ +   E  L  +F+  G + + +         +G   +++D   +A   I  L 
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKH-----YPEKGCCFIKYDTHEQAAVCIVALA 84

Query: 222 NQNLFERRITV 232
           N     R +  
Sbjct: 85  NFPFQGRNLRT 95

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 497 NPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIG 555
            P+    +   + +S+     T  + N+P   T  +L   F+N G I   +    KG   
Sbjct: 8   PPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG-CC 66

Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKII 582
            +++D+   A   I  +      G+ +
Sbjct: 67  FIKYDTHEQAAVCIVALANFPFQGRNL 93

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
            K+FV  L Y   +  LR+ F   G +E   +  D+  GKSRG+G V       A +   
Sbjct: 18  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR-AAAERAC 76

Query: 219 MLNNQNLFERRITV 232
              N  +  R+  V
Sbjct: 77  KDPNPIIDGRKANV 90

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 17/82 (20%), Positives = 25/82 (30%), Gaps = 4/82 (4%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIKEA 107
            +    GD+    ++ D  TGK RG   V         +A        +  GRK  +  A
Sbjct: 36  KYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIID--GRKANVNLA 93

Query: 108 VEDKGGRRNMGGGGGVDRDLSA 129
                 R    G        S+
Sbjct: 94  YLGAKPRSLQTGFAIGVSGPSS 115

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 57.3 bits (138), Expect = 1e-10
 Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 161 KVFVANLDYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
            V V+N+DY++  K+L++     F   GKV++VE++   D   +    V+ ++  +A+ +
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGA 68

Query: 217 ISMLNNQNLFERRITVRMDR 236
           ++ L+   +  ++I V +  
Sbjct: 69  VNSLHRYKIGSKKILVSLAT 88

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 61.0 bits (147), Expect = 2e-10
 Identities = 13/77 (16%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 160 NKVFVANLDYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQ 215
           + +++ NL+ K+ + +L++    +F   G++  ++I + +  K RG   V F     A  
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 216 SISMLNNQNLFERRITV 232
           ++  +     +++ + +
Sbjct: 68  ALRSMQGFPFYDKPMRI 84

>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 = 53.0 bits (126), Expect = 8e-08
 Identities = 27/157 (17%), Positives = 43/157 (27%), Gaps = 2/157 (1%)

Query: 432 SQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQ 491
                   + +            P T   R   +M G   Y      +   G +      
Sbjct: 123 KAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPP 182

Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIK-FAEIKG 550
                          +   S N     + + NLP       L   F      K    + G
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242

Query: 551 KGDIGLVRFDSEWTAKRAIDMMDRTRI-DGKIIDVTF 586
           + DI  V FD+E  A  A D +   +I     + ++F
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF 279

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 9/77 (11%)

Query: 518 TVVVKNLPPTITWQELR----DKFRNCGDIKFAEI----KGKGDIGLVRFDSEWTAKRAI 569
           T+ + NL   I   EL+      F   G I    +    K +G    V F    +A  A+
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRG-QAFVIFKEVSSATNAL 69

Query: 570 DMMDRTRIDGKIIDVTF 586
             M       K + + +
Sbjct: 70  RSMQGFPFYDKPMRIQY 86

>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 = 42.2 bits (98), Expect = 3e-04
 Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 4/67 (5%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
           F+ NL  + +E  L  +F      + V +   +         VEFD+ V+A  +   L  
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQG 266

Query: 223 QNLFERR 229
             + +  
Sbjct: 267 FKITQNN 273

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 56.2 bits (136), Expect = 2e-10
 Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 160 NKVFVANL------DYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
           + + V N+        +  +  + ++F   GK+ N     + DGK++G+  +E+  P  A
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHA 60

Query: 214 VQSISMLNNQNLFERRI 230
           V ++   +   L ++  
Sbjct: 61  VDAVKNADGYKLDKQHT 77

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 15/74 (20%), Positives = 24/74 (32%), Gaps = 12/74 (16%)

Query: 518 TVVVKNLP------PTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAK 566
            +VV N+P             +   F   G I          K KG    + + S   A 
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKG-YIFLEYASPAHAV 61

Query: 567 RAIDMMDRTRIDGK 580
            A+   D  ++D +
Sbjct: 62  DAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE 96
           S  G +T      ++ GK +G   +E+ SP     AV     ++
Sbjct: 28 FSKFGKITNDFY-PEEDGKTKGYIFLEYASPAHAVDAVKNADGYK 71

>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 = 61.8 bits (149), Expect = 2e-10
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             +FVA ++Y   E KLR  F + G ++ + +   K  GK RG+  +E++H  +   +  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 219 MLNNQNLFERRITVRMDR 236
             + + +  RR+ V ++R
Sbjct: 163 HADGKKIDGRRVLVDVER 180

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 56.6 bits (137), Expect = 3e-10
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 160 NKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           +++F+ NL    V ++ L  +F   G +  + I          FG ++FD+P     +I 
Sbjct: 23  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIE 75

Query: 219 MLNNQNLFERRITVRMDRVADR 240
             + +  F +++ + +     R
Sbjct: 76  XESQEMNFGKKLILEVSSSNAR 97

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 21/104 (20%), Positives = 37/104 (35%), Gaps = 15/104 (14%)

Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLP-PTITWQELRDKFRNCGD 542
           GS            PR     +R            + + NLP   ++ ++L   F   G 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMKSR------------LFIGNLPLKNVSKEDLFRIFSPYGH 49

Query: 543 IKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           I    IK     G ++FD+  + + AI+   +    GK + +  
Sbjct: 50  IMQINIK-NA-FGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV 91

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

 Score = 56.6 bits (137), Expect = 3e-10
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
           P    V+   +   + ++ +R+ F   G++  + +  +K     G+  V F     A  +
Sbjct: 23  PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-----GYSFVRFSTHESAAHA 77

Query: 217 ISMLNNQNLFERRITVR 233
           I  +N   +    +   
Sbjct: 78  IVSVNGTTIEGHVVKCY 94

>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 = 5e-10
 Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 4/96 (4%)

Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KG 550
           SG  GN +        +   S+ +  TV    +   +T Q +R  F   G I    +   
Sbjct: 3   SGSSGNTKQL--RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 551 KGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           KG    VRF +  +A  AI  ++ T I+G ++   +
Sbjct: 61  KG-YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW 95

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 155 NCPLINKVFVANLDYK-VDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
           N P  +++F+ NL  K V ++ L  +F   G +  + I          FG ++FD+P   
Sbjct: 6   NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSV 58

Query: 214 VQSISMLNNQNLFERRITVRMDRVADR 240
             +I   + +  F +++ + +     R
Sbjct: 59  RDAIECESQEMNFGKKLILEVSSSNAR 85

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

 Score = 43.7 bits (104), Expect = 7e-06
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 521 VKNLPP-TITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDG 579
           + NLP   ++ ++L   F   G I    IK     G ++FD+  + + AI+   +    G
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQINIK-NA-FGFIQFDNPQSVRDAIECESQEMNFG 72

Query: 580 KIIDVTF 586
           K + +  
Sbjct: 73  KKLILEV 79

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

 Score = 41.0 bits (97), Expect = 6e-05
 Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 7/66 (10%)

Query: 56  GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
           G +  + I             ++F +P  VR A+    +    G+KL+++ +  +   + 
Sbjct: 36  GHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQF 88

Query: 116 NMGGGG 121
           + G  G
Sbjct: 89  DHGDHG 94

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 56.5 bits (136), Expect = 4e-10
 Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 10/88 (11%)

Query: 162 VFVANLDYKVDEKKLREVFR---LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           V +  L +    + ++       +   V  V     ++G+  G   VE +   + V+   
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESE-DDVKLAL 78

Query: 219 MLNNQNLFERRITVR------MDRVADR 240
             + +++  R I V       MD V   
Sbjct: 79  KKDRESMGHRYIEVFKSHRTEMDWVLKH 106

>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 = 55.8 bits (135), Expect = 4e-10
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 7/73 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N ++V   D  +    LR  F   G + ++ +        R    V ++    A Q+++ 
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAE 68

Query: 220 LNNQNLFERRITV 232
           LN   +   ++ V
Sbjct: 69  LNGTQVESVQLKV 81

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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 14/85 (16%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 504 SNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDS 561
           S+ S  +     +   + V      +T   LR  F   G+I    +   +     V ++ 
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRN-CAFVTYEK 58

Query: 562 EWTAKRAIDMMDRTRIDGKIIDVTF 586
             +A +A+  ++ T+++   + V  
Sbjct: 59  MESADQAVAELNGTQVESVQLKVNI 83

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 55.8 bits (135), Expect = 5e-10
 Identities = 17/102 (16%), Positives = 42/102 (41%), Gaps = 8/102 (7%)

Query: 134 NSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY-KVDEKKLREVFRLAGKVENVEIA 192
           +S   G +  L    + +      + ++VF+ NL+   V +  +  +F   G+V    + 
Sbjct: 2   SSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV- 60

Query: 193 LDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM 234
                  +G+  V++ +   A  ++   N + L  + + + M
Sbjct: 61  ------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96

>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 = 45.8 bits (109), Expect = 2e-06
 Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 3/96 (3%)

Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPP-TITWQELRDKFRNCGDIKFAEIKG 550
           SG  G       SN +           V + NL    +   ++   F   G +    +  
Sbjct: 3   SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH- 61

Query: 551 KGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           KG    V++ +E  A+ A+   +   + G+ +D+  
Sbjct: 62  KG-YAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 56.4 bits (136), Expect = 6e-10
 Identities = 16/89 (17%), Positives = 32/89 (35%), Gaps = 11/89 (12%)

Query: 162 VFVANLDYKVDEKKLREVF----RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
           V +  L +    +++   F     + G  E +      DG+  G   V F     A  ++
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 218 SMLNNQNLFERRITVR------MDRVADR 240
              +   L +R I +       + +V +R
Sbjct: 86  RK-HKDLLGKRYIELFRSTAAEVQQVLNR 113

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 55.5 bits (134), Expect = 7e-10
 Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           V +  L +   ++++ + F     V N + + +D  G+S G   V+F     A +++   
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK- 76

Query: 221 NNQNLFERRITV 232
           + + +  R I +
Sbjct: 77  HKERIGHRYIEI 88

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 46.7 bits (111), Expect = 1e-06
 Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 8/88 (9%)

Query: 504 SNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGD------IKFAEIKGKGDIGL 556
           S+ S   S +   D  V ++ LP   + +E+   F           +             
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
           V+F S+  A++A+    + RI  + I++
Sbjct: 62  VQFASQEIAEKALK-KHKERIGHRYIEI 88

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           + +  D  G+  G A V+F S ++  KA+ K H+     R + I ++
Sbjct: 46  MTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKS 91

>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 Length = 136

 Score = 56.5 bits (136), Expect = 7e-10
 Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 11/93 (11%)

Query: 161 KVFVANLDYKVDEKKLREVFR---LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
            V +  L +    + ++       +      V     ++G+  G   VE     + V+  
Sbjct: 46  VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSE-DDVKMA 104

Query: 218 SMLNNQNLFERRITVR------MDRVADRLDGP 244
              + +++  R I V       MD V     GP
Sbjct: 105 LKKDRESMGHRYIEVFKSHRTEMDWVLKH-SGP 136

>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 Length = 136

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 20/112 (17%), Positives = 38/112 (33%), Gaps = 14/112 (12%)

Query: 485 SGQASIQSGGYGNPRAGLDS---NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCG 541
                +  G +     G         M      E   V ++ LP + + +++++   +C 
Sbjct: 10  HSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCT 69

Query: 542 D---------IKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
                     I   E +  G+   V   SE   K A+   DR  +  + I+V
Sbjct: 70  IHDGAAGVHFIYTREGRQSGE-AFVELGSEDDVKMALK-KDRESMGHRYIEV 119

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 55.2 bits (133), Expect = 9e-10
 Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 162 VFVANLDYKVDEKKLREVF---RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           +    L +    + +   F   R+      +   L++DGK RG   +E +   + VQ   
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE-QDVQKAL 72

Query: 219 MLNNQNLFERRITV------RMDRVADRL 241
             +   + +R + V       +D +   L
Sbjct: 73  EKHRMYMGQRYVEVYEINNEDVDALMKSL 101

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 54.8 bits (132), Expect = 9e-10
 Identities = 18/82 (21%), Positives = 26/82 (31%), Gaps = 4/82 (4%)

Query: 155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
             PL   V+V NL        L+   R  G V             R    + +     A 
Sbjct: 15  GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTW----QGPRRRAFLHYPDSAAAQ 70

Query: 215 QSISMLNNQNLFERRITVRMDR 236
           Q++S L    L    + V + R
Sbjct: 71  QAVSCLQGLRLGTDTLRVALAR 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 49.1 bits (117), Expect = 9e-08
 Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 1/70 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
            V V NLP      +L+   R  G +      +G      + +     A++A+  +   R
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLR 80

Query: 577 IDGKIIDVTF 586
           +    + V  
Sbjct: 81  LGTDTLRVAL 90

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP--VEAVQS 216
            + V  L +K  E+ L+E F   G+V  V++  D   G S+GFG V F        V S
Sbjct: 17  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
            + ST G+V  V++  D  TG  +G   V F   +   K +++ H  +  GR    K   
Sbjct: 34  EYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMID--GRWCDCKLPN 91

Query: 109 EDKGGRRNMGGG 120
             +        G
Sbjct: 92  SKQSQDSGPSSG 103

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 11/89 (12%)

Query: 504 SNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIG 555
           S+ S      +++ + ++V  LP   T Q+L++ F   G++   ++         KG  G
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG-FG 60

Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
            VRF    T  +   M  R  IDG+  D 
Sbjct: 61  FVRFTEYETQVKV--MSQRHMIDGRWCDC 87

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 54.6 bits (132), Expect = 2e-09
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLA-GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +FV +L   VD+  L E F          ++ LD+ G S+G+G V+F   +E  ++++  
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71

Query: 221 NNQ-NLFERRITVRM 234
                L  + + + +
Sbjct: 72  QGAVGLGSKPVRLSV 86

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  L ++  ++ LRE F   G+V+   +  D    +SRGFG V F      V  +  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLA 60

Query: 220 LNNQNLFERRITVR 233
            +   L  + I  +
Sbjct: 61  QSRHELDSKTIDPK 74

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

 Score = 54.5 bits (131), Expect = 2e-09
 Identities = 11/77 (14%), Positives = 28/77 (36%), Gaps = 6/77 (7%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLA----GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQ 215
             V + N++ +V ++KL+ +        G +  ++I +D    + G   + F     A  
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDI--LDIVVDLSDDNSGKAYIVFATQESAQA 87

Query: 216 SISMLNNQNLFERRITV 232
            +            + +
Sbjct: 88  FVEAFQGYPFQGNPLVI 104

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

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 8/97 (8%)

Query: 498 PRAGLDSNRSMNQSSNIE-RDTVVVKNLPPTITWQELR----DKFRNCG---DIKFAEIK 549
            R  +DS    +   + E    V++ N+ P +  ++L+        + G   DI      
Sbjct: 10  ERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD 69

Query: 550 GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
                  + F ++ +A+  ++        G  + +TF
Sbjct: 70  DNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106

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

 Score = 39.1 bits (91), Expect = 6e-04
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 53  STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
           S+ GD+  ++I+ D +    G A + F + +  +  V     +  +G  LVI  +   +
Sbjct: 55  SSQGDI--LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAI-DMMDRTR 576
           T+ V  L  TIT  +LR+ F   G+I+   +  +     ++F +   A+ A     ++  
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLI 73

Query: 577 IDGKIIDVTF 586
           ++G+ ++V +
Sbjct: 74  VNGRRLNVKW 83

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
             I  ++V  L   + E  LR  F   G++  + +   +         ++F     A  +
Sbjct: 10  KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-----QCAFIQFATRQAAEVA 64

Query: 217 I-SMLNNQNLFERRITVR 233
                N   +  RR+ V+
Sbjct: 65  AEKSFNKLIVNGRRLNVK 82

>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 = 53.4 bits (129), Expect = 3e-09
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            +++V  L        L   F   G +  ++       K   F  ++++    A  + + 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-----KGDSFAYIQYESLDAAQAACAK 72

Query: 220 LNNQNLF--ERRITV 232
           +    L   +RR+ V
Sbjct: 73  MRGFPLGGPDRRLRV 87

>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 = 47.2 bits (113), Expect = 5e-07
 Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 8/88 (9%)

Query: 494 GYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKG 552
           G       +   ++    +      + V  L P  +   L  +F   G I+  +  KG  
Sbjct: 1   GSSGSSGKIGYGKANP--TT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS 54

Query: 553 DIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
               ++++S   A+ A   M    + G 
Sbjct: 55  -FAYIQYESLDAAQAACAKMRGFPLGGP 81

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 53.6 bits (129), Expect = 4e-09
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGK-VENVEIALDKD--GKSRGFGTVEFDHPVEAVQS 216
            ++F+  +      +++ E      + V +V +        K+RGF  VE++    A  +
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 217 ISMLNNQN--LFERRITVR 233
              L      L+  +I V 
Sbjct: 69  RRKLMPGRIQLWGHQIAVD 87

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 48.3 bits (115), Expect = 3e-07
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 10/86 (11%)

Query: 511 SSNIERDTVVVKNLPPTITWQELRDKFRNCGD-------IKFAEIKGKGD-IGLVRFDSE 562
           S +     + +  +P     +E+ ++     +          A  K K      V ++S 
Sbjct: 3   SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62

Query: 563 WTAKRAIDMM--DRTRIDGKIIDVTF 586
             A  A   +   R ++ G  I V +
Sbjct: 63  RAAAMARRKLMPGRIQLWGHQIAVDW 88

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L +   +K L++ F   G+V +  I +D + G+SRGFG + F     +V+ +  
Sbjct: 13  KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA-ASVEKVLD 71

Query: 220 LNNQNLFERRITVR 233
                L  R I  +
Sbjct: 72  QKEHRLDGRVIDPK 85

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 37.9 bits (89), Expect = 7e-04
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
            + +  G+V    I  D +TG+ RG   + F+    V K +++       GR +  K+A
Sbjct: 30  DYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEH-RLDGRVIDPKKA 87

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 52.6 bits (126), Expect = 1e-08
 Identities = 17/106 (16%), Positives = 36/106 (33%), Gaps = 6/106 (5%)

Query: 483 GGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGD 542
           G S      S G     + +  +RS    S      + ++ LP  +T  E+       G 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR----VIHIRKLPIDVTEGEVISLGLPFGK 57

Query: 543 IKFAEIKGKGDIGLVRFDSEWTAKRAIDM--MDRTRIDGKIIDVTF 586
           +    +    +   +  ++E  A   ++        + G+ I + F
Sbjct: 58  VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF 103

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 42.6 bits (100), Expect = 4e-05
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM-- 219
           + +  L   V E ++  +    GKV N+ +      K +    +E +    A   ++   
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYT 88

Query: 220 LNNQNLFERRITVRM 234
                L  + I ++ 
Sbjct: 89  SVTPVLRGQPIYIQF 103

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.2 bits (125), Expect = 1e-08
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 160 NKVFVANLDYKVDEK---KLREVFRLAGKVENVEIALDKDGK----SRGFGTVEFDHPVE 212
           N VFV  L  ++ +    K  E F   GK+  V I                 V +    +
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 213 AVQSISMLNNQNLFERRITV 232
           A+++I  +NN  +  R +  
Sbjct: 76  ALRAIQCVNNVVVDGRTLKA 95

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 12/85 (14%)

Query: 514 IERDTVVVKNLPPTITWQEL---RDKFRNCGDIKFAEI---------KGKGDIGLVRFDS 561
           ++++ V V  L   +   E+    + F   G I    I         +G      V +  
Sbjct: 13  VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72

Query: 562 EWTAKRAIDMMDRTRIDGKIIDVTF 586
              A RAI  ++   +DG+ +  + 
Sbjct: 73  SEDALRAIQCVNNVVVDGRTLKASL 97

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT-- 575
            V V+ L  ++   +L +     G I +  +       LV F++  +AK  +        
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPV 76

Query: 576 RIDGKIIDVTF 586
            I G+     +
Sbjct: 77  YIAGQQAFFNY 87

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 5/74 (6%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V V  L   V E  L E     G +  V +        +    VEF++   A + ++   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMM-----PFKRQALVEFENIDSAKECVTFAA 72

Query: 222 NQNLFERRITVRMD 235
           +  ++        +
Sbjct: 73  DVPVYIAGQQAFFN 86

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 51.9 bits (125), Expect = 2e-08
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  L ++  E+ LR  +   GK+ +  +  D    +SRGFG V F      V +   
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM-AEVDAAMA 87

Query: 220 LNNQNLFERRITVR 233
               ++  R +  +
Sbjct: 88  ARPHSIDGRVVEPK 101

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 38.4 bits (90), Expect = 8e-04
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVN-KMHRFETKGRKLVIKEA 107
           ++    G +T   ++ D  + + RG   V F S   V  A+  + H  +  GR +  K A
Sbjct: 46  NYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSID--GRVVEPKRA 103

Query: 108 VEDKGGRRNMGGGGG 122
           V     R   G G  
Sbjct: 104 VA----REESGSGPS 114

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 6/74 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + VFV      + E +LRE F   G V +V I        R F  V F    +  QS+  
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP----KPFRAFAFVTFADD-QIAQSL-C 59

Query: 220 LNNQNLFERRITVR 233
             +  +    + + 
Sbjct: 60  GEDLIIKGISVHIS 73

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 15/71 (21%), Positives = 19/71 (26%), Gaps = 6/71 (8%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
              S  GDV  V I        R  A V F    + +    +      KG  + I  A  
Sbjct: 24  EFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGEDLII--KGISVHISNAEP 77

Query: 110 DKGGRRNMGGG 120
                     G
Sbjct: 78  KHNSNSGPSSG 88

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 5/66 (7%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKG--KGDIGLVRFDSEWTAKRAIDMMDRTRID 578
           V      +T  ELR+ F   GD+    I    +     V F  +  A+      +   I 
Sbjct: 10  VGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA-FAFVTFADDQIAQSL--CGEDLIIK 66

Query: 579 GKIIDV 584
           G  + +
Sbjct: 67  GISVHI 72

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  LD+   ++ LR  F   G+V +  I  DK   +SRGFG V+F  P   V ++  
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP-NCVGTVLA 76

Query: 220 LNNQNLFERRITV 232
                L  R I  
Sbjct: 77  SRPHTLDGRNIDP 89

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 10/79 (12%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENV------EIALDKDGKSRGFGTVEFDHPVEAV 214
           +++V N+ + + E+ + + F    ++  +       +   +  + + F  +EF    E  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 215 QSISMLNNQNLFERRITVR 233
           Q+++  +      + + +R
Sbjct: 68  QAMA-FDGIIFQGQSLKIR 85

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  L ++  ++ LRE F   G+V+   +  D    +SRGFG V F      V  +  
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLA 85

Query: 220 LNNQNLFERRITV 232
            +   L  + I  
Sbjct: 86  QSRHELDSKTIDP 98

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

 Score = 48.6 bits (116), Expect = 2e-07
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT-- 575
            V ++ L   +   +L +  +  G I +  +  K    LV F+    A  A++       
Sbjct: 23  VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQI 82

Query: 576 RIDGKIIDVTF 586
            I G    V +
Sbjct: 83  YIAGHPAFVNY 93

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

 Score = 44.0 bits (104), Expect = 8e-06
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 5/74 (6%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V +  L   V E  L E  +  G +  V +        +    VEF+  + A  +++   
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM-----PKKRQALVEFEDVLGACNAVNYAA 78

Query: 222 NQNLFERRITVRMD 235
           +  ++       ++
Sbjct: 79  DNQIYIAGHPAFVN 92

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 49.2 bits (117), Expect = 2e-07
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQS 216
            KVFV  L   +DE ++   FR  G +        +       +G+  + F     +VQ+
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE-SSVQA 67

Query: 217 ISMLNNQNLFERRITVRMDRVADR 240
           +     +   +  + V    + D+
Sbjct: 68  LIDACLEEDGKLYLCVSSPTIKDK 91

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +KVFV      +  ++L++ F   G+V +V I        R F  V F    +  QS+  
Sbjct: 12  SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADD-KVAQSL-C 65

Query: 220 LNNQNLFERRITVR 233
             +  +    + + 
Sbjct: 66  GEDLIIKGISVHIS 79

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 508 MNQSSNIERDT--VVVKNLPPTITWQELRDKFRNCGDIKFAEIKG--KGDIGLVRFDSEW 563
           M  S +       V V      +T +EL+  F   G++    I    +     V F  + 
Sbjct: 1   MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRA-FAFVTFADDK 59

Query: 564 TAKRAIDMMDRTRIDGKIIDV 584
            A+      +   I G  + +
Sbjct: 60  VAQSLC--GEDLIIKGISVHI 78

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 14/67 (20%), Positives = 20/67 (29%), Gaps = 7/67 (10%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
                 G+V  V I        R  A V F    + +    +      KG  + I  A  
Sbjct: 30  QFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDLII--KGISVHISNAE- 82

Query: 110 DKGGRRN 116
            K  + N
Sbjct: 83  PKHNKLN 89

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.5 bits (113), Expect = 5e-07
 Identities = 12/85 (14%), Positives = 31/85 (36%), Gaps = 2/85 (2%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
           S+   +  S +    + ++ LP  +T  E+       G +    +    +   +  ++E 
Sbjct: 4   SHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEE 63

Query: 564 TAKRAID--MMDRTRIDGKIIDVTF 586
            A   ++        + G+ I + F
Sbjct: 64  AANTMVNYYTSVTPVLRGQPIYIQF 88

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 42.2 bits (99), Expect = 3e-05
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS--M 219
           + +  L   V E ++  +    GKV N+ +      K +    +E +    A   ++   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYT 73

Query: 220 LNNQNLFERRITVRM 234
                L  + I ++ 
Sbjct: 74  SVTPVLRGQPIYIQF 88

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 49.1 bits (116), Expect = 7e-07
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 1/60 (1%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
             L   G V  +++        +GS  V F S +  +K V      + K   L+I    +
Sbjct: 128 EWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD 186

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 48.7 bits (115), Expect = 8e-07
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 1/80 (1%)

Query: 155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
           N      V++           ++E     G+V N+++        +G   V FD   E+ 
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSI-ESA 163

Query: 215 QSISMLNNQNLFERRITVRM 234
           +       Q   E  + +  
Sbjct: 164 KKFVETPGQKYKETDLLILF 183

>4aez_B MAD2, mitotic spindle checkpoint component MAD2; cell cycle, KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe} Length = 203

 Score = 48.6 bits (115), Expect = 1e-06
 Identities = 14/46 (30%), Positives = 29/46 (63%)

Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDEND 310
           +  +  W+  +K+QKL L+I+++ + E LERW F ++   ++D+  
Sbjct: 68  VSQLHKWMFAKKIQKLILVITSKCSGEDLERWQFNVEMVDTADQFQ 113

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 46.6 bits (110), Expect = 2e-06
 Identities = 23/104 (22%), Positives = 41/104 (39%), Gaps = 8/104 (7%)

Query: 489 SIQSGG--YGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFA 546
           S+QSG        A +D+  +M   S + R  ++V+NL   +T   L   F   G +   
Sbjct: 1   SVQSGNLALAASAAAVDAGMAMAGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKI 58

Query: 547 EI--KGKGDIGLVRFDSEWTAKRAIDMMDRTRI--DGKIIDVTF 586
               K      L+++    +A+ A   +D   I      + + F
Sbjct: 59  ITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 102

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 44.2 bits (104), Expect = 1e-05
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           + V NL Y V    L ++F   G V  +         ++    +++  PV A  +   L+
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLD 87

Query: 222 NQNLFERRITVRMD 235
            QN++    T+R+D
Sbjct: 88  GQNIYNACCTLRID 101

>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 = 44.4 bits (105), Expect = 6e-06
 Identities = 11/86 (12%), Positives = 29/86 (33%), Gaps = 3/86 (3%)

Query: 504 SNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSE 562
           S+ S     +     V+ ++ LP  +T  E+       G +    +    +   +   +E
Sbjct: 2   SSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATE 61

Query: 563 WTAKRAID--MMDRTRIDGKIIDVTF 586
             A   ++        +  + I + +
Sbjct: 62  EAAITMVNYYSAVTPHLRNQPIYIQY 87

>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 = 41.7 bits (98), Expect = 4e-05
 Identities = 12/75 (16%), Positives = 29/75 (38%), Gaps = 7/75 (9%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS--M 219
           + +  L  +V E ++  +    GKV N+ +      K +    +E      A+  ++   
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYS 72

Query: 220 LNNQNLFERRITVRM 234
               +L  + I ++ 
Sbjct: 73  AVTPHLRNQPIYIQY 87

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 45.5 bits (107), Expect = 8e-06
 Identities = 29/114 (25%), Positives = 47/114 (41%), Gaps = 7/114 (6%)

Query: 126 DLSALLQ-NNSSKFGNTYGLSPQFLESLGINCPLINKVF---VANLDYKVDEKKLREVFR 181
              A LQ  NS + GN    +       G+     + V    V NL Y V    L ++F 
Sbjct: 9   SAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFS 68

Query: 182 LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD 235
             G V    I   K+ + +    +++  PV A  +   L+ QN++    T+R+D
Sbjct: 69  KFGTVLK-IITFTKNNQFQAL--LQYADPVSAQHAKLSLDGQNIYNACCTLRID 119

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 42.8 bits (100), Expect = 7e-05
 Identities = 23/104 (22%), Positives = 41/104 (39%), Gaps = 8/104 (7%)

Query: 489 SIQSGG--YGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFA 546
           S+QSG        A +D+  +M   S + R  ++V+NL   +T   L   F   G +   
Sbjct: 19  SVQSGNLALAASAAAVDAGMAMAGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKI 76

Query: 547 EI--KGKGDIGLVRFDSEWTAKRAIDMMDRTRI--DGKIIDVTF 586
               K      L+++    +A+ A   +D   I      + + F
Sbjct: 77  ITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120

>2vfx_A Mitotic spindle assembly checkpoint protein MAD2A; CDC2, nucleus, mitosis, anaphase, cell cycle, CE division, spindle checkpoint; HET: PE4 PE3; 1.95A {Homo sapiens} PDB: 2qyf_A 2v64_A 1s2h_A 1go4_A 3gmh_A 1klq_A 2v64_D 1duj_A Length = 206

 Score = 45.8 bits (108), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKT 320
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A    +    
Sbjct: 70  VEQLKDWLYKSSVQKLVVVISNIESGEVLERWQFDIESDKTAKDDSAPREKSQKAI 125

>3abd_A Mitotic spindle assembly checkpoint protein MAD2B; horma, DNA replication, translesion DNA SYNT cell cycle, cell division, mitosis, DNA damage; HET: DNA; 1.90A {Homo sapiens} PDB: 3abe_C* Length = 227

 Score = 44.8 bits (105), Expect = 2e-05
 Identities = 8/49 (16%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAAS 313
           L  V   L +  V+K+ ++I ++     +E++ F++        +  + 
Sbjct: 84  LHCVKPLLEKNDVEKVVVVILDKEH-RPVEKFVFEITQPPLLSISSDSL 131

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 96

 Score = 40.8 bits (95), Expect = 9e-05
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 516 RDTVVVKNLPPTITWQELRDKFR----NCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDM 571
              + V NLP     + + ++ R    NCG  K   I G     ++RF ++ +A+RA   
Sbjct: 9   HTLLYVYNLPANKDGKSVSNRLRRLSDNCGG-KVLSITG--CSAILRFINQDSAERAQKR 65

Query: 572 MDRTRIDGKIIDVTF 586
           M+   + G  I V+F
Sbjct: 66  MENEDVFGNRIIVSF 80

>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 = 39.9 bits (93), Expect = 2e-04
 Identities = 17/99 (17%), Positives = 34/99 (34%), Gaps = 4/99 (4%)

Query: 493 GGYGNPRAG--LDSNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEIK 549
           G  G+  A   L  +  +   S   +  VV    L   ++  +L      CG +    + 
Sbjct: 1   GSSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60

Query: 550 GKGDIGLVRFDSEWTAKRAIDMMDRTRI-DGKIIDVTFF 587
                   R+ +   +KRA   ++   + D     +T +
Sbjct: 61  PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY 99

>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 = 38.4 bits (89), Expect = 8e-04
 Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V    L   V   +L  V    G V+ + +  +K      +    +    E+ ++   LN
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-----PYSFARYRTTEESKRAYVTLN 84

Query: 222 NQNLFERR 229
            + + +  
Sbjct: 85  GKEVVDDL 92

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

 Score = 40.5 bits (94), Expect = 7e-04
 Identities = 18/109 (16%), Positives = 31/109 (28%), Gaps = 16/109 (14%)

Query: 487 QASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITW---------QELRDKF 537
               +   Y     G+ S R  N+       T+ V  +   +             +R  F
Sbjct: 112 FGREKFADYREDMGGIGSFRKKNK-------TLYVGGIDGALNSKHLKPAQIESRIRFVF 164

Query: 538 RNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
              GDI         + G V+F  +  A+ A + M    +         
Sbjct: 165 SRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWD 213

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	587
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.98
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.95
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.95
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.94
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.94
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.94
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.94
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.93
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.93
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.92
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.92
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.92
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.9
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.81
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.75
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.75
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.75
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.75
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.75
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.74
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.74
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.74
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.74
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.74
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.74
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.74
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.74
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.74
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.73
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.73
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.73
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.73
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.73
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.73
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.72
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.72
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.72
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.72
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.72
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.72
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.72
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.72
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.72
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.72
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.72
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.71
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.71
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.71
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.71
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.71
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.71
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.71
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.71
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.71
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.71
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.71
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.71
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.71
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.71
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.71
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.7
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.7
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.7
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.7
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.7
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.7
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.7
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.7
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.7
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.7
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.7
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.7
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.7
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.7
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.7
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.7
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.7
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.7
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.7
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.7
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.69
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.69
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.69
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.69
2div_A	99	TRNA selenocysteine associated protein; structural	99.69
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.69
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.69
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.69
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.69
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.69
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.69
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.69
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.69
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.69
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.69
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.69
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.69
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.68
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.68
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.68
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.68
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.68
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.68
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.68
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.68
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.68
2div_A	99	TRNA selenocysteine associated protein; structural	99.68
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.68
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.68
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.68
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.68
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.68
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.67
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.67
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.67
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.67
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.67
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.67
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.67
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.67
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.67
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.67
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.67
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.66
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.66
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.66
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.66
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.66
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.66
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.66
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.66
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.66
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.66
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.66
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.66
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.66
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.66
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.66
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.65
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.65
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.65
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.65
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.65
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.65
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.65
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.65
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.65
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.65
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.65
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.65
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.64
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.64
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.64
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.64
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.45
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.64
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.64
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.64
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.64
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.64
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.64
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.64
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.64
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.64
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.64
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.64
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.64
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.63
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.63
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.63
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.63
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.63
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.63
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.63
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.63
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.63
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.63
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.63
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.63
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.63
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.63
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.63
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.63
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.63
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.63
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.62
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.62
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.62
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.62
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.62
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.62
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.62
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.62
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.61
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.61
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.61
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.61
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.61
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.61
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.61
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.61
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.61
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.61
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.6
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.6
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.6
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.6
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.6
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.6
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.6
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.6
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.6
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.6
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.59
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.59
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.59
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.58
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.58
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.58
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.58
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.58
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.58
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.58
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.58
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.58
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.58
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.58
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.57
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.57
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.57
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.57
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.57
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.57
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.56
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.34
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.56
1x5p_A	97	Negative elongation factor E; structure genomics,	99.56
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.56
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.56
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.55
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.55
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.54
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.54
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.54
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.53
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.53
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.53
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.52
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.52
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.52
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.51
1x5p_A	97	Negative elongation factor E; structure genomics,	99.51
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.51
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.5
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.48
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.47
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.47
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.46
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.45
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.42
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.42
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.41
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.41
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.41
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.39
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.39
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.34
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.28
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.25
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.22
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.2
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.19
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.18
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.17
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.08
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.03
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.97
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.85
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.73
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.62
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.6
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.2
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.99
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.81
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.66
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.63
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.13
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.07
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.93
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.83
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.72
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.66
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.55
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.42
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.29
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.24
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.49
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.01
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.94
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.41

>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=100.00  E-value=2.2e-40  Score=334.56  Aligned_cols=161  Identities=11%  Similarity=0.138  Sum_probs=139.3

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ...+..++|||+|||+++|+++| ++|++||+|.+|+|++++.+ ++|||||+|.+.++|++|++ +++..|.|++|.|.
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVS  113 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEE
Confidence            34457789999999999999999 89999999999999998755 58999999999999999994 89999999999999


Q ss_pred             ecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcC-
Q psy1534         106 EAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAG-  184 (587)
Q Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-  184 (587)
                      ++.                                                  .++|||+|||+++++++|+++|+.|| 
T Consensus       114 ~~~--------------------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~  143 (292)
T 2ghp_A          114 HLT--------------------------------------------------ECTLWMTNFPPSYTQRNIRDLLQDINV  143 (292)
T ss_dssp             ECC--------------------------------------------------SCEEEEECCCTTCCHHHHHHHHHHTTC
T ss_pred             ECC--------------------------------------------------CCEEEEECCCCCCCHHHHHHHHHHhCC
Confidence            864                                                  35899999999999999999999999 


Q ss_pred             CeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         185 KVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       185 ~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      .|..|.|++++.+.++|||||+|.+.++|.+|++.||+..+.|++|.|.++.+..
T Consensus       144 ~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          144 VALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             CCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             CeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence            9999999999888899999999999999999999999999999999999987553

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=6.1e-40  Score=329.96  Aligned_cols=152  Identities=22%  Similarity=0.316  Sum_probs=141.7

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..++|||+|||+++|+++| ++|++|| |.+|++     ++++|||||+|.+.++|++|++.|++..|.|++|.|.++..
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~   94 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT   94 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCC
Confidence            5589999999999999999 8999999 999988     45689999999999999999999999999999999998652


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                                                                       .++|||+|||+++++++|+++|++||.|..|
T Consensus        95 -------------------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~  125 (284)
T 3smz_A           95 -------------------------------------------------DALLCVANLPPSLTQQQFEELVRPFGSLERC  125 (284)
T ss_dssp             -------------------------------------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEE
T ss_pred             -------------------------------------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEE
Confidence                                                             2589999999999999999999999999999


Q ss_pred             EEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         190 EIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       190 ~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .+++++ +|+++|||||+|.+.++|.+|++.||+..+.|++|.|.++.+
T Consensus       126 ~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~  174 (284)
T 3smz_A          126 FLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDA  174 (284)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCG
T ss_pred             EEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            999987 499999999999999999999999999999999999998754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=2.2e-33  Score=269.60  Aligned_cols=167  Identities=23%  Similarity=0.340  Sum_probs=150.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +..+|||+|||+++|+++| ++|++||+|++|+|++|+ +++++|||||+|.+.++|++|++.+++..+.|+.|+|.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            4568999999999999999 899999999999999997 89999999999999999999999999999999999999887


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      .....                                         .....++|||+|||+++++++|+++|++||.|.+
T Consensus        94 ~~~~~-----------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~  132 (213)
T 4f02_A           94 RDPSL-----------------------------------------RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS  132 (213)
T ss_dssp             CCTHH-----------------------------------------HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEE
T ss_pred             ccccc-----------------------------------------cccccccceECCcccccHHHHHHHHHhhcCCeEE
Confidence            33210                                         0012368999999999999999999999999999


Q ss_pred             EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         189 VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       189 v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      |+|+++.. .++|||||+|.+.++|++||+.|||..|.|++|.|+++.++.
T Consensus       133 ~~i~~d~~-~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          133 CKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             EEEEEETT-EEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             EEeeccCC-CCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            99999864 479999999999999999999999999999999999987653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.8e-33  Score=253.87  Aligned_cols=163  Identities=18%  Similarity=0.277  Sum_probs=150.3

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK  111 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~  111 (587)
                      ++|||+|||.++++++| ++|++||+|.+|+|+++++++++|||||+|.+.++|++|++.|++..+.|++|.|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999 89999999999999999988999999999999999999999999999999999999987442


Q ss_pred             CCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEE
Q psy1534         112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEI  191 (587)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i  191 (587)
                      ..                                         ...+.++|||+|||+++++++|+++|++||.|.++.+
T Consensus        81 ~~-----------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i  119 (166)
T 3md3_A           81 QS-----------------------------------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV  119 (166)
T ss_dssp             CC-----------------------------------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEE
T ss_pred             CC-----------------------------------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEE
Confidence            10                                         1234579999999999999999999999999999999


Q ss_pred             eeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         192 ALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       192 ~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ++++. +.++|||||+|.+.++|.+|++.||+..+.|++|+|.+++
T Consensus       120 ~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          120 MWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             EECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             EecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            99964 9999999999999999999999999999999999999985

>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=100.00  E-value=2.2e-32  Score=252.17  Aligned_cols=162  Identities=22%  Similarity=0.362  Sum_probs=150.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +.++|||+|||.++++++| ++|++||+|.+|+|++++ +|+++|||||+|.+.++|++|++.|++..+.|++|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            4578999999999999999 899999999999999996 89999999999999999999999999999999999999987


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      ++..                                           ....++|||+|||.++++++|+++|++||.|..
T Consensus        82 ~~~~-------------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~  118 (168)
T 1b7f_A           82 PGGE-------------------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ  118 (168)
T ss_dssp             CCSS-------------------------------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEE
T ss_pred             CCcc-------------------------------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEE
Confidence            4421                                           123579999999999999999999999999999


Q ss_pred             EEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEc
Q psy1534         189 VEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMD  235 (587)
Q Consensus       189 v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a  235 (587)
                      +.+++++ +++++|||||+|.+.++|.+|++.||+..+.|  ++|+|++|
T Consensus       119 ~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999998 59999999999999999999999999999987  99999885

>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=100.00  E-value=4.3e-32  Score=256.99  Aligned_cols=175  Identities=23%  Similarity=0.340  Sum_probs=149.6

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      .+...++|||+|||+++|+++| ++|++||+|.+|+|++++ +|+++|||||+|.+.++|++|++. ++..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            3456779999999999999999 899999999999999997 899999999999999999999976 9999999999999


Q ss_pred             ecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC
Q psy1534         106 EAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK  185 (587)
Q Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~  185 (587)
                      ++........                                     .......++|||+|||+++++++|+++|++||.
T Consensus        88 ~~~~~~~~~~-------------------------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~  130 (196)
T 1l3k_A           88 RAVSREDSQR-------------------------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK  130 (196)
T ss_dssp             ECCC------------------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSC
T ss_pred             cccCcccccc-------------------------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCC
Confidence            9874421100                                     001233579999999999999999999999999


Q ss_pred             eeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCC
Q psy1534         186 VENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRL  241 (587)
Q Consensus       186 i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~  241 (587)
                      |..|.|++++ +++++|||||+|.+.++|.+|+.. ++..|.|+.|.|+++.++...
T Consensus       131 i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             eEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            9999999998 499999999999999999999976 899999999999999887643

>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=100.00  E-value=5.1e-32  Score=249.32  Aligned_cols=161  Identities=22%  Similarity=0.420  Sum_probs=148.1

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      .++|||+|||+++++++| ++|++||+|.+|++++++ +|+++|||||+|.++++|++|++.|++..+.|++|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            478999999999999999 899999999999999997 999999999999999999999999999999999999999874


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                      ...                                           ....++|||+|||.++++++|+++|++||.|.++
T Consensus        82 ~~~-------------------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~  118 (167)
T 1fxl_A           82 SSA-------------------------------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS  118 (167)
T ss_dssp             CCG-------------------------------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEE
T ss_pred             Ccc-------------------------------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEE
Confidence            321                                           1124689999999999999999999999999999


Q ss_pred             EEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeE--EEEEEc
Q psy1534         190 EIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR--ITVRMD  235 (587)
Q Consensus       190 ~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~--l~v~~a  235 (587)
                      .+++++ +++++|||||+|.+.++|.+|++.|||..+.|+.  |.|+||
T Consensus       119 ~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            999988 5899999999999999999999999999999975  777765

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

Probab=100.00  E-value=1.7e-32  Score=263.89  Aligned_cols=179  Identities=20%  Similarity=0.349  Sum_probs=153.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||.++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.|++..|.|++|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4578999999999999999 899999999999999997 99999999999999999999999999999999999998876


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      ......                                .............++|||+|||.++++++|+++|++||.|.+
T Consensus       107 ~~~~~~--------------------------------~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  154 (216)
T 2qfj_A          107 NIGQAQ--------------------------------PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS  154 (216)
T ss_dssp             CCGGGH--------------------------------HHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEE
T ss_pred             Cccccc--------------------------------hhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeE
Confidence            332100                                000000001234579999999999999999999999999999


Q ss_pred             EEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCC
Q psy1534         189 VEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADRL  241 (587)
Q Consensus       189 v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~~  241 (587)
                      |+|++++ +++++|||||+|.+.++|.+|++.||+..|.|++|.|.++......
T Consensus       155 v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             EEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            9999997 4999999999999999999999999999999999999999887543

>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=99.98  E-value=8e-32  Score=250.12  Aligned_cols=164  Identities=21%  Similarity=0.322  Sum_probs=147.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CC--CcceEEEEEECCHHHHHHHHHHhCCceeC---CeEEE
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TG--KPRGSAIVEFQSPDLVRKAVNKMHRFETK---GRKLV  103 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g--~skG~aFV~F~~~e~A~~Al~~l~g~~l~---gr~i~  103 (587)
                      ..++|||+|||+++++++| ++|++||+|.+|+|++++ ++  +++|||||+|.+.++|++|++.|++..+.   ++++.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            4679999999999999999 899999999999999997 54  89999999999999999999999998876   68888


Q ss_pred             EEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhc
Q psy1534         104 IKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLA  183 (587)
Q Consensus       104 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~  183 (587)
                      +.++..+..                                          .....++|||+|||+++++++|+++|++|
T Consensus        82 ~~~~~~~~~------------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~  119 (175)
T 3nmr_A           82 MKPADSEKN------------------------------------------NAVEDRKLFIGMISKKCTENDIRVMFSSF  119 (175)
T ss_dssp             EEECGGGCC------------------------------------------SCGGGSEEEEESCCTTCCHHHHHHHHGGG
T ss_pred             Ecccccccc------------------------------------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhC
Confidence            888774421                                          11235799999999999999999999999


Q ss_pred             CCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CeEEEEEEcc
Q psy1534         184 GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF---ERRITVRMDR  236 (587)
Q Consensus       184 G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~v~~a~  236 (587)
                      |.|.+|.++++++|+++|||||+|.+.++|.+|++.|||..+.   +++|.|+||.
T Consensus       120 G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          120 GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            9999999999988999999999999999999999999998876   4999999873

>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=99.97  E-value=3.6e-32  Score=250.63  Aligned_cols=162  Identities=24%  Similarity=0.392  Sum_probs=147.3

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +.++|||+|||+++|+++| ++|++||+|.+|+|++++ +|+++|||||+|.+.++|++|++.  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            3578999999999999999 899999999999999996 899999999999999999999984  678999999999887


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      .+..                                           ....++|||+|||+++++++|+++|++||.|.+
T Consensus        80 ~~~~-------------------------------------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~  116 (167)
T 2cjk_A           80 PRDE-------------------------------------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIID  116 (167)
T ss_dssp             CHHH-------------------------------------------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSE
T ss_pred             chhh-------------------------------------------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEE
Confidence            3321                                           012468999999999999999999999999999


Q ss_pred             EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         189 VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       189 v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      |.+++++. ++++|||||+|.+.++|.+|++ +++..+.|++|.|+++.++
T Consensus       117 ~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          117 AQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             EEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99999974 9999999999999999999997 8999999999999998765

>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=99.97  E-value=8e-31  Score=263.38  Aligned_cols=197  Identities=12%  Similarity=0.123  Sum_probs=171.0

Q ss_pred             CCCchhHHHHHHcCCCCCccccccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEEC
Q psy1534           3 SPVTETELVEQIAHQDFPMFQRIETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQ   80 (587)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~   80 (587)
                      ++-+...|...+++..+....-.-...+...+|||+|||+++++++| ++|++||+|.+|+|++++ +|+++|||||+|.
T Consensus        66 ~~~~A~~A~~~l~~~~~~g~~i~v~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~  145 (284)
T 3smz_A           66 NGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM  145 (284)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             CHHHHHHHHHHcCCCeeCCeEEEEEecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEEC
Confidence            34455667777777766544222233456789999999999999999 899999999999999997 9999999999999


Q ss_pred             CHHHHHHHHHHhCCceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCc
Q psy1534          81 SPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLIN  160 (587)
Q Consensus        81 ~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (587)
                      +.++|.+|++.|++..+.|++|.|.++.++....                                        .....+
T Consensus       146 ~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~----------------------------------------~~~~~~  185 (284)
T 3smz_A          146 KKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTP----------------------------------------ALLHSR  185 (284)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECCGGGCCT----------------------------------------TTTSCS
T ss_pred             CHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCc----------------------------------------ccCCcc
Confidence            9999999999999999999999999998543110                                        123457


Q ss_pred             EEEEecCCCCC-cHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         161 KVFVANLDYKV-DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       161 ~l~V~nLp~~~-te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      +|||+|||+++ ++++|+++|++||.|.+|.|+++.+|+++|||||+|.+.++|.+|++.|||..+.|++|.|.++.++.
T Consensus       186 ~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             EEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             EEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            99999999995 99999999999999999999999999999999999999999999999999999999999999997765

>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=99.97  E-value=2.6e-30  Score=245.75  Aligned_cols=192  Identities=16%  Similarity=0.193  Sum_probs=145.8

Q ss_pred             CCCCcEEEcCCC-CCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQ-GDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp-~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ++..+|||+||| +++++++| ++|++||+|.+|+|+++    +||||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            456799999999 89999999 89999999999999986    4799999999999999999999999999999999998


Q ss_pred             ccccCCCCC-CCCCCCCC--CchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcC
Q psy1534         108 VEDKGGRRN-MGGGGGVD--RDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAG  184 (587)
Q Consensus       108 ~~~~~~~~~-~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G  184 (587)
                      ..+...... .....+..  .+....   ....+    .  ...........++.++|||+|||+++++++|+++|++||
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~---~~~r~----~--~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G  148 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSES---RNNRF----S--TPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELG  148 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTC---TTCSC----S--SHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHT
T ss_pred             cCCccCCCcccccccCCccccccCCC---ccccc----c--CcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcC
Confidence            744321000 00000000  000000   00000    0  000001111235678999999999999999999999999


Q ss_pred             Ce--eEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCe----EEEEEEc
Q psy1534         185 KV--ENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFER----RITVRMD  235 (587)
Q Consensus       185 ~i--~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~----~l~v~~a  235 (587)
                      .|  .+|+++.++ +.++|||||+|.+.++|.+||..||+..|.|+    ++.|+++
T Consensus       149 ~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          149 VKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            99  899998876 55679999999999999999999999999876    6777775

>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=99.97  E-value=5.6e-30  Score=237.09  Aligned_cols=156  Identities=21%  Similarity=0.302  Sum_probs=141.8

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccC----C-------CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTV----G-------DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK   98 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~----G-------~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~   98 (587)
                      ..++|||+|||+++|+++| ++|++|    |       .|.++++.++     +|||||+|.++++|++|+ .||+..+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~-----~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT-----TTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC-----CCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            4579999999999999999 899999    7       8888887654     799999999999999999 89999999


Q ss_pred             CeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHH
Q psy1534          99 GRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLRE  178 (587)
Q Consensus        99 gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~  178 (587)
                      |++|.|.++....                                           .....++|||+|||+++++++|++
T Consensus        77 g~~i~v~~~~~~~-------------------------------------------~~~~~~~l~v~nlp~~~t~~~l~~  113 (172)
T 2g4b_A           77 GQSLKIRRPHDYQ-------------------------------------------PLPGAHKLFIGGLPNYLNDDQVKE  113 (172)
T ss_dssp             TEECEEECCSSCC-------------------------------------------CCTTTTCEEEECCCTTCCHHHHHH
T ss_pred             CceeeecCCcccC-------------------------------------------CCCCCCEEEEEcCCCcCCHHHHHH
Confidence            9999999876332                                           111256899999999999999999


Q ss_pred             HHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         179 VFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       179 ~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +|++||.|.+|.+++++ +++++|||||+|.+.++|.+|++.||+..+.|++|.|++|
T Consensus       114 ~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          114 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99999999999999997 5999999999999999999999999999999999999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.97  E-value=2.8e-29  Score=237.98  Aligned_cols=181  Identities=18%  Similarity=0.236  Sum_probs=147.3

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccC----C-------CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTV----G-------DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK   98 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~----G-------~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~   98 (587)
                      ..++|||+|||+++++++| ++|++|    |       .|.++++.     +++|||||+|.+.++|++|+ .||+..|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            4689999999999999999 899999    5       67777664     45899999999999999999 89999999


Q ss_pred             CeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHH
Q psy1534          99 GRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLRE  178 (587)
Q Consensus        99 gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~  178 (587)
                      |++|.|.++..........  .    ..        ...       .+.  ..........++|||+|||+++++++|++
T Consensus        77 g~~i~v~~~~~~~~~~~~~--~----~~--------~~~-------~~~--~~~~~~~~~~~~l~v~nl~~~~~~~~l~~  133 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMS--E----NP--------SVY-------VPG--VVSTVVPDSAHKLFIGGLPNYLNDDQVKE  133 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSS--S----CS--------SCC-------CTT--SSCCCSSCCCCEEEEECCCTTCCHHHHHH
T ss_pred             CceEEEeCCCCCCCCCCCc--C----CC--------cCC-------CCC--CccCCCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            9999999987442111000  0    00        000       000  00011234578999999999999999999


Q ss_pred             HHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q psy1534         179 VFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVADR  240 (587)
Q Consensus       179 ~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~~  240 (587)
                      +|++||.|.+|.+++++ ++.++|||||+|.+.++|.+|++.||+..+.|++|.|+++.++.+
T Consensus       134 ~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          134 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             HHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             HHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999999999999997 599999999999999999999999999999999999999987754

>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=99.97  E-value=1.4e-30  Score=241.98  Aligned_cols=165  Identities=18%  Similarity=0.313  Sum_probs=143.3

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+...++|||+|||+++++++| ++|++||.|..+.+....+++++|||||+|.+.++|++|+ .|++..|.|++|+|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            3456789999999999999999 7899999887743333348899999999999999999999 5999999999999999


Q ss_pred             cccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCe
Q psy1534         107 AVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKV  186 (587)
Q Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i  186 (587)
                      +..+...                                         .....++|||+|||+++++++|+++|++||.|
T Consensus        88 ~~~~~~~-----------------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v  126 (175)
T 1fje_B           88 PKGRDSK-----------------------------------------KVRAARTLLAKNLSFNITEDELKEVFEDALEI  126 (175)
T ss_dssp             CCCSSCS-----------------------------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEE
T ss_pred             CCCcccc-----------------------------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeE
Confidence            8844210                                         11235799999999999999999999999987


Q ss_pred             eEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         187 ENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       187 ~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      ..+    ..+++++|||||+|.+.++|.+|++.|||..+.|++|.|+++.++
T Consensus       127 ~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          127 RLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             EEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            765    456889999999999999999999999999999999999998765

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.96  E-value=6.9e-29  Score=248.98  Aligned_cols=202  Identities=17%  Similarity=0.193  Sum_probs=148.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-----HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-----SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-----~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      .+..++|||+|||+++++++|     ++|++||+|.+|+|++  ++++||||||+|.+.++|++|++.||+..|.|++|+
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            356789999999999999995     5899999999999886  788999999999999999999999999999999999


Q ss_pred             EEecccccCC--CCCCCC-CCCCCCch--------hhhhccCC------------------------c------------
Q psy1534         104 IKEAVEDKGG--RRNMGG-GGGVDRDL--------SALLQNNS------------------------S------------  136 (587)
Q Consensus       104 V~~a~~~~~~--~~~~~~-~~~~~~~~--------~~~~~~~~------------------------~------------  136 (587)
                      |.++..+...  +..+.. .+......        ........                        .            
T Consensus        84 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  163 (282)
T 3pgw_A           84 IQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPY  163 (282)
T ss_pred             EEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCC
Confidence            9998743311  000000 00000000        00000000                        0            


Q ss_pred             ----ccCCCCCCCh---------------hhh--hccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC
Q psy1534         137 ----KFGNTYGLSP---------------QFL--ESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK  195 (587)
Q Consensus       137 ----~~~~~~~~~~---------------~~~--~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  195 (587)
                          .........+               ...  .......++.++|||+|||.++++++|+++|++||.|.+|+|+.++
T Consensus       164 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~  243 (282)
T 3pgw_A          164 MPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR  243 (282)
T ss_pred             CCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC
Confidence                0000000000               000  0001234467899999999999999999999999999999999764


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEEcc
Q psy1534         196 DGKSRGFGTVEFDHPVEAVQSISMLNNQNLF-ERRITVRMDR  236 (587)
Q Consensus       196 ~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~a~  236 (587)
                          +|||||+|.+.++|.+|++.|||..|. |+.|+|.|++
T Consensus       244 ----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          244 ----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             ----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence                589999999999999999999999999 9999999985

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

Probab=99.96  E-value=1.5e-29  Score=255.18  Aligned_cols=173  Identities=19%  Similarity=0.221  Sum_probs=147.4

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCC-CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVG-DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G-~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....+|||+|||+++++++| ++|++|| +|.+|+|++++.+.++|||||+|.+.++|.+|++.|++..|.|++|.|.+
T Consensus       114 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          114 HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             ECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             ECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            346789999999999999999 8999999 99999999998888999999999999999999999999999999999999


Q ss_pred             cccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCC-CcHHHHHHHHHhcCC
Q psy1534         107 AVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYK-VDEKKLREVFRLAGK  185 (587)
Q Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~  185 (587)
                      +.++......                                    .......++|||+|||++ +++++|+++|++||.
T Consensus       194 a~~~~~~~~~------------------------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~  237 (292)
T 2ghp_A          194 SNPLEKSKRT------------------------------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGS  237 (292)
T ss_dssp             CCCC---------------------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSC
T ss_pred             CCCCcccccc------------------------------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCC
Confidence            8844321100                                    012334679999999999 999999999999999


Q ss_pred             eeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         186 VENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       186 i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      |..|+|+++..  +.++|||||+|.+.++|.+|+ .|||..|.|++|.|.++.++
T Consensus       238 v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          238 IEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             EEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             eeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999999987  999999999999999999999 99999999999999999875

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.96  E-value=6.9e-29  Score=241.02  Aligned_cols=193  Identities=16%  Similarity=0.234  Sum_probs=148.8

Q ss_pred             CCCCCcEEEcCCCC-CCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQG-DASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~-~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+...+|||+|||+ ++++++| ++|++||+|.+|+|++++    +|||||+|.+.++|++|++.|++..|.|++|.|.+
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45678999999999 9999999 899999999999999985    78999999999999999999999999999999999


Q ss_pred             cccccCCCCCCC-CCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcC-
Q psy1534         107 AVEDKGGRRNMG-GGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAG-  184 (587)
Q Consensus       107 a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-  184 (587)
                      +..+........ .......+.....   ..    ....  ..........++.++|||+|||+++++++|+++|++|| 
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~---~~----~~~~--~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~  177 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSP---LH----RFKK--PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG  177 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCS---SC----CCCS--TTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSC
T ss_pred             ecCccccCccccccccccccccccCc---cc----ccCC--ccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCC
Confidence            974422111000 0000000000000   00    0000  00011112345678999999999999999999999999 


Q ss_pred             CeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEEccCC
Q psy1534         185 KVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF-ERRITVRMDRVA  238 (587)
Q Consensus       185 ~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~a~~~  238 (587)
                      .|.+|+|+.+    .+|||||+|.+.++|.+|++.||+..+. |++|+|.|++++
T Consensus       178 ~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          178 VVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999663    3689999999999999999999999999 999999998764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.96  E-value=2.8e-28  Score=234.01  Aligned_cols=81  Identities=21%  Similarity=0.360  Sum_probs=74.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+.++|||+|||++++|++|+++|++||.|.+|+|++|+. ++++|||||+|.+.++|++||+.+|+..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            3568999999999999999999999999999999999985 999999999999999999999999999999999998775


Q ss_pred             cC
Q psy1534         236 RV  237 (587)
Q Consensus       236 ~~  237 (587)
                      ..
T Consensus        93 ~~   94 (213)
T 4f02_A           93 QR   94 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.96  E-value=2e-28  Score=242.61  Aligned_cols=156  Identities=23%  Similarity=0.262  Sum_probs=143.6

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++|||+|||+++|+++| ++|++||+|.+|+|.++     +|||||+|.+.++|++|++.|++..|.|++|.|.++.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~   94 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            45568999999999999999 89999999999999764     7999999999999999999999999999999999987


Q ss_pred             cccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE
Q psy1534         109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN  188 (587)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~  188 (587)
                      .                                                 .++|||+|||+.+++++|+++|+.||.|.+
T Consensus        95 ~-------------------------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~  125 (261)
T 3sde_A           95 H-------------------------------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEK  125 (261)
T ss_dssp             C-------------------------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEE
T ss_pred             c-------------------------------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEE
Confidence            2                                                 258999999999999999999999999999


Q ss_pred             EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC-CceeC---CeEEEEEEccCCC
Q psy1534         189 VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN-NQNLF---ERRITVRMDRVAD  239 (587)
Q Consensus       189 v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~-g~~~~---g~~l~v~~a~~~~  239 (587)
                      |.|+++.+|+++|||||+|.+.++|.+|+..|| +..+.   +++|.|.++....
T Consensus       126 v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          126 AVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             EEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             EEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            999999889999999999999999999999994 55555   9999999987654

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

Probab=99.96  E-value=1e-28  Score=234.21  Aligned_cols=191  Identities=17%  Similarity=0.249  Sum_probs=147.2

Q ss_pred             CCCcEEEcCCCC-CCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQG-DASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~-~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||. ++++++| ++|++||+|.+|+|++++    +|||||+|.+.++|++|++.|++..|.|++|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            357899999999 9999999 899999999999999875    6899999999999999999999999999999999988


Q ss_pred             cccCCCCCCCCC-CCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcC-Ce
Q psy1534         109 EDKGGRRNMGGG-GGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAG-KV  186 (587)
Q Consensus       109 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~i  186 (587)
                      .+.......... .....+....   ....+..      ..........++.++|||+|||..+++++|+++|++|| .|
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~---~~~r~~~------~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v  148 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNS---PLHRFKK------PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV  148 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCC---CTTSSSS------CCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCC
T ss_pred             CCCcCCCCcCCccccccccccCC---chhhccC------ccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCc
Confidence            443211110000 0000000000   0000000      00000111235678999999999999999999999999 99


Q ss_pred             eEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEEccCC
Q psy1534         187 ENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF-ERRITVRMDRVA  238 (587)
Q Consensus       187 ~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~a~~~  238 (587)
                      .+|.|+.+.    +|||||+|.+.++|.+|++.||+..+. |++|+|.|++++
T Consensus       149 ~~v~i~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          149 KGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CEEEESSTT----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             eEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            999997643    789999999999999999999999999 999999998764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.95  E-value=3.8e-27  Score=216.38  Aligned_cols=78  Identities=23%  Similarity=0.461  Sum_probs=73.5

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ++|||+|||+++++++|+++|++||.|.+|.|++++.++++|||||+|.+.++|.+|++.||+..+.|++|.|.++..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCC
Confidence            489999999999999999999999999999999999889999999999999999999999999999999999988643

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.95  E-value=1e-26  Score=214.07  Aligned_cols=80  Identities=24%  Similarity=0.423  Sum_probs=75.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      +.++|||+|||+++++++|+++|++||.|.+|.+++++ +++++|||||+|.+.++|.+|++.|++..+.|++|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            35799999999999999999999999999999999987 48999999999999999999999999999999999998865


Q ss_pred             C
Q psy1534         237 V  237 (587)
Q Consensus       237 ~  237 (587)
                      +
T Consensus        82 ~   82 (168)
T 1b7f_A           82 P   82 (168)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.95  E-value=3.3e-26  Score=210.35  Aligned_cols=79  Identities=28%  Similarity=0.488  Sum_probs=75.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|+.||.|.+|.+++++ +++++|||||+|.+.++|.+|++.||+..+.|++|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            5799999999999999999999999999999999998 599999999999999999999999999999999999988653

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.95  E-value=2.5e-25  Score=223.03  Aligned_cols=83  Identities=14%  Similarity=0.350  Sum_probs=75.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHH----HHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLR----EVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRI  230 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  230 (587)
                      +..+.++|||+|||+++++++|+    ++|++||.|.+|+|++  +++++|||||+|.+.++|.+||+.||+..|.|+.|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            34567899999999999999977    8999999999999886  57889999999999999999999999999999999


Q ss_pred             EEEEccCCC
Q psy1534         231 TVRMDRVAD  239 (587)
Q Consensus       231 ~v~~a~~~~  239 (587)
                      +|.+++...
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999986554

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

Probab=99.94  E-value=3.6e-26  Score=219.60  Aligned_cols=79  Identities=25%  Similarity=0.481  Sum_probs=71.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|+.||.|.+|+|++++ +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            5799999999999999999999999999999999988 589999999999999999999999999999999999976543

>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=99.94  E-value=6.6e-26  Score=214.28  Aligned_cols=81  Identities=20%  Similarity=0.372  Sum_probs=74.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|.+||+. ++..+.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            3468999999999999999999999999999999999985 89999999999999999999976 999999999999886


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      ...
T Consensus        90 ~~~   92 (196)
T 1l3k_A           90 VSR   92 (196)
T ss_dssp             CC-
T ss_pred             cCc
Confidence            543

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.94  E-value=1.2e-25  Score=213.63  Aligned_cols=78  Identities=27%  Similarity=0.365  Sum_probs=72.6

Q ss_pred             CCcEEEEecCC-CCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp-~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ++++|||+||| +.+++++|+++|++||.|.+|+|++++    +|||||+|.+.++|++||+.|||..+.|++|.|.+++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            46799999999 899999999999999999999998863    7999999999999999999999999999999999987


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      .+.
T Consensus        79 ~~~   81 (205)
T 3tyt_A           79 QPA   81 (205)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            554

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.94  E-value=1.3e-25  Score=208.15  Aligned_cols=68  Identities=28%  Similarity=0.413  Sum_probs=64.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCC---CcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG---KSRGFGTVEFDHPVEAVQSISMLNNQNLF  226 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g---~~~g~afV~f~~~~~A~~Al~~l~g~~~~  226 (587)
                      .++|||+|||+++++++|+++|++||.|.+|+|++++.+   +++|||||+|.+.++|++|++.||+..+.
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~   73 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVL   73 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCC
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEc
Confidence            579999999999999999999999999999999999864   89999999999999999999999998765

>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=99.93  E-value=6.1e-25  Score=213.14  Aligned_cols=80  Identities=23%  Similarity=0.334  Sum_probs=74.6

Q ss_pred             CCCCcEEEEecCCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .++.++|||+|||+ ++++++|+++|++||.|.+|+|++++    +|||||+|.+.++|++|++.||+..+.|++|.|.+
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45678999999999 99999999999999999999999875    78999999999999999999999999999999999


Q ss_pred             ccCCC
Q psy1534         235 DRVAD  239 (587)
Q Consensus       235 a~~~~  239 (587)
                      ++...
T Consensus       107 a~~~~  111 (229)
T 2adc_A          107 SKHQN  111 (229)
T ss_dssp             CSCCC
T ss_pred             ecCcc
Confidence            87654

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

Probab=99.93  E-value=1.2e-24  Score=206.08  Aligned_cols=77  Identities=23%  Similarity=0.373  Sum_probs=72.4

Q ss_pred             CcEEEEecCCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+ ++++++|+++|++||.|.+|++++++    +|||||+|.+.++|.+|++.||+..+.|++|.|.++..
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~   78 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   78 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecC
Confidence            47999999999 99999999999999999999999875    78999999999999999999999999999999999876


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      ..
T Consensus        79 ~~   80 (198)
T 1qm9_A           79 QN   80 (198)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=99.93  E-value=1e-24  Score=201.50  Aligned_cols=70  Identities=11%  Similarity=0.196  Sum_probs=66.2

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC------CCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK------GDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~------~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .+|+|+|||.++|+++|+++|++||.|..+.+..+      +|+|||+|++.++|++|++.|||..|+|++|+|.+
T Consensus        95 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  170 (172)
T 2g4b_A           95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  170 (172)
T ss_dssp             TCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            49999999999999999999999999999999665      47999999999999999999999999999999985

>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=99.92  E-value=1.7e-25  Score=205.86  Aligned_cols=75  Identities=29%  Similarity=0.517  Sum_probs=69.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .++|||+|||+++++++|+++|++||.|.+|.|++++. |+++|||||+|.+.++|++|++.  +..+.|+.|.|.++
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            57999999999999999999999999999999999974 99999999999999999999984  67889998877664

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.92  E-value=4.9e-24  Score=201.71  Aligned_cols=71  Identities=11%  Similarity=0.191  Sum_probs=67.0

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC------CCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK------GDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~------~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .++|||.|||+++|+++|+++|++||.|..+.+..+      +|+|||+|.+.++|++||+.|||..|+|++|+|.+
T Consensus       114 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            469999999999999999999999999999999765      58999999999999999999999999999999986

>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=99.92  E-value=2.2e-25  Score=206.80  Aligned_cols=82  Identities=16%  Similarity=0.269  Sum_probs=70.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|+.||.+..+.+.....++++|||||+|.+.++|.+|+ .||+..+.|++|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecC
Confidence            44578999999999999999999999999876633333335888999999999999999999 59999999999999887


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      ...
T Consensus        89 ~~~   91 (175)
T 1fje_B           89 KGR   91 (175)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            543

>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=99.90  E-value=2.6e-23  Score=205.80  Aligned_cols=75  Identities=25%  Similarity=0.401  Sum_probs=69.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++|+++|+++|+.||.|.+|.|.++     +|||||+|.+.++|.+|+..||+..+.|++|.|.++
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            345689999999999999999999999999999999764     799999999999999999999999999999999774

>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=99.88  E-value=2.3e-22  Score=183.29  Aligned_cols=150  Identities=20%  Similarity=0.278  Sum_probs=114.9

Q ss_pred             EEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccC
Q psy1534          60 YVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFG  139 (587)
Q Consensus        60 ~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (587)
                      +++|+.+.. +++|||||+|.+.++|++|++.+++....+..+.+............                  ..   
T Consensus         2 ~~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~---   59 (158)
T 2kn4_A            2 QYKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG------------------SH---   59 (158)
T ss_dssp             EEEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECC------------------CC---
T ss_pred             cEEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccccc------------------cc---
Confidence            567777754 58999999999999999999988764433333333322211000000                  00   


Q ss_pred             CCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHH
Q psy1534         140 NTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSIS  218 (587)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~  218 (587)
                               ...........++|||+|||+++++++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++||+
T Consensus        60 ---------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~  130 (158)
T 2kn4_A           60 ---------HHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD  130 (158)
T ss_dssp             ---------CSSCCCCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHH
T ss_pred             ---------ccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHH
Confidence                     00001123346899999999999999999999999999999999997 49999999999999999999999


Q ss_pred             HhCCceeCCeEEEEEEccCCCC
Q psy1534         219 MLNNQNLFERRITVRMDRVADR  240 (587)
Q Consensus       219 ~l~g~~~~g~~l~v~~a~~~~~  240 (587)
                      .||+..|.|++|.|+++++...
T Consensus       131 ~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A          131 AMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             HSTTEESSSSEEEEEEECCSSC
T ss_pred             HhCCCEECCeEEEEEECCCCCC
Confidence            9999999999999999987653

>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=99.86  E-value=6.4e-22  Score=169.94  Aligned_cols=80  Identities=14%  Similarity=0.277  Sum_probs=73.2

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +...+|||+|||+++++++| ++|++||+|.+|+|++|+. .+||||||+|.+.++|++||+.|++..|.|++|+|.++.
T Consensus         3 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45678999999999999999 8999999999999999863 489999999999999999999999999999999999987


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus        82 ~~   83 (115)
T 4f25_A           82 SR   83 (115)
T ss_dssp             CC
T ss_pred             Cc
Confidence            44

>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=99.84  E-value=7.8e-21  Score=171.42  Aligned_cols=139  Identities=22%  Similarity=0.331  Sum_probs=113.1

Q ss_pred             CCcceEEEEEECCHHHHHHHHHHh-CCceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChh
Q psy1534          69 GKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQ  147 (587)
Q Consensus        69 g~skG~aFV~F~~~e~A~~Al~~l-~g~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (587)
                      ...+|+++|+|.+.++|++|++.+ |+..+.| +|.+.++..+......                  ...         .
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~------------------~~~---------~   61 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEG------------------SHH---------H   61 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECS------------------SSS---------C
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccc------------------ccc---------c
Confidence            356899999999999999999999 9999999 9999988733210000                  000         0


Q ss_pred             hhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy1534         148 FLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE  227 (587)
Q Consensus       148 ~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  227 (587)
                      ..........+.++|||+|||+++++++|+++|++||.|.+|.|+++    ++|||||+|.+.++|.+|++.||+..|.|
T Consensus        62 ~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g  137 (150)
T 2i2y_A           62 HHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCG  137 (150)
T ss_dssp             CCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSS
T ss_pred             cccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            00001113345689999999999999999999999999999999987    58999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q psy1534         228 RRITVRMDRVAD  239 (587)
Q Consensus       228 ~~l~v~~a~~~~  239 (587)
                      ++|+|+++.++.
T Consensus       138 ~~l~v~~a~~~~  149 (150)
T 2i2y_A          138 CRVRVELSNGEK  149 (150)
T ss_dssp             SCCEEEECCCCC
T ss_pred             eEEEEEEcCCCC
Confidence            999999988764

>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=99.81  E-value=1.1e-19  Score=151.25  Aligned_cols=79  Identities=14%  Similarity=0.340  Sum_probs=75.5

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....+|||+|||+++|+++| ++|++||+|.+|+|++|+ +|++||||||+|.+.++|++|++.|||..|.|++|+|.++
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45678999999999999999 899999999999999997 8999999999999999999999999999999999999998


Q ss_pred             c
Q psy1534         108 V  108 (587)
Q Consensus       108 ~  108 (587)
                      .
T Consensus        97 k   97 (99)
T 4fxv_A           97 R   97 (99)
T ss_dssp             C
T ss_pred             e
Confidence            6

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.79  E-value=4.6e-19  Score=147.51  Aligned_cols=80  Identities=29%  Similarity=0.428  Sum_probs=76.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+++|||+|||+++|+++|+++|++||.|.+|+|++|+. |+++|||||+|.+.++|++|++.|||..|.|++|+|++|+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            467999999999999999999999999999999999985 9999999999999999999999999999999999999987


Q ss_pred             C
Q psy1534         237 V  237 (587)
Q Consensus       237 ~  237 (587)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

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

Probab=99.79  E-value=3.4e-19  Score=151.21  Aligned_cols=82  Identities=21%  Similarity=0.178  Sum_probs=77.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      +++.++|||+|||+++++++| ++|++||+|++|+|++|+ ++++||||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            456789999999999999999 899999999999999997 899999999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +.+.
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8743

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.76  E-value=8.7e-19  Score=144.17  Aligned_cols=79  Identities=18%  Similarity=0.261  Sum_probs=73.7

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCC--eEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCc----eeCCeE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGD--VTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRF----ETKGRK  101 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~--V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~----~l~gr~  101 (587)
                      ....+|||+|||+++|+++| ++|++||.  |.+|+|++|+ +|++||||||+|.+.++|++|++.||+.    .|.||+
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            46689999999999999999 89999995  6799999997 8999999999999999999999999986    599999


Q ss_pred             EEEEecc
Q psy1534         102 LVIKEAV  108 (587)
Q Consensus       102 i~V~~a~  108 (587)
                      |.|.++.
T Consensus        87 i~V~~Ak   93 (95)
T 2lkz_A           87 IGVDFAK   93 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEEcc
Confidence            9999986

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

Probab=99.75  E-value=6e-18  Score=143.48  Aligned_cols=83  Identities=27%  Similarity=0.336  Sum_probs=78.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ++.++|||+|||+++++++|+++|++||.|.+|+|++|+. ++++|||||+|.+.++|++||+.||+..+.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4567999999999999999999999999999999999986 999999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            6543

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.75  E-value=4.2e-18  Score=145.98  Aligned_cols=81  Identities=26%  Similarity=0.462  Sum_probs=75.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .++|||+|||+++++++|+++|++||.|.+|+|++++. .++|||||+|.+.++|++||+.||+..|.|++|.|.++..+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            46899999999999999999999999999999999864 57999999999999999999999999999999999998775


Q ss_pred             CC
Q psy1534         239 DR  240 (587)
Q Consensus       239 ~~  240 (587)
                      ..
T Consensus        84 ~~   85 (115)
T 4f25_A           84 KE   85 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.75  E-value=6e-19  Score=144.43  Aligned_cols=79  Identities=19%  Similarity=0.310  Sum_probs=73.2

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCC-CeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhC-CceeCCeEEEEEecc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVG-DVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMH-RFETKGRKLVIKEAV  108 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G-~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~-g~~l~gr~i~V~~a~  108 (587)
                      ++|||+|||+++|+++| ++|++|| +|++|+|++|+ ++++||||||+|.+.++|++|++.++ +..|.|++|+|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            68999999999999999 8999999 89999999997 89999999999999999999999874 578999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      +++
T Consensus        82 ~~~   84 (91)
T 2lxi_A           82 PKP   84 (91)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            553

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=5e-18  Score=140.28  Aligned_cols=83  Identities=16%  Similarity=0.362  Sum_probs=78.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ++..++|||+|||.++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            457789999999999999999 899999999999999997 899999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        82 a~~~~   86 (95)
T 2dnz_A           82 VTERL   86 (95)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            98554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1e-17  Score=140.72  Aligned_cols=84  Identities=15%  Similarity=0.241  Sum_probs=78.7

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..+...+|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            3456789999999999999999 899999999999999996 99999999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++.++.
T Consensus        91 ~a~~~~   96 (103)
T 2cq0_A           91 WAKPST   96 (103)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            998554

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.75  E-value=1.9e-18  Score=141.39  Aligned_cols=82  Identities=23%  Similarity=0.406  Sum_probs=75.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcC-CeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEEEc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAG-KVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML-NNQNLFERRITVRMD  235 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G-~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~a  235 (587)
                      +++|||+|||+++||++|+++|++|| .|.+|+|++|+. ++++|||||+|.+.++|++||+.+ ++..+.|++|.|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 799999999985 999999999999999999999987 456799999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      .++.+
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1e-17  Score=139.87  Aligned_cols=84  Identities=17%  Similarity=0.242  Sum_probs=78.9

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ......++|||+|||+++++++| ++|++||+|.+|+|+++++++++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34457789999999999999999 89999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccc
Q psy1534         106 EAVED  110 (587)
Q Consensus       106 ~a~~~  110 (587)
                      ++.++
T Consensus        92 ~a~~~   96 (100)
T 2do4_A           92 ISNSG   96 (100)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            99854

>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=99.74  E-value=9.1e-18  Score=141.50  Aligned_cols=85  Identities=21%  Similarity=0.312  Sum_probs=79.2

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC---eEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG---RKL  102 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g---r~i  102 (587)
                      ...+..++|||+|||+++++++| ++|++||+|.+|+|+++++++++|||||+|.+.++|++|++.||+..+.+   ++|
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34456789999999999999999 89999999999999999999999999999999999999999999999998   999


Q ss_pred             EEEeccccc
Q psy1534         103 VIKEAVEDK  111 (587)
Q Consensus       103 ~V~~a~~~~  111 (587)
                      +|.++..+.
T Consensus        90 ~V~~a~~~~   98 (105)
T 2dnh_A           90 VVKFADTDK   98 (105)
T ss_dssp             EEEESCSSC
T ss_pred             EEEECccCc
Confidence            999998554

>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=99.74  E-value=1.2e-17  Score=143.33  Aligned_cols=86  Identities=13%  Similarity=0.240  Sum_probs=79.7

Q ss_pred             cCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          26 ETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        26 ~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      ....+..++|||+|||+++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344456789999999999999999 899999999999999997 999999999999999999999999999999999999


Q ss_pred             EEeccccc
Q psy1534         104 IKEAVEDK  111 (587)
Q Consensus       104 V~~a~~~~  111 (587)
                      |.++.++.
T Consensus        99 V~~a~~~~  106 (115)
T 2cpz_A           99 VQLKRSKN  106 (115)
T ss_dssp             EECCCCSC
T ss_pred             EEEcCCCC
Confidence            99998554

>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=99.74  E-value=8e-18  Score=140.22  Aligned_cols=83  Identities=22%  Similarity=0.221  Sum_probs=78.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ....++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456789999999999999999 899999999999999997 999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98654

>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=99.74  E-value=6.5e-18  Score=137.11  Aligned_cols=81  Identities=19%  Similarity=0.235  Sum_probs=74.6

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +...+|||+|||.++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35678999999999999999 899999999999999996 9999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            743

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.4e-17  Score=139.89  Aligned_cols=84  Identities=19%  Similarity=0.263  Sum_probs=78.5

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      .......+|||+|||+++++++| ++|++||+|.+|+|+++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34457789999999999999999 89999999999999999 99999999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++.++.
T Consensus        89 ~a~~~~   94 (103)
T 2d9p_A           89 LAQRKE   94 (103)
T ss_dssp             ECSSCC
T ss_pred             Eecccc
Confidence            998554

>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=99.74  E-value=6.5e-18  Score=142.39  Aligned_cols=86  Identities=19%  Similarity=0.239  Sum_probs=79.9

Q ss_pred             cCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          26 ETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        26 ~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      ....+...+|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            344567789999999999999999 899999999999999997 999999999999999999999999999999999999


Q ss_pred             EEeccccc
Q psy1534         104 IKEAVEDK  111 (587)
Q Consensus       104 V~~a~~~~  111 (587)
                      |.++..++
T Consensus        89 v~~a~~~~   96 (105)
T 1x5u_A           89 VNKASAHN   96 (105)
T ss_dssp             EEETTTTS
T ss_pred             EEECCCCC
Confidence            99998554

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.74  E-value=1.2e-18  Score=153.76  Aligned_cols=125  Identities=22%  Similarity=0.252  Sum_probs=79.7

Q ss_pred             eEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhcc
Q psy1534          73 GSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESL  152 (587)
Q Consensus        73 G~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (587)
                      -++|++|++...|.+|++.+++....++.- +.+..+                                           
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~~-------------------------------------------   40 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGRP-------------------------------------------   40 (135)
T ss_dssp             -------------------------------CCSCCS-------------------------------------------
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcCCC-------------------------------------------
Confidence            367888888888899998888765544321 000000                                           


Q ss_pred             CCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         153 GINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       153 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      .......++|||+|||+++++++|+++|++||.|..|.|++++. ++++|||||+|.+.++|++||+.||+..|.|++|+
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~  120 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  120 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            00122357999999999999999999999999999999999874 89999999999999999999999999999999999


Q ss_pred             EEEccCCCCC
Q psy1534         232 VRMDRVADRL  241 (587)
Q Consensus       232 v~~a~~~~~~  241 (587)
                      |++++.....
T Consensus       121 V~~a~~~~~~  130 (135)
T 2lea_A          121 VQMARYGRPP  130 (135)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=9.8e-18  Score=138.22  Aligned_cols=82  Identities=22%  Similarity=0.267  Sum_probs=76.7

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34467789999999999999999 899999999999999997 7999999999999999999999999999999999999


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      .+++
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=139.37  Aligned_cols=83  Identities=24%  Similarity=0.365  Sum_probs=77.5

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      .....++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++ |++..|.|++|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            3457789999999999999999 899999999999999997 89999999999999999999998 99999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++.++.
T Consensus        85 ~a~~~~   90 (99)
T 2dgs_A           85 RAEPRD   90 (99)
T ss_dssp             ECCCCC
T ss_pred             ECCCCc
Confidence            998554

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.8e-18  Score=140.17  Aligned_cols=82  Identities=18%  Similarity=0.262  Sum_probs=77.4

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEE-EEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYV-EILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v-~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      +..++|||+|||+++++++| ++|++||+|.+| +|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            46789999999999999999 899999999999 999995 999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +.++.
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            98554

>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=99.74  E-value=1.3e-17  Score=133.98  Aligned_cols=78  Identities=21%  Similarity=0.239  Sum_probs=74.5

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      .+|||+|||.++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..+.|++|+|.++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            47999999999999999 899999999999999996 9999999999999999999999999999999999999999854

>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=99.73  E-value=6.4e-18  Score=136.49  Aligned_cols=80  Identities=25%  Similarity=0.290  Sum_probs=75.7

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            457789999999999999999 899999999999999995 999999999999999999999999999999999999998


Q ss_pred             cc
Q psy1534         107 AV  108 (587)
Q Consensus       107 a~  108 (587)
                      +.
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.3e-17  Score=137.67  Aligned_cols=82  Identities=18%  Similarity=0.244  Sum_probs=76.8

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ..++..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999 899999999999999997 8999999999999999999999999999999999999


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      .++.
T Consensus        90 ~~a~   93 (95)
T 2cqc_A           90 SGPS   93 (95)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9886

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=9.4e-18  Score=140.60  Aligned_cols=84  Identities=24%  Similarity=0.259  Sum_probs=78.6

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..+..++|||+|||+++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3457789999999999999999 899999999999999996 89999999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..+.
T Consensus        88 ~a~~~~   93 (102)
T 2cqb_A           88 LAKPMR   93 (102)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998554

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=7e-18  Score=141.67  Aligned_cols=85  Identities=24%  Similarity=0.237  Sum_probs=78.8

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .......+|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34456789999999999999999 899999999999999997 7999999999999999999999999999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus        88 ~~a~~~~   94 (103)
T 2dnm_A           88 QVARYGR   94 (103)
T ss_dssp             EECSSCC
T ss_pred             EECCcCC
Confidence            9998543

>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=99.73  E-value=1.1e-17  Score=143.54  Aligned_cols=82  Identities=17%  Similarity=0.307  Sum_probs=77.8

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ....+|||+|||+++++++| ++|++||+|++|+|+++++++++|||||+|.+.++|++|++.||+..|.|++|+|.++.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46689999999999999999 89999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      ++.
T Consensus        85 ~~~   87 (116)
T 2fy1_A           85 KPS   87 (116)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            554

>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=99.73  E-value=9.6e-18  Score=138.56  Aligned_cols=81  Identities=20%  Similarity=0.297  Sum_probs=76.4

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+..++|||+|||+++++++| ++|++||+|++|+|+++++++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3456689999999999999999 899999999999999998899999999999999999999999999999999999998


Q ss_pred             cc
Q psy1534         107 AV  108 (587)
Q Consensus       107 a~  108 (587)
                      +.
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=6.6e-18  Score=141.56  Aligned_cols=86  Identities=21%  Similarity=0.273  Sum_probs=79.5

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+..++|||+|||+++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34457789999999999999999 899999999999999997 8999999999999999999999999999999999999


Q ss_pred             EecccccC
Q psy1534         105 KEAVEDKG  112 (587)
Q Consensus       105 ~~a~~~~~  112 (587)
                      .++.++..
T Consensus        87 ~~a~~~~~   94 (102)
T 1x5s_A           87 DQAGKSSD   94 (102)
T ss_dssp             EEEECCCC
T ss_pred             EECCCCCC
Confidence            99986543

>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=99.73  E-value=1.7e-17  Score=151.90  Aligned_cols=141  Identities=19%  Similarity=0.257  Sum_probs=79.1

Q ss_pred             EEECCHHHHHHHHHHhCCceeC--CeEEEEEecccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCC
Q psy1534          77 VEFQSPDLVRKAVNKMHRFETK--GRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGI  154 (587)
Q Consensus        77 V~F~~~e~A~~Al~~l~g~~l~--gr~i~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (587)
                      .+|++.++|+.|+..|++....  |+.+.+.+..+.....             +....       +   ..+........
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~-------------~~~~~-------~---s~~~~~~~~~~   67 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHS-------------YERVR-------N---EDDDELEPGPQ   67 (165)
T ss_dssp             ------------------------------------------------------------------------------CC
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccC-------------ccccc-------c---CCCCCCCCCCC
Confidence            7999999999999998875554  5555444432111000             00000       0   00000001111


Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|++++ ++.++|||||+|.+.++|++||+.||+..|.|++|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            23456899999999999999999999999999999999997 49999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q psy1534         234 MDRVADR  240 (587)
Q Consensus       234 ~a~~~~~  240 (587)
                      ++..+..
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9987664

>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=99.73  E-value=2.6e-17  Score=133.57  Aligned_cols=81  Identities=25%  Similarity=0.365  Sum_probs=75.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      +.++|||+|||+++++++|+++|++||.|.+|.|++++ .++++|||||+|.+.++|++|++.||+..+.|++|+|++++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            46799999999999999999999999999999999997 59999999999999999999999999999999999999987


Q ss_pred             CC
Q psy1534         237 VA  238 (587)
Q Consensus       237 ~~  238 (587)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            65

>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=99.72  E-value=2.6e-17  Score=140.16  Aligned_cols=85  Identities=20%  Similarity=0.330  Sum_probs=79.0

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhC------CceeC
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMH------RFETK   98 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~------g~~l~   98 (587)
                      ......++|||+|||+++++++| ++|++||+|.+|+|++|+ +++++|||||+|.+.++|++|++.||      +..|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            44557789999999999999999 899999999999999997 89999999999999999999999999      99999


Q ss_pred             CeEEEEEeccccc
Q psy1534          99 GRKLVIKEAVEDK  111 (587)
Q Consensus        99 gr~i~V~~a~~~~  111 (587)
                      |++|+|.++..+.
T Consensus        90 g~~l~v~~a~~~~  102 (111)
T 1x4h_A           90 GRQLKVDLAVTRD  102 (111)
T ss_dssp             SCEEEEECCCCCC
T ss_pred             CEEEEEEECCCCc
Confidence            9999999998553

>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=99.72  E-value=3.5e-17  Score=131.49  Aligned_cols=80  Identities=25%  Similarity=0.429  Sum_probs=76.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .+|||+|||+++++++|+++|++||.|.+|.+++++. ++++|||||+|.+.++|++|++.||+..+.|++|+|++++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            5899999999999999999999999999999999964 999999999999999999999999999999999999999876


Q ss_pred             C
Q psy1534         239 D  239 (587)
Q Consensus       239 ~  239 (587)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.72  E-value=1.9e-17  Score=140.06  Aligned_cols=84  Identities=18%  Similarity=0.213  Sum_probs=77.6

Q ss_pred             ccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          25 IETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        25 ~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      .+...+...+|||+|||+++++++| ++|++||+|.+|+|+++++++++|||||+|.+.++|++|++.||+..|.|++|+
T Consensus        22 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           22 GGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             --CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3445567789999999999999999 899999999999999999999999999999999999999999999999999999


Q ss_pred             EEecc
Q psy1534         104 IKEAV  108 (587)
Q Consensus       104 V~~a~  108 (587)
                      |.++.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99875

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.72  E-value=4e-17  Score=139.97  Aligned_cols=85  Identities=18%  Similarity=0.232  Sum_probs=79.1

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .......+|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34457789999999999999999 899999999999999996 9999999999999999999999999999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++.++.
T Consensus        90 ~~a~~~~   96 (115)
T 2dgo_A           90 NWATRKP   96 (115)
T ss_dssp             EESSCCC
T ss_pred             EEccCCC
Confidence            9998554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=3.3e-17  Score=137.54  Aligned_cols=83  Identities=18%  Similarity=0.179  Sum_probs=76.7

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+...+|||+|||+++++++| ++|++|| |.+|+|++++ +++++|||||+|.+.++|++|+ .||+..|.|++|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            44456789999999999999999 8999997 9999999997 8999999999999999999999 89999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus        88 ~~a~~~~   94 (103)
T 2dng_A           88 DIAEGRK   94 (103)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9998554

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.72  E-value=1.8e-17  Score=138.00  Aligned_cols=82  Identities=17%  Similarity=0.312  Sum_probs=77.1

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEE--------EEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCce
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTY--------VEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFE   96 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~--------v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~   96 (587)
                      ..++...+|||+|||+++++++| ++|++||.|.+        |+|++++ +|+++|||||+|.+.++|++|++.||+..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            45567889999999999999999 89999999999        9999996 89999999999999999999999999999


Q ss_pred             eCCeEEEEEecc
Q psy1534          97 TKGRKLVIKEAV  108 (587)
Q Consensus        97 l~gr~i~V~~a~  108 (587)
                      |.|++|+|.++.
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999874

>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=99.72  E-value=7e-18  Score=144.72  Aligned_cols=104  Identities=16%  Similarity=0.221  Sum_probs=92.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ++..++|||+|||+++++++| ++|++||+|.+|+|+++  +.++|||||+|.+.++|++|++.||+..|.|+.|.|.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            456789999999999999999 89999999999999976  455899999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCC
Q psy1534         108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGK  185 (587)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~  185 (587)
                      ..+..                                               .    .+++...++++|+++|++||.
T Consensus        83 ~~~~~-----------------------------------------------~----~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           83 NANRA-----------------------------------------------F----QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CHHHH-----------------------------------------------T----TTSCHHHHHHHHHHHHHHHCC
T ss_pred             cCChh-----------------------------------------------h----hhhhHhHhHHHHHHHHHHhCC
Confidence            84431                                               0    456778899999999999984

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.6e-17  Score=136.80  Aligned_cols=82  Identities=16%  Similarity=0.248  Sum_probs=76.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC----CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD----TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~----~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      +..++|||+|||+++++++| ++|++||+|.+|+|++++    +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            56789999999999999999 899999999999999985    3489999999999999999999999999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++.++.
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9998554

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=4.3e-17  Score=136.02  Aligned_cols=83  Identities=20%  Similarity=0.452  Sum_probs=79.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+++++++++|||||+|.+.++|++|++.||+..+.|++|+|.+++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   94 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN   94 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            45689999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ++.
T Consensus        95 ~~~   97 (100)
T 2do4_A           95 SGP   97 (100)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            765

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.72  E-value=1e-17  Score=137.77  Aligned_cols=80  Identities=18%  Similarity=0.328  Sum_probs=74.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCC--eeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCc----eeCCeEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGK--VENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQ----NLFERRI  230 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~--i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~----~~~g~~l  230 (587)
                      .-.+|||+|||+++|+++|+++|++||.  |.+|+|++|+. ++++|||||+|.+.++|++||+.||+.    .|.||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            3579999999999999999999999995  67999999985 999999999999999999999999986    5899999


Q ss_pred             EEEEccC
Q psy1534         231 TVRMDRV  237 (587)
Q Consensus       231 ~v~~a~~  237 (587)
                      .|++|+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999875

>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=99.72  E-value=1.9e-17  Score=137.06  Aligned_cols=80  Identities=25%  Similarity=0.323  Sum_probs=75.9

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      .++|||+|||.++++++| ++|++||+|.+|+|++++ +|+++|||||+|.+.++|++|++.||+..|.|++|+|.++..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            478999999999999999 899999999999999996 899999999999999999999999999999999999999985


Q ss_pred             cc
Q psy1534         110 DK  111 (587)
Q Consensus       110 ~~  111 (587)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.7e-17  Score=140.04  Aligned_cols=81  Identities=14%  Similarity=0.227  Sum_probs=76.4

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            45578999999999999999 899999999999999997 8999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      ..+
T Consensus       101 ~~~  103 (106)
T 1p27_B          101 FVR  103 (106)
T ss_dssp             EES
T ss_pred             cCC
Confidence            854

>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=99.72  E-value=1.7e-17  Score=140.40  Aligned_cols=86  Identities=16%  Similarity=0.402  Sum_probs=79.6

Q ss_pred             ccCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q psy1534          25 IETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL  102 (587)
Q Consensus        25 ~~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i  102 (587)
                      .+...+..++|||+|||.++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.|++..|.|++|
T Consensus        19 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           19 LQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             SCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             cccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3455667789999999999999999 899999999999999996 89999999999999999999999999999999999


Q ss_pred             EEEecccc
Q psy1534         103 VIKEAVED  110 (587)
Q Consensus       103 ~V~~a~~~  110 (587)
                      +|.++.++
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            99998744

>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=99.72  E-value=1.9e-17  Score=140.84  Aligned_cols=85  Identities=16%  Similarity=0.230  Sum_probs=78.4

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+...+|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            33456678999999999999999 899999999999999996 9999999999999999999999999999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus       101 ~~a~~~~  107 (110)
T 1oo0_B          101 DWCFVKG  107 (110)
T ss_dssp             EESEESS
T ss_pred             EEcccCC
Confidence            9998543

>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=99.72  E-value=2.6e-17  Score=138.39  Aligned_cols=83  Identities=11%  Similarity=0.169  Sum_probs=76.6

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-C-CCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-T-GKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~-g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      ...+...+|||+|||+++++++| ++|++|| |.+|+|++++ + ++++|||||+|.+.++|++|| .||+..|.|++|+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   87 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEE
Confidence            34456789999999999999999 8999999 9999999997 5 999999999999999999999 9999999999999


Q ss_pred             EEeccccc
Q psy1534         104 IKEAVEDK  111 (587)
Q Consensus       104 V~~a~~~~  111 (587)
                      |.++..+.
T Consensus        88 V~~a~~~~   95 (104)
T 1wi8_A           88 VDVADQAQ   95 (104)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99998654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.9e-17  Score=138.89  Aligned_cols=85  Identities=26%  Similarity=0.344  Sum_probs=78.9

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeC-C-CCCcceEEEEEECCHHHHHHHHHHh-CCceeCCeEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILND-D-TGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKL  102 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d-~-~g~skG~aFV~F~~~e~A~~Al~~l-~g~~l~gr~i  102 (587)
                      ...+...+|||+|||+++++++| ++|++||+|++|+|+++ + +++++|||||+|.+.++|++|++.| |+..|.|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34457789999999999999999 89999999999999999 4 9999999999999999999999999 9999999999


Q ss_pred             EEEeccccc
Q psy1534         103 VIKEAVEDK  111 (587)
Q Consensus       103 ~V~~a~~~~  111 (587)
                      +|.++..+.
T Consensus        90 ~v~~a~~~~   98 (107)
T 2cph_A           90 VLEWADSEV   98 (107)
T ss_dssp             EEEECCCCC
T ss_pred             EEEeCCCCC
Confidence            999998554

>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=99.72  E-value=5.1e-17  Score=135.31  Aligned_cols=85  Identities=25%  Similarity=0.420  Sum_probs=79.7

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|++++ .++++|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            446899999999999999999999999999999999998 5999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      .++...
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            887643

>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=99.71  E-value=6.6e-17  Score=135.66  Aligned_cols=84  Identities=19%  Similarity=0.266  Sum_probs=77.1

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ......++|||+|||+++++++| ++|++||+|.+|+|++++.+ ++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34457789999999999999999 89999999999999998755 89999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..+.
T Consensus        89 ~a~~~~   94 (103)
T 2cq3_A           89 NATARV   94 (103)
T ss_dssp             ECCSSC
T ss_pred             EcccCC
Confidence            998554

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=2.2e-17  Score=138.86  Aligned_cols=84  Identities=12%  Similarity=0.133  Sum_probs=78.4

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-Hhccc-CCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCce-eCCeEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLST-VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE-TKGRKLVI  104 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~-~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~-l~gr~i~V  104 (587)
                      ......+|||+|||+++++++| ++|++ ||+|.+|+|+++++++++|||||+|.+.++|++|++.|++.. |.|++|+|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            3456789999999999999999 89999 999999999999999999999999999999999999999999 99999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++.++.
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9998554

>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=99.71  E-value=3.5e-18  Score=139.71  Aligned_cols=78  Identities=14%  Similarity=0.263  Sum_probs=70.5

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCC--CeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVG--DVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G--~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .+|||+|||+++++++| ++|++||  +|.+|+|++|+ +|++||||||+|.+.++|++|++.||+..|.|++|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            47999999999999999 8999999  99999999997 99999999999999999999999999999999999999998


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=4.7e-17  Score=134.39  Aligned_cols=84  Identities=26%  Similarity=0.446  Sum_probs=79.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ++.++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            3468999999999999999999999999999999999985 999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      ..+..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=9e-18  Score=140.53  Aligned_cols=79  Identities=23%  Similarity=0.183  Sum_probs=74.7

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....++|||+|||+++|+++| ++|++||+|.+|+|++|+++++||||||+|.+.++|++|++ +++..|.|++|.|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            345689999999999999999 89999999999999999889999999999999999999998 8999999999999987


Q ss_pred             c
Q psy1534         108 V  108 (587)
Q Consensus       108 ~  108 (587)
                      .
T Consensus        87 ~   87 (103)
T 1s79_A           87 D   87 (103)
T ss_dssp             H
T ss_pred             h
Confidence            7

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=8.7e-17  Score=137.59  Aligned_cols=82  Identities=21%  Similarity=0.242  Sum_probs=77.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .+..++|||+|||+++++++| ++|++||+|++|+|+++++++++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            356789999999999999999 8999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      ...
T Consensus        92 ~~~   94 (114)
T 2do0_A           92 ERA   94 (114)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            743

>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=99.71  E-value=4.8e-17  Score=139.47  Aligned_cols=86  Identities=26%  Similarity=0.432  Sum_probs=80.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .+..++|||+|||+++++++|+++|++||.|.+|+|++++ +++++|||||+|.+.++|++||+.||+..|.|++|+|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999998 499999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      ++++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9877643

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=3.6e-17  Score=145.27  Aligned_cols=85  Identities=20%  Similarity=0.318  Sum_probs=78.7

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ......++|||+|||.++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456679999999999999999 899999999999999997 8999999999999999999999999999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus       117 ~~a~~~~  123 (139)
T 1u6f_A          117 ALAASGH  123 (139)
T ss_dssp             EESSCCC
T ss_pred             EECCCCC
Confidence            9998554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.8e-17  Score=136.51  Aligned_cols=86  Identities=23%  Similarity=0.340  Sum_probs=79.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            3456899999999999999999999999999999999997 499999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      +.++...
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9877643

>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=99.71  E-value=5.3e-17  Score=136.26  Aligned_cols=83  Identities=14%  Similarity=0.168  Sum_probs=75.9

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....++|||+|||+++++++| ++|++||+|++|+|++++.. ++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            3456789999999999999999 89999999999999998643 689999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        90 a~~~~   94 (103)
T 2cqi_A           90 ATTPS   94 (103)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            98554

>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=99.71  E-value=5.4e-17  Score=136.72  Aligned_cols=85  Identities=21%  Similarity=0.341  Sum_probs=79.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC---eEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE---RRITVR  233 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g---~~l~v~  233 (587)
                      +..++|||+|||+++++++|+++|++||.|.+|.|+++++++++|||||+|.+.++|++||+.||+..+.+   ++|.|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            45789999999999999999999999999999999999989999999999999999999999999999998   999999


Q ss_pred             EccCCCCC
Q psy1534         234 MDRVADRL  241 (587)
Q Consensus       234 ~a~~~~~~  241 (587)
                      +++.+..+
T Consensus        93 ~a~~~~~~  100 (105)
T 2dnh_A           93 FADTDKES  100 (105)
T ss_dssp             ESCSSCCC
T ss_pred             ECccCccc
Confidence            99887643

>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=99.71  E-value=4.4e-17  Score=132.23  Aligned_cols=79  Identities=22%  Similarity=0.291  Sum_probs=73.2

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..+..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++. ++..|.|++|.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEEE
Confidence            3457789999999999999999 899999999999999997 899999999999999999999964 8889999999998


Q ss_pred             ec
Q psy1534         106 EA  107 (587)
Q Consensus       106 ~a  107 (587)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.4e-17  Score=138.32  Aligned_cols=79  Identities=15%  Similarity=0.145  Sum_probs=72.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhC--CceeCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH--RFETKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~--g~~l~gr~i~V~  105 (587)
                      ++...+|||+|||+++++++| ++|++||+|++|+|+++     ||||||+|.+.++|++|++.|+  +..|.|++|+|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            457789999999999999999 89999999999999986     7999999999999999999886  478999999999


Q ss_pred             ecccccC
Q psy1534         106 EAVEDKG  112 (587)
Q Consensus       106 ~a~~~~~  112 (587)
                      ++..+..
T Consensus        88 ~A~~~~~   94 (105)
T 1sjq_A           88 FSNHKEL   94 (105)
T ss_dssp             CCSSSSC
T ss_pred             EcCCCCC
Confidence            9985543

>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=99.71  E-value=4.1e-17  Score=131.74  Aligned_cols=80  Identities=33%  Similarity=0.543  Sum_probs=75.7

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            456899999999999999999999999999999999986 4889999999999999999999999999999999999997


Q ss_pred             c
Q psy1534         236 R  236 (587)
Q Consensus       236 ~  236 (587)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.9e-17  Score=135.14  Aligned_cols=84  Identities=30%  Similarity=0.406  Sum_probs=78.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE-EEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENV-EIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +.++|||+|||+++++++|+++|++||.|.+| +|++++ .++++|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            46899999999999999999999999999999 999996 4999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      .++...
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            877643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=6.3e-17  Score=134.74  Aligned_cols=85  Identities=25%  Similarity=0.469  Sum_probs=78.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++||+ ||+..|.|++|+|++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999975 8999999999999999999998 999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      +.++...
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9877643

>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=99.71  E-value=5.4e-17  Score=134.02  Aligned_cols=81  Identities=37%  Similarity=0.558  Sum_probs=76.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+++++++++|||||+|.+.++|++|++.||+..+.|++|+|++++
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            44689999999999999999999999999999999999889999999999999999999999999999999999999976


Q ss_pred             C
Q psy1534         237 V  237 (587)
Q Consensus       237 ~  237 (587)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.71  E-value=3e-17  Score=137.30  Aligned_cols=82  Identities=18%  Similarity=0.116  Sum_probs=74.8

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+....+|||+|||+++|+++| ++|++||.| +|+|++|+++++||||||+|.+.++|++|| .+|+..|.+|.|+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEE
Confidence            3456789999999999999999 899999955 999999999999999999999999999999 5799999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +....
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            88543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.7e-17  Score=136.91  Aligned_cols=85  Identities=31%  Similarity=0.493  Sum_probs=79.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            3568999999999999999999999999999999999875 899999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      +++...
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887644

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.2e-16  Score=136.80  Aligned_cols=85  Identities=58%  Similarity=0.792  Sum_probs=79.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|+++++++++|||||+|.+.++|++||+.||+..|.|+.|.|+++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      +....
T Consensus        92 ~~~~~   96 (114)
T 2do0_A           92 ERALP   96 (114)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            76543

>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=99.71  E-value=1.8e-17  Score=139.93  Aligned_cols=84  Identities=18%  Similarity=0.285  Sum_probs=78.0

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCcee---CCeEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFET---KGRKL  102 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l---~gr~i  102 (587)
                      ..+...+|||+|||.++++++| ++|++||+|.+|+|++|+ +++++|||||+|.+.++|++|++.||+..+   .+++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            3456789999999999999999 899999999999999997 899999999999999999999999999988   89999


Q ss_pred             EEEeccccc
Q psy1534         103 VIKEAVEDK  111 (587)
Q Consensus       103 ~V~~a~~~~  111 (587)
                      +|.++..+.
T Consensus        89 ~v~~a~~~~   97 (106)
T 2dgp_A           89 QVKPADSES   97 (106)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCccc
Confidence            999998554

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.71  E-value=1.3e-16  Score=136.69  Aligned_cols=86  Identities=23%  Similarity=0.352  Sum_probs=80.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+++++++|+++|+.||.|..|.|++++ .++++|||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999997 599999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      +..+...
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9877643

>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=99.70  E-value=6.4e-17  Score=133.85  Aligned_cols=81  Identities=21%  Similarity=0.403  Sum_probs=77.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +++|||+|||.++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..+.|+.|.|+++.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            57999999999999999999999999999999999975 89999999999999999999999999999999999999987


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            75

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.1e-17  Score=138.23  Aligned_cols=84  Identities=21%  Similarity=0.298  Sum_probs=78.0

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++||+. ++..|.|++|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            34567789999999999999999 899999999999999996 899999999999999999999998 999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus        90 ~~a~~~~   96 (105)
T 2dh8_A           90 KPCTPRG   96 (105)
T ss_dssp             CCSCCSS
T ss_pred             EEccCCC
Confidence            9998554

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=7.8e-17  Score=133.03  Aligned_cols=82  Identities=30%  Similarity=0.329  Sum_probs=77.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .++.++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..+.|++|+|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999999986 89999999999999999999999999999999999999


Q ss_pred             ccC
Q psy1534         235 DRV  237 (587)
Q Consensus       235 a~~  237 (587)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=6.3e-17  Score=138.95  Aligned_cols=83  Identities=17%  Similarity=0.203  Sum_probs=77.2

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ......++|||+|||+++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++|++.|++ .|.|++|+|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            44557789999999999999999 899999999999999997 899999999999999999999999998 899999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++..+
T Consensus        91 ~~a~~~   96 (116)
T 2cqd_A           91 NLAYLG   96 (116)
T ss_dssp             EESTTT
T ss_pred             EEcccC
Confidence            999744

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=6.2e-17  Score=132.52  Aligned_cols=81  Identities=15%  Similarity=0.204  Sum_probs=76.1

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ......+|||+|||+++++++| ++|++| .|.+|+|+++.+|+++|||||+|.+.++|++|++ ||+..|.|++|.|.+
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3456789999999999999999 899999 9999999999999999999999999999999999 999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +.++
T Consensus        84 a~~~   87 (91)
T 2dgw_A           84 EKSG   87 (91)
T ss_dssp             ESSC
T ss_pred             CCcC
Confidence            9854

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=6.1e-17  Score=135.86  Aligned_cols=85  Identities=25%  Similarity=0.509  Sum_probs=79.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+++ .++++|||||+|.+.++|++||+.||+..|.|++|.|+++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            345689999999999999999999999999999999998 8899999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      +++..+
T Consensus        91 ~~~~~~   96 (103)
T 2d9p_A           91 QRKEER   96 (103)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            887643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.70  E-value=2.6e-17  Score=141.85  Aligned_cols=82  Identities=17%  Similarity=0.291  Sum_probs=75.8

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33456679999999999999999 899999999999999996 8999999999999999999999999999999999999


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      ++++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9873

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.70  E-value=5.8e-18  Score=141.24  Aligned_cols=79  Identities=22%  Similarity=0.224  Sum_probs=75.0

Q ss_pred             CCcEEEcCCCC------CCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCC-eEE
Q psy1534          32 EVPVVMDLIQG------DASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG-RKL  102 (587)
Q Consensus        32 ~~~vfV~nlp~------~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g-r~i  102 (587)
                      .++|||+|||+      ++++++| ++|++||+|.+|+|++|+ +|++||||||+|.+.++|++|++.||+..|.| ++|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            56899999999      9999999 899999999999999997 79999999999999999999999999999999 999


Q ss_pred             EEEecccc
Q psy1534         103 VIKEAVED  110 (587)
Q Consensus       103 ~V~~a~~~  110 (587)
                      +|.++.++
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99999843

>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=99.70  E-value=1.7e-16  Score=133.19  Aligned_cols=85  Identities=26%  Similarity=0.444  Sum_probs=78.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|+|++++.+ ++|||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345689999999999999999999999999999999998754 8999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cq3_A           91 TARVMT   96 (103)
T ss_dssp             CSSCCC
T ss_pred             ccCCCC
Confidence            887643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=7.8e-17  Score=133.89  Aligned_cols=84  Identities=27%  Similarity=0.517  Sum_probs=77.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC--C--CcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--G--KSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--g--~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      +.++|||+|||+++++++|+++|++||.|..|.|++++.  |  +++|||||+|.+.++|++|++.||+..|.|++|.|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            467999999999999999999999999999999998764  4  889999999999999999999999999999999999


Q ss_pred             EccCCCCC
Q psy1534         234 MDRVADRL  241 (587)
Q Consensus       234 ~a~~~~~~  241 (587)
                      ++..+...
T Consensus        84 ~a~~~~~~   91 (98)
T 2cpf_A           84 ISERATKP   91 (98)
T ss_dssp             CSSCSSCC
T ss_pred             EccCCCCC
Confidence            99877643

>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=99.70  E-value=7.9e-17  Score=138.19  Aligned_cols=85  Identities=27%  Similarity=0.469  Sum_probs=79.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+++++++++|||||+|.+.++|++|++.||+..|.|++|+|++++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            34679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q psy1534         237 VADRL  241 (587)
Q Consensus       237 ~~~~~  241 (587)
                      .....
T Consensus        85 ~~~~~   89 (116)
T 2fy1_A           85 KPSFQ   89 (116)
T ss_dssp             CSSCS
T ss_pred             CCCCC
Confidence            76643

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.4e-17  Score=139.25  Aligned_cols=84  Identities=23%  Similarity=0.368  Sum_probs=77.9

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeE--------EEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCcee
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVT--------YVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFET   97 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~--------~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l   97 (587)
                      .....++|||+|||+++++++| ++|++||.|.        .|+|++++ +++++|||||+|.+.++|++|++.||+..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            3456789999999999999999 8999999999        69999995 999999999999999999999999999999


Q ss_pred             CCeEEEEEeccccc
Q psy1534          98 KGRKLVIKEAVEDK  111 (587)
Q Consensus        98 ~gr~i~V~~a~~~~  111 (587)
                      .|++|+|.++..+.
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999998554

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=4.5e-17  Score=136.70  Aligned_cols=86  Identities=27%  Similarity=0.392  Sum_probs=79.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+++++++|+++|++||.|..|.|++++. ++++|||||+|.+.++|++||+.||+..|.|++|.|++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34568999999999999999999999999999999999986 89999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      ++.....
T Consensus        90 a~~~~~~   96 (103)
T 2dnm_A           90 ARYGRRD   96 (103)
T ss_dssp             CSSCCSC
T ss_pred             CCcCCCC
Confidence            9876543

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.70  E-value=1.4e-17  Score=137.60  Aligned_cols=80  Identities=20%  Similarity=0.215  Sum_probs=73.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+...+|||+|||+++++++| ++|++||+|.+|++++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            445689999999999999999 899999999999999886 899999999999999999999999999999999999998


Q ss_pred             cc
Q psy1534         107 AV  108 (587)
Q Consensus       107 a~  108 (587)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=6.2e-17  Score=135.57  Aligned_cols=85  Identities=27%  Similarity=0.469  Sum_probs=79.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+.++|||+|||+++++++|+++|++||.|..|.|++++. ++++|||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4568999999999999999999999999999999999875 889999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      +.+...
T Consensus        90 ~~~~~~   95 (102)
T 1x5s_A           90 GKSSDN   95 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            877643

>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=99.70  E-value=2.1e-17  Score=137.37  Aligned_cols=83  Identities=20%  Similarity=0.210  Sum_probs=76.8

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..+...+|||+|||+++++++| ++|++||+|.+|++++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            4456788999999999999999 899999999999888886 99999999999999999999999999999999999999


Q ss_pred             ecccc
Q psy1534         106 EAVED  110 (587)
Q Consensus       106 ~a~~~  110 (587)
                      ++..+
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98743

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

Probab=99.70  E-value=4.3e-17  Score=133.75  Aligned_cols=83  Identities=20%  Similarity=0.431  Sum_probs=76.8

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+...+|||+|||+++++++| ++|++||+|.+|+|+++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3457789999999999999999 89999999999999985 888999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +....
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98543

>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=99.70  E-value=2.2e-17  Score=144.32  Aligned_cols=84  Identities=18%  Similarity=0.248  Sum_probs=78.4

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ..++..++|||+|||+++++++| ++|++||+|++|+|++|+ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            44567789999999999999999 899999999999999997 8999999999999999999999999999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++..+
T Consensus       121 ~~a~~~  126 (129)
T 2kxn_B          121 DFSITK  126 (129)
T ss_dssp             SCCSSS
T ss_pred             EEecCC
Confidence            999854

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.2e-17  Score=134.97  Aligned_cols=80  Identities=14%  Similarity=0.116  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCeEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN--NQNLFERRITVR  233 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~  233 (587)
                      .++.++|||+|||++++|++|+++|++||.|.+|.|+++     +|||||+|.+.++|++|++.|+  +..|.|++|.|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            455789999999999999999999999999999999986     6999999999999999999886  478999999999


Q ss_pred             EccCCCC
Q psy1534         234 MDRVADR  240 (587)
Q Consensus       234 ~a~~~~~  240 (587)
                      +++.+..
T Consensus        88 ~A~~~~~   94 (105)
T 1sjq_A           88 FSNHKEL   94 (105)
T ss_dssp             CCSSSSC
T ss_pred             EcCCCCC
Confidence            9877653

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=6.5e-17  Score=133.25  Aligned_cols=81  Identities=32%  Similarity=0.468  Sum_probs=76.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .++.++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            34568999999999999999999999999999999999986 89999999999999999999999999999999999999


Q ss_pred             cc
Q psy1534         235 DR  236 (587)
Q Consensus       235 a~  236 (587)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.70  E-value=2.8e-17  Score=143.37  Aligned_cols=84  Identities=13%  Similarity=0.215  Sum_probs=78.1

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..+...+|||+|||+++++++| ++|++||+|.+|+|++++ ++.++|||||+|.+.++|++|++.||+..|.|++|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3445679999999999999999 899999999999999997 99999999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..+.
T Consensus        98 ~a~~~~  103 (126)
T 3ex7_B           98 WCFVRG  103 (126)
T ss_dssp             ESEESS
T ss_pred             EecCCC
Confidence            998554

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=1.4e-17  Score=139.32  Aligned_cols=75  Identities=21%  Similarity=0.243  Sum_probs=70.7

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK  111 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~  111 (587)
                      .+|||+|||+++++++| ++|++||+|.+|+|+++    ++|||||+|.+.++|++|++.|++..+.|++|+|.++..+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            37999999999999999 89999999999999987    78999999999999999999999999999999999998554

>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=99.70  E-value=2e-16  Score=132.69  Aligned_cols=84  Identities=15%  Similarity=0.297  Sum_probs=77.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++++.. ++|||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            345689999999999999999999999999999999998654 6899999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      +.+..
T Consensus        91 ~~~~~   95 (103)
T 2cqi_A           91 TTPSS   95 (103)
T ss_dssp             CCTTC
T ss_pred             CCCcc
Confidence            87653

>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=99.70  E-value=8.2e-17  Score=145.95  Aligned_cols=86  Identities=15%  Similarity=0.057  Sum_probs=79.3

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+...+|||+|||+++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++||+.||+..|.|++|+|
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            33456789999999999999999 899999999999999997 8999999999999999999999999999999999999


Q ss_pred             EecccccC
Q psy1534         105 KEAVEDKG  112 (587)
Q Consensus       105 ~~a~~~~~  112 (587)
                      .++.....
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99985443

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.70  E-value=4.2e-17  Score=147.30  Aligned_cols=80  Identities=19%  Similarity=0.237  Sum_probs=75.0

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCC--CeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVG--DVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G--~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ...+|||+|||+++++++| ++|++||  +|.+|+|++|+ +|++||||||+|.+.++|++||+.||+..|.|++|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            4579999999999999999 8999999  99999999997 999999999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9743

>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=99.70  E-value=3.3e-17  Score=136.12  Aligned_cols=78  Identities=18%  Similarity=0.161  Sum_probs=70.4

Q ss_pred             CCCCCcEEEcCCCC-CCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEE
Q psy1534          29 APLEVPVVMDLIQG-DASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR--FETKGRKLVI  104 (587)
Q Consensus        29 ~~~~~~vfV~nlp~-~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g--~~l~gr~i~V  104 (587)
                      ..+.++|||+|||+ ++++++| ++|++||+|.+|+|+++     ||||||+|++.++|++|++.|++  ..|.|++|+|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            34678999999999 9999999 89999999999999976     58999999999999999999885  5699999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++.+.+
T Consensus        87 ~~a~~~~   93 (102)
T 1x4d_A           87 HLSQKYK   93 (102)
T ss_dssp             EEECCCT
T ss_pred             EECCCCC
Confidence            9998543

>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=99.70  E-value=1.2e-16  Score=136.00  Aligned_cols=86  Identities=23%  Similarity=0.359  Sum_probs=79.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhC------CceeCCe
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLN------NQNLFER  228 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~------g~~~~g~  228 (587)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++||+.||      +..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            34568999999999999999999999999999999999985 8999999999999999999999999      9999999


Q ss_pred             EEEEEEccCCCCC
Q psy1534         229 RITVRMDRVADRL  241 (587)
Q Consensus       229 ~l~v~~a~~~~~~  241 (587)
                      +|+|+++.++...
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999999877543

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

Probab=99.69  E-value=4.1e-17  Score=134.13  Aligned_cols=78  Identities=19%  Similarity=0.249  Sum_probs=70.7

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCce--eCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE--TKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~--l~gr~i~V~  105 (587)
                      .++.++|||+|||+++|+++| ++|++||+|++|+|+++     ||||||+|++.++|++|++.|++..  |.||+|+|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            456788999999999999999 89999999999999864     7999999999999999999999864  889999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..++
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998553

>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=99.69  E-value=6.2e-17  Score=131.87  Aligned_cols=79  Identities=23%  Similarity=0.396  Sum_probs=74.6

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|+ .||+..|.|++|+|.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3478999999999999999 899999999999999997 9999999999999999999999 999999999999999987


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.69  E-value=1.5e-17  Score=135.87  Aligned_cols=81  Identities=16%  Similarity=0.337  Sum_probs=71.2

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcC--CeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAG--KVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G--~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+|||+|||+++++++|+++|++||  .|.+|+|++++. |+++|||||+|.+.++|++|++.||+..+.|+.|+|+++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            3799999999999999999999999  999999999984 9999999999999999999999999999999999999988


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7653

>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=99.69  E-value=9.1e-17  Score=135.31  Aligned_cols=85  Identities=31%  Similarity=0.448  Sum_probs=79.7

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3456899999999999999999999999999999999998 499999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            987754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=3.8e-17  Score=136.05  Aligned_cols=82  Identities=21%  Similarity=0.295  Sum_probs=77.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeE-EEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeE----
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVT-YVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK----  101 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~-~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~----  101 (587)
                      ....++|||+|||+++++++| ++|++||+|. +|+|++++ +++++|||||+|.+.++|++|++.||+..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            356789999999999999999 8999999999 99999997 9999999999999999999999999999999999    


Q ss_pred             EEEEecccc
Q psy1534         102 LVIKEAVED  110 (587)
Q Consensus       102 i~V~~a~~~  110 (587)
                      |+|.++...
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998744

>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=99.69  E-value=5.4e-17  Score=136.42  Aligned_cols=82  Identities=22%  Similarity=0.231  Sum_probs=76.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEE-EEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTY-VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....+|||+|||+++++++| ++|++||.|.+ |+|+++.+|+++|||||+|.+.++|++||+. ++..|.||.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            346689999999999999999 89999999998 9999999999999999999999999999987 99999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +.+++
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            88554

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.3e-17  Score=134.78  Aligned_cols=80  Identities=16%  Similarity=0.201  Sum_probs=74.1

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.||+..|.|+.|+|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            356789999999999999999 889999999999999996 899999999999999999999999999999999988765


Q ss_pred             cc
Q psy1534         107 AV  108 (587)
Q Consensus       107 a~  108 (587)
                      ..
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.69  E-value=1.8e-16  Score=134.03  Aligned_cols=82  Identities=23%  Similarity=0.454  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ...+.++|||+|||+.+++++|+++|++||.|.+|.|+++++++++|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q psy1534         235 DR  236 (587)
Q Consensus       235 a~  236 (587)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.69  E-value=1.5e-16  Score=131.52  Aligned_cols=81  Identities=26%  Similarity=0.377  Sum_probs=75.7

Q ss_pred             CCcEEEEecCCCCCcHHHHH----HHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLR----EVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..++|||+|||+++++++|+    ++|++||.|.+|+|++++.+  +|||||+|.+.++|++||+.||+..+.|++|+|+
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   85 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVS   85 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            45799999999999999999    99999999999999998766  8899999999999999999999999999999999


Q ss_pred             EccCCCC
Q psy1534         234 MDRVADR  240 (587)
Q Consensus       234 ~a~~~~~  240 (587)
                      ++++...
T Consensus        86 ~a~~~~~   92 (96)
T 2dgx_A           86 LATGASG   92 (96)
T ss_dssp             ECCCSSC
T ss_pred             EcCCCCC
Confidence            9977653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=9.7e-17  Score=134.88  Aligned_cols=86  Identities=21%  Similarity=0.297  Sum_probs=80.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHh-cCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCCeEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRL-AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQN-LFERRITVR  233 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~-~~g~~l~v~  233 (587)
                      ..+.++|||+|||+++++++|+++|++ ||.|.+|.|+++++++++|||||+|.+.++|.+||+.||+.. +.|++|.|+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            345689999999999999999999999 999999999999989999999999999999999999999999 999999999


Q ss_pred             EccCCCCC
Q psy1534         234 MDRVADRL  241 (587)
Q Consensus       234 ~a~~~~~~  241 (587)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99776543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.69  E-value=1.5e-17  Score=130.86  Aligned_cols=73  Identities=22%  Similarity=0.368  Sum_probs=69.9

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++ |++..|.|++|.|+++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            6999999999999999 899999999999999997 89999999999999999999997 8999999999999875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.69  E-value=4.2e-17  Score=140.34  Aligned_cols=82  Identities=21%  Similarity=0.202  Sum_probs=76.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCC---eEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGD---VTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~---V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .....+|||+|||+++|+++| ++|++||.   |.+|+|+++++|++||||||+|.+.++|++||+ ||+..|.||.|+|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            456688999999999999999 89999999   899999999889999999999999999999998 8999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++.+++
T Consensus        93 ~~a~~~~   99 (118)
T 2db1_A           93 FKSHRTE   99 (118)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998443

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=1.3e-16  Score=134.82  Aligned_cols=86  Identities=23%  Similarity=0.502  Sum_probs=79.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeC-C-CCCcceEEEEEecCHHHHHHHHHHh-CCceeCCeEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD-K-DGKSRGFGTVEFDHPVEAVQSISML-NNQNLFERRITV  232 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-~-~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v  232 (587)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+++ + .++++|||||+|.+.++|++||+.| |+..|.|++|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            345689999999999999999999999999999999998 4 5999999999999999999999999 999999999999


Q ss_pred             EEccCCCCC
Q psy1534         233 RMDRVADRL  241 (587)
Q Consensus       233 ~~a~~~~~~  241 (587)
                      +++.++...
T Consensus        92 ~~a~~~~~~  100 (107)
T 2cph_A           92 EWADSEVTV  100 (107)
T ss_dssp             EECCCCCCC
T ss_pred             EeCCCCCCC
Confidence            999887543

>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=99.69  E-value=1e-16  Score=135.23  Aligned_cols=86  Identities=23%  Similarity=0.335  Sum_probs=79.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCcee---CCeEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNL---FERRIT  231 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~~l~  231 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..+   .+++|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            34568999999999999999999999999999999999986 99999999999999999999999999988   899999


Q ss_pred             EEEccCCCCC
Q psy1534         232 VRMDRVADRL  241 (587)
Q Consensus       232 v~~a~~~~~~  241 (587)
                      |+++..+.+.
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999877643

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.69  E-value=1.3e-16  Score=126.28  Aligned_cols=74  Identities=20%  Similarity=0.209  Sum_probs=69.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+..|||+||++.+||++|+++|.+||+|.++++..     ++|||||+|.+.++|++|++.||+.++.|++|+|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            356899999999999999999999999999999976     58999999999999999999999999999999999983

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2.9e-16  Score=134.78  Aligned_cols=84  Identities=26%  Similarity=0.430  Sum_probs=77.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|++||+.|++ .|.|++|+|++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            34568999999999999999999999999999999999975 99999999999999999999999998 89999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      +....+
T Consensus        93 a~~~~~   98 (116)
T 2cqd_A           93 AYLGAK   98 (116)
T ss_dssp             STTTCC
T ss_pred             cccCCC
Confidence            977653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.3e-16  Score=134.62  Aligned_cols=83  Identities=25%  Similarity=0.381  Sum_probs=78.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..|.|++|.|+++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            4468999999999999999999999999999999999986 999999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8764

>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=99.68  E-value=1.4e-16  Score=135.17  Aligned_cols=83  Identities=16%  Similarity=0.216  Sum_probs=75.0

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ......++|||+|||+++++++| ++|++||+|++|+|+.+  +.++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34456789999999999999999 89999999999999654  5578999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..++
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            998554

>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=99.68  E-value=4.8e-17  Score=132.26  Aligned_cols=80  Identities=20%  Similarity=0.338  Sum_probs=74.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCC-cceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGK-PRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~-skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...+|||+|||+++++++| ++|++||+|.+|+|++++ ++. ++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            5689999999999999999 899999999999999987 444 8999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      .++
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            744

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

Probab=99.68  E-value=1.2e-16  Score=131.40  Aligned_cols=80  Identities=18%  Similarity=0.199  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCeEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQN--LFERRITV  232 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~--~~g~~l~v  232 (587)
                      ..+++++|||+|||+++++++|+++|++||.|.+|.++++     ||||||+|.+.++|.+|++.|++..  +.|++|.|
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            3456889999999999999999999999999999999864     7899999999999999999999875  78999999


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      .+++.+.
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9997654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=132.86  Aligned_cols=82  Identities=24%  Similarity=0.423  Sum_probs=77.1

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE--------EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVEN--------VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNL  225 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~  225 (587)
                      ..++.++|||+|||+++++++|+++|++||.|.+        |+|++++. ++++|||||+|.+.++|++|++.||+..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            4556789999999999999999999999999999        99999975 99999999999999999999999999999


Q ss_pred             CCeEEEEEEcc
Q psy1534         226 FERRITVRMDR  236 (587)
Q Consensus       226 ~g~~l~v~~a~  236 (587)
                      .|++|+|++++
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999874

>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=99.68  E-value=2.3e-16  Score=131.15  Aligned_cols=80  Identities=13%  Similarity=0.157  Sum_probs=71.7

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHh--CCceeCCeEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM--HRFETKGRKLVI  104 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l--~g~~l~gr~i~V  104 (587)
                      ..++.++|||+|||+++++++| ++|++||+|.+|+|+++     ||||||+|.+.++|++|++.|  ++..|.|++|+|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            3456789999999999999999 89999999999999875     799999999999999999977  468899999999


Q ss_pred             EecccccC
Q psy1534         105 KEAVEDKG  112 (587)
Q Consensus       105 ~~a~~~~~  112 (587)
                      .++..+..
T Consensus        86 ~~a~~~~~   93 (101)
T 2cq1_A           86 QYSNHKEL   93 (101)
T ss_dssp             EECSCSSC
T ss_pred             EEcCcccC
Confidence            99985543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.68  E-value=2.2e-16  Score=132.46  Aligned_cols=83  Identities=22%  Similarity=0.349  Sum_probs=77.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..+.++|||+|||+++++++|+++|++|| |.+|.|++++. ++++|||||+|.+.++|++|| .||+..|.|++|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34568999999999999999999999996 99999999985 999999999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2dng_A           90 AEGRKQ   95 (103)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            987654

>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=99.68  E-value=9.8e-17  Score=135.71  Aligned_cols=85  Identities=24%  Similarity=0.477  Sum_probs=79.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..+..++|||+|||+.+++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..|.|++|+|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            455678999999999999999999999999999999999975 8999999999999999999999999999999999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      +++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            987653

>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=99.68  E-value=2.9e-16  Score=131.73  Aligned_cols=83  Identities=19%  Similarity=0.222  Sum_probs=75.8

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .......+|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++  ++..|.|++|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v   87 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEE
Confidence            34456789999999999999999 899999999999999996 89999999999999999999998  478999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus        88 ~~a~~~~   94 (103)
T 2cqg_A           88 KLPNSKQ   94 (103)
T ss_dssp             ECCCTTC
T ss_pred             EecCCCC
Confidence            9998553

>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=99.68  E-value=3.6e-17  Score=143.65  Aligned_cols=81  Identities=20%  Similarity=0.179  Sum_probs=75.9

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCC---eEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGD---VTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~---V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .....+|||+|||+++|+++| ++|++||.   |.+|+|++|++|++||||||+|.+.++|++||+ ||+..|.||+|+|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            446678999999999999999 89999999   899999999889999999999999999999998 9999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++.++
T Consensus       120 ~~a~~~  125 (136)
T 2hgl_A          120 FKSHRT  125 (136)
T ss_dssp             EECCHH
T ss_pred             EECChH
Confidence            998744

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=9.7e-17  Score=136.02  Aligned_cols=84  Identities=17%  Similarity=0.208  Sum_probs=73.4

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ......++|||+|||+++++++| ++|++||+|.+|+|++++ +|+++|||||+|.+.++|++|++.+ +..|.|++|.|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V   98 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDP   98 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEE
Confidence            34457789999999999999999 899999999999999997 8999999999999999999999886 59999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus        99 ~~a~~~~  105 (109)
T 2rs2_A           99 KVAFPRR  105 (109)
T ss_dssp             EECCCCC
T ss_pred             EEccCCC
Confidence            9998543

>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=99.68  E-value=4e-17  Score=139.65  Aligned_cols=82  Identities=22%  Similarity=0.290  Sum_probs=76.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCe-EEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDV-TYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V-~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ....++|||+|||+++++++| ++|++||.| .+|+|++|++|+++|||||+|.+.++|++||+. |+..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            456789999999999999999 899999999 899999999999999999999999999999987 99999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +.++.
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            98443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.6e-16  Score=128.74  Aligned_cols=82  Identities=21%  Similarity=0.265  Sum_probs=76.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|+.| .|.+|.|+++.+|+++|||||+|.+.++|++||+ ||+..|.|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            3446899999999999999999999999 9999999999779999999999999999999999 9999999999999998


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      ..+.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.68  E-value=1.2e-16  Score=138.98  Aligned_cols=84  Identities=18%  Similarity=0.227  Sum_probs=78.1

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ......+|||+|||+++++++| ++|++||+|++|+|+++++|+++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3455679999999999999999 899999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +....
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            98543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=6.4e-17  Score=137.17  Aligned_cols=83  Identities=18%  Similarity=0.244  Sum_probs=76.0

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ......++|||+|||.++++++| ++|++||+|.+|+|++++. .++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            44457789999999999999999 8999999999999999864 489999999999999999999999999999999999


Q ss_pred             ecccc
Q psy1534         106 EAVED  110 (587)
Q Consensus       106 ~a~~~  110 (587)
                      ++..+
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98744

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=132.83  Aligned_cols=84  Identities=18%  Similarity=0.301  Sum_probs=78.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCee-EEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeE----
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVE-NVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR----  229 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~-~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~----  229 (587)
                      ..+.++|||+|||+++++++|+++|++||.|. +|+|++++. ++++|||||+|.+.++|++|++.||+..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34568999999999999999999999999999 999999984 999999999999999999999999999999999    


Q ss_pred             EEEEEccCCC
Q psy1534         230 ITVRMDRVAD  239 (587)
Q Consensus       230 l~v~~a~~~~  239 (587)
                      |+|.++++..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999987664

>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=99.68  E-value=1.5e-16  Score=133.70  Aligned_cols=83  Identities=27%  Similarity=0.450  Sum_probs=77.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .+.++|||+|||+++++++|+++|++|| |.+|.|++++.  ++++|||||+|.+.++|++|| .||+..|.|++|.|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4468999999999999999999999999 99999999985  899999999999999999999 9999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      +.++...
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9887644

>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=99.68  E-value=2.2e-17  Score=138.86  Aligned_cols=81  Identities=28%  Similarity=0.395  Sum_probs=76.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|++||+|.+|+|++++ +|+++|||||+|.+.++|++|++.||+..|.|++|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            5579999999999999999 899999999999999996 89999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      .+.
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            543

>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=99.68  E-value=1.7e-16  Score=128.99  Aligned_cols=81  Identities=22%  Similarity=0.395  Sum_probs=75.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .++|||+|||+++++++|+++|++||.|.+|.|++++.  ++++|||||+|.+.++|++|++.||+..+.|+.|+|+++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            57999999999999999999999999999999999885  3489999999999999999999999999999999999987


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      +..
T Consensus        84 ~~~   86 (88)
T 4a8x_A           84 APW   86 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

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

Probab=99.68  E-value=2e-16  Score=129.74  Aligned_cols=83  Identities=35%  Similarity=0.557  Sum_probs=77.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+++ .++++|||||+|.+.++|++|++.||+..+.|++|+|++++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            45689999999999999999999999999999999984 68899999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      +...
T Consensus        85 ~~~~   88 (92)
T 2dgv_A           85 NASG   88 (92)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.8e-16  Score=132.45  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=74.1

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....++|||+|||+++++++| ++|++||+|   +|+++.+++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4457789999999999999999 899999987   677778899999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98554

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.68  E-value=3.6e-16  Score=138.82  Aligned_cols=87  Identities=30%  Similarity=0.517  Sum_probs=80.9

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|++++. ++++|||||+|.+.++|++||+.||+..|.|+.|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            445678999999999999999999999999999999999985 8999999999999999999999999999999999999


Q ss_pred             EccCCCCC
Q psy1534         234 MDRVADRL  241 (587)
Q Consensus       234 ~a~~~~~~  241 (587)
                      +++.+...
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99887643

>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=99.68  E-value=2e-16  Score=134.35  Aligned_cols=84  Identities=24%  Similarity=0.384  Sum_probs=78.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|+..||+..|.|++|.|++
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34568999999999999999999999999999999999874 99999999999999999999999999999999999999


Q ss_pred             ccCCC
Q psy1534         235 DRVAD  239 (587)
Q Consensus       235 a~~~~  239 (587)
                      +.++.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98765

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=6.2e-17  Score=135.42  Aligned_cols=79  Identities=15%  Similarity=0.149  Sum_probs=74.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|++++.++++|||||+|.+.++|.+||. +++..+.|+.|.|.++..
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            3579999999999999999999999999999999999889999999999999999999998 899999999999998755

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=7e-17  Score=138.64  Aligned_cols=81  Identities=19%  Similarity=0.201  Sum_probs=75.6

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++||+. ++..|.|++|+|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            34578999999999999999 899999999999999996 899999999999999999999987 999999999999999


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      ..+.
T Consensus       104 ~~~~  107 (116)
T 1x4b_A          104 VARE  107 (116)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            8554

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.67  E-value=4.2e-17  Score=135.99  Aligned_cols=81  Identities=27%  Similarity=0.329  Sum_probs=77.1

Q ss_pred             CcEEEEecCCC------CCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCC-eEE
Q psy1534         159 INKVFVANLDY------KVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE-RRI  230 (587)
Q Consensus       159 ~~~l~V~nLp~------~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-~~l  230 (587)
                      .++|||+|||+      ++++++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|++||+.|||..+.| ++|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            57999999999      999999999999999999999999986 9999999999999999999999999999999 999


Q ss_pred             EEEEccCCC
Q psy1534         231 TVRMDRVAD  239 (587)
Q Consensus       231 ~v~~a~~~~  239 (587)
                      +|.++.+..
T Consensus        86 ~V~~a~~~~   94 (100)
T 3ns6_A           86 FLYTMKDVE   94 (100)
T ss_dssp             EEEESHHHH
T ss_pred             EEEECchhh
Confidence            999987653

>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=99.67  E-value=2.3e-16  Score=134.21  Aligned_cols=82  Identities=16%  Similarity=0.145  Sum_probs=74.8

Q ss_pred             CCCCcEEEcCCCCCCCHHHH----HhcccCCCeEEEEEeeCC-CC---CcceEEEEEECCHHHHHHHHHHhCCceeCCeE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI----SHLSTVGDVTYVEILNDD-TG---KPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK  101 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l----~~F~~~G~V~~v~i~~d~-~g---~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~  101 (587)
                      ....+|||+|||+++++++|    ++|++||+|.+|+|++++ ++   +++|||||+|.+.++|++|++.||+..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            45689999999999999998    679999999999999986 43   56699999999999999999999999999999


Q ss_pred             EEEEeccccc
Q psy1534         102 LVIKEAVEDK  111 (587)
Q Consensus       102 i~V~~a~~~~  111 (587)
                      |+|.++..+.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998664

>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=99.67  E-value=1.5e-16  Score=131.55  Aligned_cols=79  Identities=20%  Similarity=0.224  Sum_probs=72.9

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-----HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-----SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-----~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ....+|||+|||+++++++|     ++|++||+|.+|+|++|+..  ||||||+|.+.++|++|++.||+..|.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            35678999999999999998     57999999999999999754  899999999999999999999999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++...
T Consensus        85 ~~a~~~   90 (96)
T 2dgx_A           85 SLATGA   90 (96)
T ss_dssp             EECCCS
T ss_pred             EEcCCC
Confidence            999744

>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=99.67  E-value=1.1e-16  Score=133.07  Aligned_cols=79  Identities=13%  Similarity=0.133  Sum_probs=71.8

Q ss_pred             CCCCcEEEEecCCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEE
Q psy1534         156 CPLINKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN--QNLFERRITV  232 (587)
Q Consensus       156 ~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v  232 (587)
                      ..+.++|||+|||+ ++++++|+++|++||.|.+|.|+++     +|||||+|.+.++|.+||+.||+  ..|.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            34578999999999 9999999999999999999999876     58999999999999999999886  4599999999


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      .+++...
T Consensus        87 ~~a~~~~   93 (102)
T 1x4d_A           87 HLSQKYK   93 (102)
T ss_dssp             EEECCCT
T ss_pred             EECCCCC
Confidence            9998654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.67  E-value=4.1e-16  Score=135.53  Aligned_cols=86  Identities=22%  Similarity=0.410  Sum_probs=80.5

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+++++++++|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            45578999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      ......
T Consensus       112 ~~~~~~  117 (124)
T 2kt5_A          112 ASQIDL  117 (124)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.67  E-value=3.3e-16  Score=127.54  Aligned_cols=79  Identities=29%  Similarity=0.486  Sum_probs=75.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|.+|.+++++ +++++|||||+|.+.++|++|+ .||+..+.|++|+|+++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            4699999999999999999999999999999999997 4999999999999999999999 9999999999999999876


Q ss_pred             C
Q psy1534         238 A  238 (587)
Q Consensus       238 ~  238 (587)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.4e-16  Score=134.59  Aligned_cols=85  Identities=24%  Similarity=0.415  Sum_probs=78.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCee--------EEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVE--------NVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLF  226 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  226 (587)
                      ....++|||+|||+++++++|+++|++||.|.        .|+|++++ +++++|||||+|.+.++|++||+.||+..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34568999999999999999999999999998        69999996 4999999999999999999999999999999


Q ss_pred             CeEEEEEEccCCCC
Q psy1534         227 ERRITVRMDRVADR  240 (587)
Q Consensus       227 g~~l~v~~a~~~~~  240 (587)
                      |++|+|++++.+..
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999987654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.5e-16  Score=137.08  Aligned_cols=82  Identities=26%  Similarity=0.418  Sum_probs=76.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..+..++|||+|||+++++++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|++|++.||+..|.|++|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            445678999999999999999999999999999999999975 8999999999999999999999999999999999999


Q ss_pred             Ecc
Q psy1534         234 MDR  236 (587)
Q Consensus       234 ~a~  236 (587)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>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=99.67  E-value=3.7e-16  Score=132.27  Aligned_cols=70  Identities=31%  Similarity=0.603  Sum_probs=67.7

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccC-----ceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDG-----KIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g-----~~i~v~~  586 (587)
                      .++|||.|||+++|++||+++|++||.|..++|..+ ++|||+|++.++|++||+.||+.+|.|     ++|+|.+
T Consensus        15 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~   89 (108)
T 1x4c_A           15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   89 (108)
T ss_dssp             CCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEe
Confidence            689999999999999999999999999999999888 999999999999999999999999999     9999975

>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=99.67  E-value=2.6e-16  Score=134.63  Aligned_cols=81  Identities=15%  Similarity=0.185  Sum_probs=75.7

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCcee--------CC
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET--------KG   99 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l--------~g   99 (587)
                      .....+|||+|||+++++++| ++|++||+|.+|+|+++++++++|||||+|.+.++|++|++.||+..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            356789999999999999999 899999999999999999999999999999999999999999999999        57


Q ss_pred             eEEEEEeccc
Q psy1534         100 RKLVIKEAVE  109 (587)
Q Consensus       100 r~i~V~~a~~  109 (587)
                      ++|.|.++.+
T Consensus       102 ~~l~v~~a~p  111 (114)
T 1x5o_A          102 EPLLCKFSGP  111 (114)
T ss_dssp             SCBEEEECCC
T ss_pred             CceeEEccCC
Confidence            8899999873

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.1e-16  Score=133.02  Aligned_cols=84  Identities=30%  Similarity=0.410  Sum_probs=78.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++||+. |+..|.|+.|.|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            34568999999999999999999999999999999999975 99999999999999999999998 99999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            887654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=3.8e-17  Score=129.26  Aligned_cols=74  Identities=18%  Similarity=0.235  Sum_probs=70.8

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .+|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|++.++ ..+.|++|.|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            47999999999999999 899999999999999997 89999999999999999999999998 9999999999986

>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=99.67  E-value=1.3e-16  Score=136.55  Aligned_cols=78  Identities=21%  Similarity=0.291  Sum_probs=74.0

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      .++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|+ .||+..|.|++|+|.++..
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            458999999999999999 899999999999999997 7999999999999999999999 9999999999999999984


Q ss_pred             c
Q psy1534         110 D  110 (587)
Q Consensus       110 ~  110 (587)
                      +
T Consensus       104 ~  104 (114)
T 2cq4_A          104 E  104 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.7e-16  Score=133.94  Aligned_cols=77  Identities=23%  Similarity=0.313  Sum_probs=72.5

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      ..+|||+|||+++++++| ++|++| .|.+|+|++|++|+++|||||+|.+.++|++|| .+|+..|.||.|.|..+..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            458999999999999999 899999 899999999989999999999999999999999 68999999999999988744

>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=99.67  E-value=4.5e-16  Score=126.16  Aligned_cols=79  Identities=27%  Similarity=0.462  Sum_probs=73.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++. ++..+.|++|.|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999999975 99999999999999999999954 88899999999987


Q ss_pred             c
Q psy1534         235 D  235 (587)
Q Consensus       235 a  235 (587)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.66  E-value=1.2e-16  Score=136.31  Aligned_cols=80  Identities=15%  Similarity=0.145  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR--FETKGRKLVI  104 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g--~~l~gr~i~V  104 (587)
                      ..++.++|||+|||+++++++| ++|++||+|++|+|+++     ||||||+|++.++|++|++.|++  ..|.|++|+|
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            3456778999999999999999 89999999999999986     79999999999999999998874  6899999999


Q ss_pred             EecccccC
Q psy1534         105 KEAVEDKG  112 (587)
Q Consensus       105 ~~a~~~~~  112 (587)
                      .++..+..
T Consensus       102 ~~a~~k~~  109 (119)
T 2ad9_A          102 QFSNHKEL  109 (119)
T ss_dssp             EECSSSSC
T ss_pred             EEccCCCC
Confidence            99986543

>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=99.66  E-value=1.4e-16  Score=139.26  Aligned_cols=85  Identities=31%  Similarity=0.350  Sum_probs=79.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..++.++|||+|||+++++++|+++|++||.|..|+|++++. ++++|||||+|.+.++|++||+.||+..|.|++|.|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345578999999999999999999999999999999999975 8999999999999999999999999999999999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      ++.++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            987754

>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=99.66  E-value=3.4e-16  Score=140.92  Aligned_cols=71  Identities=21%  Similarity=0.245  Sum_probs=68.1

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC-CCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK-GDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~-~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .++|||.|||+++|+++|+++|++||.|..+++..+ +|+|||+|.+.++|++||+.|||..|.|++|+|.+
T Consensus        73 ~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             SCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            469999999999999999999999999999999876 89999999999999999999999999999999986

>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=99.66  E-value=5.8e-16  Score=131.29  Aligned_cols=83  Identities=19%  Similarity=0.309  Sum_probs=75.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|++||.|..|.|..+  ++++|||||+|.+.++|++||+.||+..|.|++|+|+++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            345689999999999999999999999999999999664  457999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      +...+
T Consensus        97 ~~~~~  101 (109)
T 1x4a_A           97 RSGRG  101 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87654

>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=99.66  E-value=2e-16  Score=132.32  Aligned_cols=79  Identities=15%  Similarity=0.205  Sum_probs=70.7

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR--FETKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g--~~l~gr~i~V~  105 (587)
                      .++.++|||+|||+++++++| ++|++||+|.+|+|+++     ||||||+|.+.++|++|++.|++  ..|.|++|+|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            356689999999999999999 89999999999999874     79999999999999999998865  45999999999


Q ss_pred             ecccccC
Q psy1534         106 EAVEDKG  112 (587)
Q Consensus       106 ~a~~~~~  112 (587)
                      ++..+..
T Consensus        87 ~a~~~~~   93 (104)
T 1wex_A           87 YSTSKRI   93 (104)
T ss_dssp             ECSSSSC
T ss_pred             EccCccc
Confidence            9986543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.6e-16  Score=133.38  Aligned_cols=83  Identities=27%  Similarity=0.462  Sum_probs=77.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .....++|||+|||.++++++|+++|++||.|.+|+|++++. .++|||||+|.+.++|++|++.||+..+.|++|+|++
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445678999999999999999999999999999999998864 4899999999999999999999999999999999999


Q ss_pred             ccCC
Q psy1534         235 DRVA  238 (587)
Q Consensus       235 a~~~  238 (587)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8765

>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=99.66  E-value=5.1e-16  Score=129.05  Aligned_cols=81  Identities=14%  Similarity=0.136  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCeEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML--NNQNLFERRITV  232 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~v  232 (587)
                      ..+++++|||+|||+++++++|+++|++||.|.+|.|+++     +|||||+|.+.++|.+|++.|  ++..+.|++|.|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            3456789999999999999999999999999999999875     799999999999999999977  567899999999


Q ss_pred             EEccCCCC
Q psy1534         233 RMDRVADR  240 (587)
Q Consensus       233 ~~a~~~~~  240 (587)
                      .+++.+..
T Consensus        86 ~~a~~~~~   93 (101)
T 2cq1_A           86 QYSNHKEL   93 (101)
T ss_dssp             EECSCSSC
T ss_pred             EEcCcccC
Confidence            99987653

>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=99.66  E-value=8.8e-16  Score=128.75  Aligned_cols=84  Identities=25%  Similarity=0.376  Sum_probs=77.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++++. ++++|||||+|.+.++|++||+  +++.|.|+.|.|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            34568999999999999999999999999999999999975 9999999999999999999998  57899999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9887644

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.66  E-value=3.8e-16  Score=123.58  Aligned_cols=71  Identities=17%  Similarity=0.135  Sum_probs=68.3

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      ..-|+|+||++.+|+++|+++|.+||+|..+.+..++|+|||+|.++++|++||+.||+.++.||.|+|.+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~   77 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAES   77 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEE
Confidence            45999999999999999999999999999999998899999999999999999999999999999999974

>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=99.66  E-value=8.3e-17  Score=169.59  Aligned_cols=84  Identities=25%  Similarity=0.517  Sum_probs=78.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|+.++ +++++|||||+|.+.++|.+||..||+..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            446899999999999999999999999999999999997 4999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      .....
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            87654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.66  E-value=1.2e-16  Score=134.41  Aligned_cols=78  Identities=18%  Similarity=0.282  Sum_probs=72.3

Q ss_pred             CCCcEEEcCCCCCC------CHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCe-EE
Q psy1534          31 LEVPVVMDLIQGDA------SLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR-KL  102 (587)
Q Consensus        31 ~~~~vfV~nlp~~~------t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr-~i  102 (587)
                      ..++|||+|||+++      ++++| ++|++||+|.+|+|+ ..+|+++|||||+|.+.++|++|++.|||..|.|+ +|
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            46789999999999      77888 899999999999998 46899999999999999999999999999999998 99


Q ss_pred             EEEeccc
Q psy1534         103 VIKEAVE  109 (587)
Q Consensus       103 ~V~~a~~  109 (587)
                      +|.++..
T Consensus        93 ~V~~a~~   99 (105)
T 2nlw_A           93 RVNLFTD   99 (105)
T ss_dssp             EEECSCC
T ss_pred             EEEEcch
Confidence            9999873

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.66  E-value=3.3e-16  Score=132.70  Aligned_cols=85  Identities=22%  Similarity=0.298  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      .....++|||+|||+++++++|+++|+.||.|.+|.|++++. ++++|||||+|.+.++|++||+.+ +..+.|+.|.|+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            344578999999999999999999999999999999999985 999999999999999999999886 599999999999


Q ss_pred             EccCCCC
Q psy1534         234 MDRVADR  240 (587)
Q Consensus       234 ~a~~~~~  240 (587)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.66  E-value=4.7e-17  Score=142.93  Aligned_cols=82  Identities=12%  Similarity=0.243  Sum_probs=76.3

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEE--EEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCc----eeCC
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTY--VEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRF----ETKG   99 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~--v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~----~l~g   99 (587)
                      .....++|||+|||+++++++| ++|++||+|..  |+|++|+ +|++||||||+|.+. +|.+|++.||+.    .|.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456779999999999999999 89999999977  9999998 999999999999999 999999999999    9999


Q ss_pred             eEEEEEecccc
Q psy1534         100 RKLVIKEAVED  110 (587)
Q Consensus       100 r~i~V~~a~~~  110 (587)
                      ++|+|.++..+
T Consensus        98 r~l~V~~a~~~  108 (131)
T 2m2b_A           98 KTINVEFAKGS  108 (131)
T ss_dssp             CCCCCEECCCS
T ss_pred             EEEEEEECCCC
Confidence            99999999854

>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=99.66  E-value=1.9e-16  Score=131.53  Aligned_cols=82  Identities=17%  Similarity=0.215  Sum_probs=75.7

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +..++|||+|||+++++++|+++|++||.|..+.+++++. ++++|||||+|.+.++|++||+.||+..|.|++|+|+++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            3467999999999999999999999999999888887764 899999999999999999999999999999999999998


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      ...
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            754

>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=99.66  E-value=9.5e-16  Score=129.71  Aligned_cols=78  Identities=26%  Similarity=0.308  Sum_probs=73.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-----eEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE-----RRITV  232 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-----~~l~v  232 (587)
                      ..++|||+|||+++++++|+++|++||.|..|.|+++      |||||+|.+.++|++||+.||+..|.|     ++|+|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEE
Confidence            4679999999999999999999999999999999886      899999999999999999999999999     99999


Q ss_pred             EEccCCCCC
Q psy1534         233 RMDRVADRL  241 (587)
Q Consensus       233 ~~a~~~~~~  241 (587)
                      +++.++.+.
T Consensus        88 ~~a~~~~~~   96 (108)
T 1x4c_A           88 KVDGPRSPS   96 (108)
T ss_dssp             EESSCCSCC
T ss_pred             EeCCCCCCC
Confidence            999886643

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.66  E-value=3.2e-16  Score=141.46  Aligned_cols=81  Identities=20%  Similarity=0.343  Sum_probs=75.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcC--CeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAG--KVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G--~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..++|||+|||+++++++|+++|+.||  .|.+|+|++|+. |+++|||||+|.+.++|++||+.||+..|.|+.|.|++
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999975 99999999999999999999999999999999999999


Q ss_pred             ccCC
Q psy1534         235 DRVA  238 (587)
Q Consensus       235 a~~~  238 (587)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8654

>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=99.66  E-value=7.1e-17  Score=134.67  Aligned_cols=80  Identities=13%  Similarity=0.188  Sum_probs=72.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC--CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD--TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ....++|||+|||+++++++| ++|++|| |.+|+|++++  +|+++|||||+|.+.++|++|+ .|++..|.|++|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            456789999999999999999 8999999 9999999996  8999999999999999999999 899999999999999


Q ss_pred             ecccc
Q psy1534         106 EAVED  110 (587)
Q Consensus       106 ~a~~~  110 (587)
                      ++..+
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98743

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.2e-16  Score=127.97  Aligned_cols=77  Identities=16%  Similarity=0.324  Sum_probs=71.4

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+..++|||+|||+++++++| ++|++||+|.+|+|+       ||||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3457789999999999999999 899999999999998       48999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        77 a~~~~   81 (90)
T 2dnq_A           77 SKNKS   81 (90)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            98554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.66  E-value=1.1e-16  Score=135.36  Aligned_cols=81  Identities=12%  Similarity=0.247  Sum_probs=71.8

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCC-CeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVG-DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G-~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ..++...+|||+|||+++++++| ++|++|| +|..|+|+.+   .++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        23 ~~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           23 KLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             --CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            44556789999999999999999 8999999 9999998643   47899999999999999999999999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++...
T Consensus       100 ~~a~~~  105 (111)
T 2jvr_A          100 ERDDNP  105 (111)
T ss_dssp             EESCC-
T ss_pred             EECCCC
Confidence            998743

>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=99.65  E-value=5.8e-17  Score=140.92  Aligned_cols=83  Identities=14%  Similarity=0.137  Sum_probs=74.4

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeC-CCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .......+|||+|||+++++++| ++|++||.|.+|.++.+ .+|+++|||||+|.+.++|++||+ ||+..|.|++|.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   98 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   98 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            34456689999999999999999 89999999999555555 599999999999999999999998 9999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++.++
T Consensus        99 ~~a~~~  104 (124)
T 1wel_A           99 HPITKK  104 (124)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            999854

>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=99.65  E-value=3.5e-16  Score=133.33  Aligned_cols=81  Identities=14%  Similarity=0.115  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN--QNLFERRITV  232 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v  232 (587)
                      ..+++++|||+|||++++|++|+++|++||.|.+|.|+++     +|||||+|.+.++|.+|++.|++  ..|.|++|.|
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            3456789999999999999999999999999999999986     79999999999999999998874  6899999999


Q ss_pred             EEccCCCC
Q psy1534         233 RMDRVADR  240 (587)
Q Consensus       233 ~~a~~~~~  240 (587)
                      .+++.+..
T Consensus       102 ~~a~~k~~  109 (119)
T 2ad9_A          102 QFSNHKEL  109 (119)
T ss_dssp             EECSSSSC
T ss_pred             EEccCCCC
Confidence            99987653

>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=99.65  E-value=9.4e-16  Score=138.95  Aligned_cols=85  Identities=24%  Similarity=0.369  Sum_probs=79.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++++. ++++|||||+|.+.++|++||+.||+..|.|++|+|++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999999986 89999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      +++...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            987653

>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=99.65  E-value=2.6e-16  Score=131.56  Aligned_cols=81  Identities=22%  Similarity=0.343  Sum_probs=74.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ...++|||+|||+++++++|+++|++|| +++|+|+++++++++|||||+|.+.++|++|| .+|++.|.+|.|+|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEECC
Confidence            3467999999999999999999999999 45999999999999999999999999999999 579999999999999887


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ...
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            655

>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=99.65  E-value=1.5e-16  Score=131.37  Aligned_cols=80  Identities=16%  Similarity=0.177  Sum_probs=73.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      +.++|||+|||+++++++|+++|++||.|..+.+++++. ++++|||||+|.+.++|++||+.||+..|.|++|+|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            457999999999999999999999999999888888765 8999999999999999999999999999999999999875


Q ss_pred             C
Q psy1534         237 V  237 (587)
Q Consensus       237 ~  237 (587)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.65  E-value=2.9e-16  Score=139.55  Aligned_cols=80  Identities=25%  Similarity=0.298  Sum_probs=74.6

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..+..++|||+|||.++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999 899999999999999996 89999999999999999999999999999999999998


Q ss_pred             ec
Q psy1534         106 EA  107 (587)
Q Consensus       106 ~a  107 (587)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>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=99.65  E-value=4.1e-17  Score=133.29  Aligned_cols=77  Identities=27%  Similarity=0.379  Sum_probs=71.7

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      ++|||+|||.++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.+ |++|++.||+..+.|++|+|.++..+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999 899999999999999997 8999999999999999 99999999999999999999999854

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=9.5e-16  Score=128.29  Aligned_cols=81  Identities=19%  Similarity=0.251  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..+..++|||+|||+++++++| ++|+.|   .+|++++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3457789999999999999999 889987   378888886 99999999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..+.
T Consensus        88 ~a~~~~   93 (102)
T 2fc8_A           88 WAKPKG   93 (102)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            998654

>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=99.65  E-value=3.9e-16  Score=136.11  Aligned_cols=86  Identities=24%  Similarity=0.357  Sum_probs=80.0

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++||+.||+..|.|+.|.|++
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            4457899999999999999999999999999999999997 599999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      +.++...
T Consensus        99 a~~~~~~  105 (126)
T 3ex7_B           99 CFVRGPP  105 (126)
T ss_dssp             SEESSSC
T ss_pred             ecCCCCC
Confidence            9877643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6e-16  Score=129.26  Aligned_cols=81  Identities=23%  Similarity=0.425  Sum_probs=74.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+.++|||+|||+++++++|+++|++||.|   +++++..++++|||||+|.+.++|++||+.||+..|.|++|+|+++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   89 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG   89 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcC
Confidence            456899999999999999999999999976   67777678999999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      ++.+
T Consensus        90 ~~~~   93 (101)
T 2fc9_A           90 PRGS   93 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=8.4e-17  Score=138.72  Aligned_cols=80  Identities=18%  Similarity=0.206  Sum_probs=74.0

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCe----EEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDV----TYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V----~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ....+|||+|||+++|+++| ++|++||+|    .+|+|++|++|++||||||+|.+.++|++||+. |+..|.+|.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            45689999999999999999 899999986    699999999999999999999999999999986 999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      ..+.++
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998744

>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=99.65  E-value=6.5e-16  Score=131.00  Aligned_cols=85  Identities=19%  Similarity=0.214  Sum_probs=77.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCC-eeEEEEe-eCCC-CCcceEEEEEecCHHHHHHHHHHhC--CceeCCeEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGK-VENVEIA-LDKD-GKSRGFGTVEFDHPVEAVQSISMLN--NQNLFERRIT  231 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~i~-~~~~-g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~  231 (587)
                      .+.++|||+|||+++++++|+++|++||. |.+|.|+ +++. ++++|||||+|.+.++|++|++.||  +..+.|++|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            34689999999999999999999999998 9999998 6664 8999999999999999999999996  5899999999


Q ss_pred             EEEccCCCCC
Q psy1534         232 VRMDRVADRL  241 (587)
Q Consensus       232 v~~a~~~~~~  241 (587)
                      |+++.++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999887643

>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=99.65  E-value=3e-16  Score=132.21  Aligned_cols=78  Identities=12%  Similarity=0.117  Sum_probs=70.1

Q ss_pred             CCCCCcEEEcCCCCC-CCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhC--CceeCCeEEEE
Q psy1534          29 APLEVPVVMDLIQGD-ASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH--RFETKGRKLVI  104 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~-~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~--g~~l~gr~i~V  104 (587)
                      .++.++|||+|||++ +++++| ++|++||+|.+|+|++     +||||||+|.+.++|++|++.|+  +..|.||+|+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999998 999999 8999999999999985     47999999999999999999886  46699999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++.++.
T Consensus        97 ~~a~~~~  103 (112)
T 1x4f_A           97 DLSEKYK  103 (112)
T ss_dssp             EEECSCS
T ss_pred             EECcccc
Confidence            9998554

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.65  E-value=4.2e-16  Score=135.44  Aligned_cols=79  Identities=24%  Similarity=0.410  Sum_probs=74.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|++||+|.+|+|++++ +++++|||||+|.+.++|++|+ .||+..|.|++|+|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3568999999999999999 899999999999999996 9999999999999999999999 899999999999999988


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.64  E-value=5.4e-17  Score=137.19  Aligned_cols=83  Identities=19%  Similarity=0.225  Sum_probs=76.7

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCC---eEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGD---VTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL  102 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~---V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i  102 (587)
                      .......+|||+|||+++|+++| ++|+.||.   |.+|+|++|+.|+++|||||+|.+.++|++||+ +|+..|.||.|
T Consensus         6 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            34457789999999999999999 89999998   999999999889999999999999999999998 89999999999


Q ss_pred             EEEecccc
Q psy1534         103 VIKEAVED  110 (587)
Q Consensus       103 ~V~~a~~~  110 (587)
                      +|.++.++
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            99998844

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.64  E-value=7.3e-17  Score=129.00  Aligned_cols=71  Identities=20%  Similarity=0.292  Sum_probs=66.2

Q ss_pred             CcEEEcCCCCCC------CHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCe-EEEE
Q psy1534          33 VPVVMDLIQGDA------SLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR-KLVI  104 (587)
Q Consensus        33 ~~vfV~nlp~~~------t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr-~i~V  104 (587)
                      ++|||+|||+++      ++++| ++|++||+|.+|+|+ ..+|+++|||||+|.+.++|++|++.|||..|.|+ +|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            689999999999      67888 899999999999988 45899999999999999999999999999999999 8876

>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=99.64  E-value=3.9e-16  Score=132.79  Aligned_cols=83  Identities=20%  Similarity=0.250  Sum_probs=76.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHH---HHHHhcCCeeEEEEeeCCC----CCcceEEEEEecCHHHHHHHHHHhCCceeCCeE
Q psy1534         157 PLINKVFVANLDYKVDEKKLR---EVFRLAGKVENVEIALDKD----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR  229 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~---~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  229 (587)
                      ...++|||+|||+++++++|+   ++|++||.|.+|.|++++.    ++++|||||+|.+.++|++||+.||+..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346799999999999999999   9999999999999998874    356799999999999999999999999999999


Q ss_pred             EEEEEccCCC
Q psy1534         230 ITVRMDRVAD  239 (587)
Q Consensus       230 l~v~~a~~~~  239 (587)
                      |+|+++.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998765

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.64  E-value=3.6e-16  Score=134.50  Aligned_cols=81  Identities=14%  Similarity=0.156  Sum_probs=75.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCC---eeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGK---VENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~---i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ...++|||+|||+++++++|+++|+.||.   |..|+|++++.|+++|||||+|.+.++|++||+ ||++.|.|+.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            34679999999999999999999999999   899999999889999999999999999999998 89999999999999


Q ss_pred             EccCC
Q psy1534         234 MDRVA  238 (587)
Q Consensus       234 ~a~~~  238 (587)
                      ++..+
T Consensus        94 ~a~~~   98 (118)
T 2db1_A           94 KSHRT   98 (118)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98654

>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=99.64  E-value=2.1e-16  Score=138.84  Aligned_cols=81  Identities=12%  Similarity=0.131  Sum_probs=75.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCC---eeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGK---VENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~---i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ...++|||+|||+++|+++|+++|++||.   |.+|+|++++.|+++|||||+|.+.++|++||+ ||+..|.||.|.|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            34679999999999999999999999999   899999999889999999999999999999998 99999999999999


Q ss_pred             EccCC
Q psy1534         234 MDRVA  238 (587)
Q Consensus       234 ~a~~~  238 (587)
                      ++..+
T Consensus       121 ~a~~~  125 (136)
T 2hgl_A          121 KSHRT  125 (136)
T ss_dssp             ECCHH
T ss_pred             ECChH
Confidence            97544

>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=99.64  E-value=3.5e-16  Score=131.45  Aligned_cols=81  Identities=26%  Similarity=0.545  Sum_probs=77.1

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++|++.||+..+.|+.|+|+++..
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            4799999999999999999999999999999999997 489999999999999999999999999999999999999887


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        88 ~~   89 (104)
T 1p1t_A           88 EK   89 (104)
T ss_dssp             TT
T ss_pred             cc
Confidence            65

>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=99.64  E-value=5.8e-16  Score=128.84  Aligned_cols=80  Identities=14%  Similarity=0.213  Sum_probs=73.4

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ...+..++|||+|||+++++++| ++|++||+|.+|+|+++     ||||||+|.+.++|++|++.||+..|.|++|+|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            33457789999999999999999 89999999999999865     7999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++.++.
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            998654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.45  E-value=1.3e-17  Score=143.19  Aligned_cols=84  Identities=17%  Similarity=0.305  Sum_probs=78.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEE--------EEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeC
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTY--------VEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETK   98 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~--------v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~   98 (587)
                      .+..++|||+|||+++++++| ++|++||+|.+        |+|++++ +++++|||||+|.+.++|++|++.||+..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            346789999999999999999 89999999999        9999996 8999999999999999999999999999999


Q ss_pred             CeEEEEEecccccC
Q psy1534          99 GRKLVIKEAVEDKG  112 (587)
Q Consensus        99 gr~i~V~~a~~~~~  112 (587)
                      |++|+|.++.++..
T Consensus        84 g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           84 GNPIKVSFATRRAD   97 (116)
Confidence            99999999986543

>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=99.64  E-value=5.7e-16  Score=129.57  Aligned_cols=80  Identities=16%  Similarity=0.109  Sum_probs=72.0

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCc--eeCCeEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ--NLFERRITVR  233 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~v~  233 (587)
                      .++.++|||+|||+++++++|+++|++||.|.+|.|+++     +|||||+|.+.++|.+|++.|++.  .+.|++|.|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            445789999999999999999999999999999999874     789999999999999999988654  5899999999


Q ss_pred             EccCCCC
Q psy1534         234 MDRVADR  240 (587)
Q Consensus       234 ~a~~~~~  240 (587)
                      +++.+..
T Consensus        87 ~a~~~~~   93 (104)
T 1wex_A           87 YSTSKRI   93 (104)
T ss_dssp             ECSSSSC
T ss_pred             EccCccc
Confidence            9987653

>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=99.64  E-value=5.2e-16  Score=125.22  Aligned_cols=77  Identities=13%  Similarity=0.256  Sum_probs=71.0

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHh-CCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l-~g~~l~gr~i~V  104 (587)
                      ...+..++|||+|||.++++++| ++|++||+|.+|+++++     ||||||+|.+.++|++|++.| ++..+.|++|+|
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            44567789999999999999999 89999999999999974     799999999999999999999 999999999999


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      .++.
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>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=99.64  E-value=4.5e-16  Score=141.39  Aligned_cols=82  Identities=23%  Similarity=0.208  Sum_probs=77.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....+|||+|||+++++++| ++|++||+|.+|+|++|+ +|+++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345679999999999999999 899999999999999996 999999999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +..+
T Consensus       147 a~~~  150 (158)
T 2kn4_A          147 ARYG  150 (158)
T ss_dssp             ECCS
T ss_pred             CCCC
Confidence            9854

>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=99.64  E-value=2.2e-16  Score=133.95  Aligned_cols=82  Identities=21%  Similarity=0.210  Sum_probs=75.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCC-eEEEEEe-eCC-CCCcceEEEEEECCHHHHHHHHHHhC--CceeCCeEEE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGD-VTYVEIL-NDD-TGKPRGSAIVEFQSPDLVRKAVNKMH--RFETKGRKLV  103 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~-V~~v~i~-~d~-~g~skG~aFV~F~~~e~A~~Al~~l~--g~~l~gr~i~  103 (587)
                      ...++|||+|||+++++++| ++|++||+ |.+|+|+ +++ +++++|||||+|.+.++|++|++.|+  +..|.|++|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45689999999999999999 89999998 9999998 666 88999999999999999999999996  5999999999


Q ss_pred             EEeccccc
Q psy1534         104 IKEAVEDK  111 (587)
Q Consensus       104 V~~a~~~~  111 (587)
                      |.++.++.
T Consensus        86 V~~a~~~~   93 (109)
T 2dis_A           86 VDWAEPEI   93 (109)
T ss_dssp             EEESCSSC
T ss_pred             EEEcCCCC
Confidence            99998543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.64  E-value=2e-16  Score=124.43  Aligned_cols=74  Identities=22%  Similarity=0.433  Sum_probs=70.4

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +|||+|||+++++++|+++|++||.|.+|.+++++. ++++|||||+|.+.++|++|++ ||+..+.|++|.|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            489999999999999999999999999999999984 9999999999999999999997 8999999999999875

>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=99.64  E-value=6.6e-16  Score=141.29  Aligned_cols=81  Identities=17%  Similarity=0.248  Sum_probs=75.7

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+|||+|||+++++++| ++|++||+|.+|+|++++ +|.++|||||+|.+.++|++||+.||+..|.|++|.|.++.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  150 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  150 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            4457999999999999999 899999999999999996 99999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      .+.
T Consensus       151 ~~~  153 (165)
T 1rk8_A          151 VKG  153 (165)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            543

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

Probab=99.64  E-value=6.1e-16  Score=134.22  Aligned_cols=83  Identities=12%  Similarity=0.232  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHH----HHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLR----EVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRI  230 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  230 (587)
                      ..++.++|||+|||+.+++++|+    ++|++||.|.+|.+.+  +++++|||||+|.+.++|.+|++.|||..|.|++|
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            34567899999999999999876    6999999999988754  57889999999999999999999999999999999


Q ss_pred             EEEEccCCC
Q psy1534         231 TVRMDRVAD  239 (587)
Q Consensus       231 ~v~~a~~~~  239 (587)
                      +|.+++.+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999988764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.64  E-value=5.3e-16  Score=131.13  Aligned_cols=80  Identities=20%  Similarity=0.194  Sum_probs=72.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcC-CeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAG-KVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .+..++|||+|||+++++++|+++|++|| .|..+.|..+   +++|||||+|.+.++|++||+.|||..|.|++|+|++
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            44568999999999999999999999999 8999988643   4789999999999999999999999999999999999


Q ss_pred             ccCC
Q psy1534         235 DRVA  238 (587)
Q Consensus       235 a~~~  238 (587)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8654

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.64  E-value=9.9e-17  Score=141.42  Aligned_cols=85  Identities=22%  Similarity=0.212  Sum_probs=78.1

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+..++|||+|||+++++++| ++|++||+|++|+|++++ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  121 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  121 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33445678999999999999999 899999999999999997 8999999999999999999999999999999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus       122 ~~a~~~~  128 (135)
T 2lea_A          122 QMARYGR  128 (135)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=9e-17  Score=129.74  Aligned_cols=79  Identities=20%  Similarity=0.362  Sum_probs=73.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++|++.||+..+.|+.|++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            3468999999999999999999999999999999999975 999999999999999999999999999999998877654

>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=99.64  E-value=8.1e-16  Score=131.55  Aligned_cols=82  Identities=20%  Similarity=0.348  Sum_probs=76.8

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--------CCe
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL--------FER  228 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--------~g~  228 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+++++++++|||||+|.+.++|++|++.||+..|        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            446899999999999999999999999999999999998899999999999999999999999999999        588


Q ss_pred             EEEEEEccCC
Q psy1534         229 RITVRMDRVA  238 (587)
Q Consensus       229 ~l~v~~a~~~  238 (587)
                      +|.|+|+.+.
T Consensus       103 ~l~v~~a~p~  112 (114)
T 1x5o_A          103 PLLCKFSGPS  112 (114)
T ss_dssp             CBEEEECCCS
T ss_pred             ceeEEccCCC
Confidence            8999998754

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

Probab=99.64  E-value=3.2e-16  Score=135.96  Aligned_cols=80  Identities=16%  Similarity=0.219  Sum_probs=72.1

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-----HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-----SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-----~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      .++..+|||+|||+++++++|     ++|++||+|.+|.+.  .++++||||||+|.+.++|++|++.|||..|.|++|+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            345678999999999999986     479999999998875  3688999999999999999999999999999999999


Q ss_pred             EEecccc
Q psy1534         104 IKEAVED  110 (587)
Q Consensus       104 V~~a~~~  110 (587)
                      |.++..+
T Consensus       104 V~~a~~~  110 (127)
T 2a3j_A          104 ITFSETP  110 (127)
T ss_dssp             EEECCCC
T ss_pred             EEEccCc
Confidence            9999844

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.64  E-value=7.2e-16  Score=129.72  Aligned_cols=82  Identities=21%  Similarity=0.310  Sum_probs=75.3

Q ss_pred             CCCcEEEEecCCCCC------cHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCe-E
Q psy1534         157 PLINKVFVANLDYKV------DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFER-R  229 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~------te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-~  229 (587)
                      ...++|||+|||+.+      ++++|+++|++||.|.+|.|+ ..+|+++|||||+|.+.++|.+||+.|||..|.|+ +
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            346899999999999      889999999999999999998 34689999999999999999999999999999998 9


Q ss_pred             EEEEEccCCC
Q psy1534         230 ITVRMDRVAD  239 (587)
Q Consensus       230 l~v~~a~~~~  239 (587)
                      |+|+++....
T Consensus        92 l~V~~a~~~~  101 (105)
T 2nlw_A           92 FRVNLFTDFD  101 (105)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEEcchHh
Confidence            9999987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=6.8e-16  Score=130.20  Aligned_cols=78  Identities=22%  Similarity=0.330  Sum_probs=73.1

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .++|||+|||+++++++|+++|+.| .|.+|.|+++++|+++|||||+|.+.++|++|| .+|++.|.||.|.|..+..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            4699999999999999999999999 899999999988999999999999999999999 68999999999999887543

>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=99.63  E-value=1.5e-16  Score=132.75  Aligned_cols=83  Identities=28%  Similarity=0.448  Sum_probs=74.5

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC--CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      .....++|||+|||+++++++|+++|+.|| |.+|.|++++  .++++|||||+|.+.++|.+|| .||+..|.|+.|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345578999999999999999999999999 9999999997  4999999999999999999999 89999999999999


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      ++++.+.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9987654

>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=99.63  E-value=6e-16  Score=129.96  Aligned_cols=82  Identities=18%  Similarity=0.223  Sum_probs=75.5

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE-EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++++++|+++|++||.|.+ |.|+++.+++++|||||+|.+.++|++||+. |+..+.||.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            34679999999999999999999999999987 8899987799999999999999999999987 999999999999988


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      ..+.
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            6554

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=9e-16  Score=131.67  Aligned_cols=82  Identities=22%  Similarity=0.404  Sum_probs=77.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|..|.|++++. ++++|||||+|.+.++|++||+. ++..|.|+.|.|+++.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            57999999999999999999999999999999999975 99999999999999999999988 99999999999999987


Q ss_pred             CCCC
Q psy1534         238 ADRL  241 (587)
Q Consensus       238 ~~~~  241 (587)
                      +...
T Consensus       106 ~~~~  109 (116)
T 1x4b_A          106 REES  109 (116)
T ss_dssp             CCCC
T ss_pred             CccC
Confidence            7643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.3e-15  Score=124.32  Aligned_cols=79  Identities=24%  Similarity=0.407  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|+       +|||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            3456899999999999999999999999999999997       579999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      +++...
T Consensus        78 ~~~~~~   83 (90)
T 2dnq_A           78 KNKSKA   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            877643

>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=99.63  E-value=3.1e-16  Score=134.11  Aligned_cols=82  Identities=16%  Similarity=0.246  Sum_probs=76.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCe-eEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKV-ENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i-~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++++++|+++|+.||.| ..|+|+++++++++|||||+|.+.++|++||+. |+..|.|++|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            346799999999999999999999999999 899999999999999999999999999999987 999999999999998


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      ..+.
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>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=99.63  E-value=8e-17  Score=126.68  Aligned_cols=73  Identities=25%  Similarity=0.327  Sum_probs=69.1

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +|||+|||+++++++| ++|++||+|.+|++++++ +++++|||||+|.+.++|++|++. ++..+.|++|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            6999999999999999 899999999999999996 899999999999999999999975 899999999999875

>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=99.63  E-value=1.6e-15  Score=128.59  Aligned_cols=82  Identities=13%  Similarity=0.309  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .....++|||+|||+++++++|+++|++||.|.+|.|+++     +|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            3445789999999999999999999999999999999986     78999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      ++++...
T Consensus        96 a~~~~~~  102 (109)
T 1x4g_A           96 GKESPDM  102 (109)
T ss_dssp             CCCCCSS
T ss_pred             cCCCCCC
Confidence            9887643

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.63  E-value=2.6e-16  Score=131.75  Aligned_cols=80  Identities=26%  Similarity=0.354  Sum_probs=74.9

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++|||+|||+++++++| ++|++||+|.+|+|+++++++++|||||+|.+.++|++|++  ++..|.|++|.|.++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            45679999999999999999 89999999999999999999999999999999999999997  9999999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      ++.
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            553

>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=99.63  E-value=1.5e-16  Score=129.97  Aligned_cols=80  Identities=30%  Similarity=0.548  Sum_probs=72.7

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      ++|||+|||+++++++|+++|++||.|.+|.+++++. ++++|||||+|.+.+ |.+|++.||+..+.|++|+|+++...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            5899999999999999999999999999999999986 999999999999999 99999999999999999999999876


Q ss_pred             CC
Q psy1534         239 DR  240 (587)
Q Consensus       239 ~~  240 (587)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>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=99.63  E-value=5.2e-16  Score=132.73  Aligned_cols=80  Identities=28%  Similarity=0.425  Sum_probs=76.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|+.||.|.+|.|++++. ++++|||||+|.+.++|++|| .||+..|.|+.|.|+++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            57999999999999999999999999999999999986 899999999999999999999 9999999999999999876


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus       104 ~~  105 (114)
T 2cq4_A          104 EK  105 (114)
T ss_dssp             HH
T ss_pred             Cc
Confidence            54

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.6e-15  Score=124.37  Aligned_cols=77  Identities=12%  Similarity=0.213  Sum_probs=71.0

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+..++|||+|||+++++++| ++|++||+|.+|+|++       +||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            3456789999999999999999 8999999999999985       4999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        79 a~~~~   83 (92)
T 2dgt_A           79 STSRL   83 (92)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            98554

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.63  E-value=4.5e-16  Score=131.44  Aligned_cols=76  Identities=16%  Similarity=0.152  Sum_probs=69.9

Q ss_pred             CcEEEcCC----CCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECC----HHH----HHHHHH--HhCCce
Q psy1534          33 VPVVMDLI----QGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQS----PDL----VRKAVN--KMHRFE   96 (587)
Q Consensus        33 ~~vfV~nl----p~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~----~e~----A~~Al~--~l~g~~   96 (587)
                      .+|||+||    |+.+++++| ++|++||+|.+|+++.|+ ||+++|||||+|.+    +++    |.+|++  .|++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            78999999    999999999 899999999999999998 99999999999996    444    899998  789999


Q ss_pred             eCCeEEEEEecc
Q psy1534          97 TKGRKLVIKEAV  108 (587)
Q Consensus        97 l~gr~i~V~~a~  108 (587)
                      |.|++|+|..-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999876

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.63  E-value=2.3e-16  Score=138.54  Aligned_cols=84  Identities=18%  Similarity=0.259  Sum_probs=77.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE--EEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCc----eeCCe
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVEN--VEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQ----NLFER  228 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~----~~~g~  228 (587)
                      ....++|||+|||+++++++|+++|++||.|..  |+|++|+ +++++|||||+|.+. +|.+|++.||+.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345689999999999999999999999999976  9999999 599999999999999 999999999999    99999


Q ss_pred             EEEEEEccCCCC
Q psy1534         229 RITVRMDRVADR  240 (587)
Q Consensus       229 ~l~v~~a~~~~~  240 (587)
                      +|.|+++++..+
T Consensus        99 ~l~V~~a~~~~~  110 (131)
T 2m2b_A           99 TINVEFAKGSKR  110 (131)
T ss_dssp             CCCCEECCCSCC
T ss_pred             EEEEEECCCCCC
Confidence            999999987653

>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=99.63  E-value=2.2e-16  Score=136.45  Aligned_cols=81  Identities=21%  Similarity=0.279  Sum_probs=73.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeE--EEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVT--YVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~--~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      .....+|||+|||+++|+++| ++|++| .|.  +|+|++|++|++||||||+|.++++|++||+. ++..|.||+|.|.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~  116 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVF  116 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEE
Confidence            346678999999999999999 899999 677  99999998899999999999999999999975 7899999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++.+++
T Consensus       117 ~a~~~e  122 (126)
T 2hgm_A          117 KSSQEE  122 (126)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=3.2e-15  Score=122.50  Aligned_cols=78  Identities=23%  Similarity=0.350  Sum_probs=72.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.+++       +||||+|.+.++|++|++.||+..+.|+.|+|+++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            44578999999999999999999999999999999985       49999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      +++.+
T Consensus        80 ~~~~~   84 (92)
T 2dgt_A           80 TSRLR   84 (92)
T ss_dssp             SCCCS
T ss_pred             cCCCC
Confidence            87754

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.63  E-value=1.7e-15  Score=131.53  Aligned_cols=80  Identities=24%  Similarity=0.430  Sum_probs=75.7

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|.+|.|++++ +++++|||||+|.+.++|++|| .||+..|.|+.|+|++++.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            5799999999999999999999999999999999997 4999999999999999999999 8999999999999999876


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.63  E-value=1.2e-15  Score=126.43  Aligned_cols=79  Identities=14%  Similarity=0.244  Sum_probs=73.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF--ERRITVR  233 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~  233 (587)
                      .++.++|||+|||+++++++|+++|++||.|.+|.+.++     +|||||+|.+.++|++|++.||+..+.  |++|+|+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            345689999999999999999999999999999999865     689999999999999999999999999  9999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      +++++.
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998765

>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=99.63  E-value=2.5e-15  Score=124.43  Aligned_cols=71  Identities=18%  Similarity=0.275  Sum_probs=68.5

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCccc--CceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRID--GKIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~--g~~i~v~~  586 (587)
                      .++|||.|||+++|++||+++|++||.|..+++..++++|||+|++.++|++||+.||+..|.  |++|+|.+
T Consensus        17 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~   89 (97)
T 1why_A           17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEE
Confidence            579999999999999999999999999999999888899999999999999999999999999  99999986

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=2.6e-16  Score=124.39  Aligned_cols=75  Identities=25%  Similarity=0.413  Sum_probs=71.7

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ++|||+|||+++++++|+++|++||.|.+|.+++++. ++++|||||+|.+.++|++|++.++ ..+.|++|.|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            4799999999999999999999999999999999975 9999999999999999999999999 9999999999986

>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=99.62  E-value=3.7e-16  Score=150.48  Aligned_cols=79  Identities=14%  Similarity=0.265  Sum_probs=74.3

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCC--CeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVG--DVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G--~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ...+|||+|||+++|+++| ++|++||  +|++|+|++|+ ++++||||||+|.+.++|++||+.||+..|.|++|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            4568999999999999999 8999999  99999999997 999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy1534         107 AVE  109 (587)
Q Consensus       107 a~~  109 (587)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            873

>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=99.62  E-value=1.2e-15  Score=129.33  Aligned_cols=79  Identities=14%  Similarity=0.223  Sum_probs=73.3

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+..++|||+|||.++++++| ++|++||+|.+|+|+++     +|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            3456789999999999999999 89999999999999986     79999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        96 a~~~~  100 (109)
T 1x4g_A           96 GKESP  100 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98554

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=8.2e-16  Score=128.42  Aligned_cols=78  Identities=28%  Similarity=0.434  Sum_probs=73.5

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      ++|||+|||+++++++|+++|++||.|.+|.|+++    ++|||||+|.+.++|++|++.||+..+.|++|.|+++..+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            48999999999999999999999999999999987    68999999999999999999999999999999999998876


Q ss_pred             CC
Q psy1534         240 RL  241 (587)
Q Consensus       240 ~~  241 (587)
                      +.
T Consensus        77 ~~   78 (101)
T 2hvz_A           77 RR   78 (101)
T ss_dssp             CS
T ss_pred             Cc
Confidence            44

>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=99.62  E-value=3.7e-15  Score=124.90  Aligned_cols=79  Identities=25%  Similarity=0.394  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+.++|||+|||+++++++|+++|++||.|..|.|++       +||||+|.+.++|++||+.||+..|.|++|.|+++.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            3468999999999999999999999999999999874       599999999999999999999999999999999998


Q ss_pred             CCCCCC
Q psy1534         237 VADRLD  242 (587)
Q Consensus       237 ~~~~~~  242 (587)
                      ++....
T Consensus        82 ~~~~~~   87 (103)
T 2dgu_A           82 PPDQKR   87 (103)
T ss_dssp             CCCCCC
T ss_pred             CCcccc
Confidence            876443

>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=99.62  E-value=9.8e-17  Score=141.33  Aligned_cols=81  Identities=20%  Similarity=0.134  Sum_probs=73.9

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .....+|||+|||+++|+++| ++|++|| |.+|+|++|++|++||||||+|.+.++|++|| .+|+..|.+|.|.|.++
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            346679999999999999999 8999999 67999999988999999999999999999999 78999999999999998


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      ..+.
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8554

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.6e-15  Score=123.75  Aligned_cols=77  Identities=12%  Similarity=0.237  Sum_probs=71.1

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+..++|||+|||+++++++| ++|++||+|.+|+|++       +||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3467789999999999999999 8999999999999985       4999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +.++.
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98553

>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=99.62  E-value=2e-15  Score=126.52  Aligned_cols=76  Identities=17%  Similarity=0.182  Sum_probs=70.2

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....++|||+|||+++++++| ++|++||+|.+|+|++       +||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            346689999999999999999 8999999999999874       69999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      ..+.
T Consensus        81 ~~~~   84 (103)
T 2dgu_A           81 KPPD   84 (103)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            8554

>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=99.62  E-value=2.1e-16  Score=135.48  Aligned_cols=83  Identities=17%  Similarity=0.235  Sum_probs=72.6

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+...+|||+|||+++++++| ++|++||.|.+|.+..+. +++++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            346689999999999999999 899999999544333332 788999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus       102 a~~~~  106 (115)
T 2cpx_A          102 GKNKK  106 (115)
T ss_dssp             CCCCS
T ss_pred             ccCCC
Confidence            98554

>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=99.61  E-value=3.3e-15  Score=123.65  Aligned_cols=78  Identities=19%  Similarity=0.445  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEecCCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         155 NCPLINKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..++.++|||+|||+ ++++++|+++|++||.|.+|.|.       +|||||+|.+.++|.+|++.||+..+.|++|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            455688999999998 99999999999999999999983       6899999999999999999999999999999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      +++.+.
T Consensus        91 ~a~~~~   96 (97)
T 2xnq_A           91 VSSSNA   96 (97)
T ss_dssp             ECCCCC
T ss_pred             ecCCCC
Confidence            987654

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

Probab=99.61  E-value=1.4e-15  Score=127.00  Aligned_cols=80  Identities=16%  Similarity=0.220  Sum_probs=73.2

Q ss_pred             CCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         154 INCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       154 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ...+..++|||+|||+++++++|+++|++||.|.+|++.+     ++|||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus        22 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             TSCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             cCCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3455678999999999999999999999999999999984     47999999999999999999999999999999999


Q ss_pred             EccCC
Q psy1534         234 MDRVA  238 (587)
Q Consensus       234 ~a~~~  238 (587)
                      +++++
T Consensus        97 ~a~~~  101 (101)
T 2la4_A           97 WGKER  101 (101)
T ss_dssp             BCCCC
T ss_pred             eccCC
Confidence            98753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.61  E-value=4.4e-16  Score=124.41  Aligned_cols=72  Identities=22%  Similarity=0.375  Sum_probs=67.2

Q ss_pred             cEEEEecCCCCC------cHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCe-EEEE
Q psy1534         160 NKVFVANLDYKV------DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFER-RITV  232 (587)
Q Consensus       160 ~~l~V~nLp~~~------te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-~l~v  232 (587)
                      ++|||+|||+.+      ++++|+++|++||.|.+|.|+ ..+|+++|||||+|.+.++|++|++.|||..+.|+ +|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            689999999999      789999999999999999988 34689999999999999999999999999999999 8876

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=3.8e-15  Score=121.55  Aligned_cols=78  Identities=22%  Similarity=0.405  Sum_probs=72.0

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++       +||||+|.+.++|++|++.||+..+.|++|+|+++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            34568999999999999999999999999999999985       49999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      .+...
T Consensus        79 ~~~~~   83 (90)
T 2dnp_A           79 TKGQK   83 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

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

Probab=99.61  E-value=7.3e-16  Score=128.72  Aligned_cols=76  Identities=13%  Similarity=0.191  Sum_probs=70.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .+..++|||+|||.++++++| ++|++||+|.+|+|++     ++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            345689999999999999999 8999999999999984     5799999999999999999999999999999999988


Q ss_pred             cc
Q psy1534         108 VE  109 (587)
Q Consensus       108 ~~  109 (587)
                      .+
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.61  E-value=2.9e-15  Score=124.55  Aligned_cols=73  Identities=30%  Similarity=0.458  Sum_probs=69.8

Q ss_pred             CCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         514 IERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       514 ~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .+.++|||.|||+++|+++|+++|++||.|..+.+.+++++|||+|++.++|++||+.||+..|.|++|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            3467999999999999999999999999999999999899999999999999999999999999999999986

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.61  E-value=2.2e-15  Score=133.77  Aligned_cols=80  Identities=33%  Similarity=0.545  Sum_probs=74.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999999975 89999999999999999999999999999999999987


Q ss_pred             c
Q psy1534         235 D  235 (587)
Q Consensus       235 a  235 (587)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.61  E-value=9.7e-16  Score=141.45  Aligned_cols=82  Identities=17%  Similarity=0.214  Sum_probs=77.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .+...+|||+|||+++++++| ++|++||+|++|+|+.++++.++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345679999999999999999 8999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            844

>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=99.61  E-value=2e-15  Score=127.12  Aligned_cols=74  Identities=14%  Similarity=0.156  Sum_probs=68.3

Q ss_pred             CCCCCeEEEeCCCCC-CChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCC--CcccCceEEEEE
Q psy1534         513 NIERDTVVVKNLPPT-ITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDR--TRIDGKIIDVTF  586 (587)
Q Consensus       513 ~~~~~~v~V~~Lp~~-~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g--~~~~g~~i~v~~  586 (587)
                      ..+..+|||+|||++ +|++||+++|++||.|..+.|.+.+++|||+|++.++|+.||+.||+  ..|.||+|+|.+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   98 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   98 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            445789999999998 99999999999999999999998899999999999999999998864  569999999975

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=4.6e-15  Score=123.38  Aligned_cols=78  Identities=15%  Similarity=0.127  Sum_probs=70.7

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccC--CCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTV--GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~--G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      ...+..++|||+|||+++++++| ++|++|  |.|.+|+++       +|||||+|.+.++|++|++.||+..|.|++|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            33456789999999999999999 899999  999999875       47999999999999999999999999999999


Q ss_pred             EEeccccc
Q psy1534         104 IKEAVEDK  111 (587)
Q Consensus       104 V~~a~~~~  111 (587)
                      |.++..+.
T Consensus        83 v~~a~~~~   90 (99)
T 2cpd_A           83 VTLAKPVD   90 (99)
T ss_dssp             EECCCCCC
T ss_pred             EEECCCCC
Confidence            99998554

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-15  Score=125.31  Aligned_cols=80  Identities=23%  Similarity=0.338  Sum_probs=72.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+..++|||+|||+++++++|+++|++||.|. +.++.+   +++|||||+|.+.++|++|++.||+..|.|++|.|+++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34468999999999999999999999999997 667664   56899999999999999999999999999999999999


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      +++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.61  E-value=1.8e-15  Score=128.40  Aligned_cols=75  Identities=21%  Similarity=0.236  Sum_probs=69.3

Q ss_pred             CCCCcEEEcCCCCC-CCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGD-ASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~-~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +..++|||+|||++ +++++| ++|++||+|.+|+|       ++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            45579999999999 999999 89999999999998       4699999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      ..++
T Consensus        98 ~~~~  101 (110)
T 1wf1_A           98 GEPK  101 (110)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8443

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.61  E-value=1.6e-15  Score=128.22  Aligned_cols=78  Identities=19%  Similarity=0.247  Sum_probs=70.6

Q ss_pred             cCCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          26 ETGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        26 ~~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ........+|||+|||+++++++| ++|++||+|++|+|+       +|||||+|.+.++|++|++.||+..|.|++|.|
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   97 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV   97 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            344567789999999999999999 899999999999998       589999999999999999999999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++..+
T Consensus        98 ~~a~~~  103 (108)
T 2jvo_A           98 VYSKLP  103 (108)
T ss_dssp             ESCSCC
T ss_pred             EEecCC
Confidence            999854

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.61  E-value=1.2e-16  Score=133.54  Aligned_cols=81  Identities=15%  Similarity=0.218  Sum_probs=73.3

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....+|||+|||+++++++| ++|++||+|.+ .++++. +++++|||||+|.+.++|++|++ ||+..|.|++|+|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345679999999999999999 89999999998 666665 89999999999999999999998 999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            98543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.61  E-value=2.3e-15  Score=127.18  Aligned_cols=79  Identities=23%  Similarity=0.416  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .....++|||+|||+++++++|+++|++||.|.+|.|+       +|||||+|.+.++|++|++.||+..+.|++|.|++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34567899999999999999999999999999999998       58999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      ++.+.+
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            987654

>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=99.60  E-value=1.1e-15  Score=126.69  Aligned_cols=82  Identities=15%  Similarity=0.349  Sum_probs=74.9

Q ss_pred             CCCCcEEEEecCCCCCcHHHHH----HHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLR----EVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      .++.++|||+|||+++++++|+    ++|++||.|.+|.+++  +++++|||||+|.+.++|.+|++.||+..+.|++|+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            4567899999999999999999    9999999999999874  466789999999999999999999999999999999


Q ss_pred             EEEccCCC
Q psy1534         232 VRMDRVAD  239 (587)
Q Consensus       232 v~~a~~~~  239 (587)
                      |++++++.
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99998765

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=3.8e-15  Score=124.61  Aligned_cols=82  Identities=22%  Similarity=0.387  Sum_probs=74.3

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..+.++|||+|||+++++++|+++|+.|   ..|.+++++ +++++|||||+|.+.++|++||+.||+..|.|+.|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3456899999999999999999999977   378888887 489999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      ++++..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            987754

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=9.5e-16  Score=127.03  Aligned_cols=79  Identities=22%  Similarity=0.350  Sum_probs=71.3

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+...+|||+|||+++++++| ++|++||+|. ++++.+   +++|||||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3456789999999999999999 8999999997 777764   6789999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +..+
T Consensus        91 a~~~   94 (97)
T 2e5j_A           91 ARQQ   94 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9854

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.60  E-value=1.1e-15  Score=126.27  Aligned_cols=79  Identities=16%  Similarity=0.223  Sum_probs=71.3

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..+...+|||+|||+++++++| ++|++||+|..|    ..+++++|||||+|.+.++|++|++.|++..|.|++|+|.+
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3446689999999999999999 899999988766    44788999999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +..+
T Consensus        88 a~~~   91 (96)
T 1fjc_A           88 TGEK   91 (96)
T ss_dssp             CSSS
T ss_pred             cCCC
Confidence            9754

>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=99.60  E-value=3.6e-15  Score=120.23  Aligned_cols=73  Identities=22%  Similarity=0.385  Sum_probs=69.5

Q ss_pred             CCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHh-CCCcccCceEEEEE
Q psy1534         514 IERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMM-DRTRIDGKIIDVTF  586 (587)
Q Consensus       514 ~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l-~g~~~~g~~i~v~~  586 (587)
                      .+.++|||.|||.++|+++|+++|++||.|..+.+.+++++|||+|++.++|++||+.| |+..|.|++|+|.+
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            34679999999999999999999999999999999998899999999999999999999 99999999999986

>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=99.60  E-value=3.2e-15  Score=123.76  Aligned_cols=77  Identities=17%  Similarity=0.325  Sum_probs=69.6

Q ss_pred             CCCCCCCcEEEcCCCC-CCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQG-DASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~-~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ...+..++|||+|||+ ++++++| ++|++||+|.+|+|.       +|||||+|.+.++|++|++.||+..+.|++|+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3445778999999998 9999999 899999999999984       689999999999999999999999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++..+
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            998743

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=8.1e-16  Score=132.56  Aligned_cols=79  Identities=18%  Similarity=0.158  Sum_probs=73.0

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCe----eEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKV----ENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i----~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .++|||+|||+++|+++|+++|++||.|    ..|.|+++++|+++|||||+|.+.++|++||+. |++.|.+|.|.|..
T Consensus        23 ~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~  101 (123)
T 2dha_A           23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFR  101 (123)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEE
Confidence            5799999999999999999999999975    689999998899999999999999999999986 99999999999988


Q ss_pred             ccCC
Q psy1534         235 DRVA  238 (587)
Q Consensus       235 a~~~  238 (587)
                      +..+
T Consensus       102 a~~~  105 (123)
T 2dha_A          102 STAA  105 (123)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7544

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=8.1e-15  Score=121.85  Aligned_cols=78  Identities=26%  Similarity=0.399  Sum_probs=71.8

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhc--CCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLA--GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..+.++|||+|||+++++++|+++|++|  |.|.+|.+.       +|||||+|.+.++|++|++.||+..|.|++|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3457899999999999999999999999  999999875       5799999999999999999999999999999999


Q ss_pred             EccCCCC
Q psy1534         234 MDRVADR  240 (587)
Q Consensus       234 ~a~~~~~  240 (587)
                      +++++.+
T Consensus        85 ~a~~~~~   91 (99)
T 2cpd_A           85 LAKPVDK   91 (99)
T ss_dssp             CCCCCCC
T ss_pred             ECCCCCC
Confidence            9987764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.60  E-value=1.2e-15  Score=127.61  Aligned_cols=81  Identities=27%  Similarity=0.512  Sum_probs=75.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|++++.++++|||||+|.+.++|++|++  ++..+.|+.|.|.++..
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCc
Confidence            4579999999999999999999999999999999999889999999999999999999997  99999999999999877


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      +..
T Consensus        86 ~~~   88 (102)
T 2xs2_A           86 KQN   88 (102)
T ss_dssp             CC-
T ss_pred             Ccc
Confidence            653

>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=99.60  E-value=2e-15  Score=129.20  Aligned_cols=69  Identities=32%  Similarity=0.607  Sum_probs=65.1

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCce-----EEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKI-----IDVT  585 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~-----i~v~  585 (587)
                      .++|||.|||+++||+||+++|++||+|..+.|..+ ++|||+|++.++|++||+.||+.+|.|++     |+|.
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~   89 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   89 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEec
Confidence            689999999999999999999999999999999887 99999999999999999999999999998     6664

>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=99.60  E-value=3.2e-15  Score=122.80  Aligned_cols=78  Identities=19%  Similarity=0.303  Sum_probs=70.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCC-eeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCC-ceeCCeEEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGK-VENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN-QNLFERRITVRM  234 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-~~~~g~~l~v~~  234 (587)
                      ...++|||+|||+++++++|+++|++||. |..+.+.      ++|||||+|.+.++|++|++.||+ ..+.|++|+|++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            44679999999999999999999999999 6666663      378999999999999999999999 999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      ++++..
T Consensus        80 a~~~~~   85 (93)
T 2cqh_A           80 SVSKKL   85 (93)
T ss_dssp             CCCCCC
T ss_pred             ccCccc
Confidence            987654

>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=99.59  E-value=4.3e-16  Score=131.57  Aligned_cols=82  Identities=13%  Similarity=0.185  Sum_probs=76.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCC---eeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGK---VENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~---i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      ....++|||+|||+++++++|+++|+.||.   |.+|.|++++.|+++|||||+|.+.++|++||+ +|+..+.|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            345689999999999999999999999988   899999999889999999999999999999998 8999999999999


Q ss_pred             EEccCC
Q psy1534         233 RMDRVA  238 (587)
Q Consensus       233 ~~a~~~  238 (587)
                      .++..+
T Consensus        87 ~~a~~~   92 (107)
T 2lmi_A           87 YEINNE   92 (107)
T ss_dssp             EECCHH
T ss_pred             EECCHH
Confidence            987654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=4.3e-15  Score=122.26  Aligned_cols=76  Identities=17%  Similarity=0.177  Sum_probs=68.0

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++|||+|||+++++++| ++|++||+|.+|  +.++ +++   ||||+|.+.++|++|++ ||+..|.|++|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            45679999999999999999 899999999997  5554 664   99999999999999999 9999999999999988


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      ..+.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7543

>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=99.59  E-value=2.8e-15  Score=128.33  Aligned_cols=83  Identities=17%  Similarity=0.296  Sum_probs=74.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCe----eEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKV----ENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i----~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      ..+.++|||+|||+++++++|+++|++||.|    ..+.+.   .++++|||||+|.+.++|++||+.||+..|.|++|.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3457899999999999999999999999998    455544   578899999999999999999999999999999999


Q ss_pred             EEEccCCCCC
Q psy1534         232 VRMDRVADRL  241 (587)
Q Consensus       232 v~~a~~~~~~  241 (587)
                      |+++..+...
T Consensus        99 v~~a~~~~~~  108 (115)
T 2cpx_A           99 IEFGKNKKQR  108 (115)
T ss_dssp             EEECCCCSCC
T ss_pred             EEEccCCCCC
Confidence            9999887643

>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=99.59  E-value=2.7e-15  Score=123.18  Aligned_cols=78  Identities=13%  Similarity=0.198  Sum_probs=69.7

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCC-eEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCC-ceeCCeEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGD-VTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHR-FETKGRKLVI  104 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~-V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g-~~l~gr~i~V  104 (587)
                      ..+..++|||+|||+++++++| ++|++||+ |..+.+.      ++|||||+|.+.++|++|++.||+ ..|.|++|+|
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            3456789999999999999999 89999999 6767664      379999999999999999999999 9999999999


Q ss_pred             Eeccccc
Q psy1534         105 KEAVEDK  111 (587)
Q Consensus       105 ~~a~~~~  111 (587)
                      .++..+.
T Consensus        78 ~~a~~~~   84 (93)
T 2cqh_A           78 DYSVSKK   84 (93)
T ss_dssp             EECCCCC
T ss_pred             EEccCcc
Confidence            9998553

>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=99.59  E-value=3.3e-15  Score=121.33  Aligned_cols=74  Identities=15%  Similarity=0.341  Sum_probs=69.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..++|||+|||+++++++| ++|++| +|.+|+|.     +++|||||+|.+.++|++|++.||+..+.|++|+|.++..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            5689999999999999999 899999 99999985     5789999999999999999999999999999999999974


Q ss_pred             c
Q psy1534         110 D  110 (587)
Q Consensus       110 ~  110 (587)
                      +
T Consensus        78 ~   78 (88)
T 1wg1_A           78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.59  E-value=7.7e-15  Score=124.52  Aligned_cols=77  Identities=18%  Similarity=0.368  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCC-CcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYK-VDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ....++|||+|||++ +++++|+++|++||.|.+|.|       ++|||||+|.+.++|++|++.||+..|.|++|+|++
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            334689999999999 999999999999999999998       378999999999999999999999999999999999


Q ss_pred             ccCCC
Q psy1534         235 DRVAD  239 (587)
Q Consensus       235 a~~~~  239 (587)
                      ++...
T Consensus        97 a~~~~  101 (110)
T 1wf1_A           97 AGEPK  101 (110)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            97654

>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=99.59  E-value=2.1e-15  Score=127.11  Aligned_cols=76  Identities=12%  Similarity=0.110  Sum_probs=68.6

Q ss_pred             CCCCcEEE--cCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCcee-----CCeE
Q psy1534          30 PLEVPVVM--DLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET-----KGRK  101 (587)
Q Consensus        30 ~~~~~vfV--~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l-----~gr~  101 (587)
                      ++.++|||  +||++++++++| ++|++||+|++|.|+.+     ||||||+|.+.++|++|++.|||..|     .+++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            45678999  779999999999 89999999999988753     79999999999999999999999998     6899


Q ss_pred             EEEEecccc
Q psy1534         102 LVIKEAVED  110 (587)
Q Consensus       102 i~V~~a~~~  110 (587)
                      |.|.++...
T Consensus        98 l~v~~a~~~  106 (114)
T 2cq2_A           98 LYLNFVEKV  106 (114)
T ss_dssp             CEEEEESCC
T ss_pred             EEEEecccC
Confidence            999998844

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

Probab=99.58  E-value=1.5e-15  Score=125.48  Aligned_cols=76  Identities=17%  Similarity=0.298  Sum_probs=69.2

Q ss_pred             CCCCCcEEEcCCCC-CCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQG-DASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~-~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+...+|||+|||+ ++++++| ++|++||+|.+|+|.       +|||||+|.+.++|++|++.||+..+.|++|+|.+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            35678999999998 9999999 899999999999985       58999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..+.
T Consensus        80 a~~~~   84 (96)
T 2kvi_A           80 SSSNA   84 (96)
T ss_dssp             EECCC
T ss_pred             cCcCC
Confidence            98543

>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=99.58  E-value=2.4e-15  Score=144.75  Aligned_cols=81  Identities=16%  Similarity=0.305  Sum_probs=75.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcC--CeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAG--KVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G--~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..++|||+|||+++++++|+++|++||  .|++|+|++|+ +++++|||||+|.+.++|++||+.||++.|.|+.|+|++
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            457999999999999999999999999  99999999997 499999999999999999999999999999999999999


Q ss_pred             ccCC
Q psy1534         235 DRVA  238 (587)
Q Consensus       235 a~~~  238 (587)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8654

>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=99.58  E-value=8.2e-16  Score=120.83  Aligned_cols=74  Identities=27%  Similarity=0.460  Sum_probs=69.9

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +|||+|||+++++++|+++|++||.|.+|.+++++. ++++|||||+|.+.++|++|++. ++..+.|++|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999875 89999999999999999999975 899999999999875

>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=99.58  E-value=4.6e-15  Score=124.99  Aligned_cols=80  Identities=13%  Similarity=0.195  Sum_probs=71.6

Q ss_pred             CCCCCcEEEE--ecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-----CC
Q psy1534         155 NCPLINKVFV--ANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL-----FE  227 (587)
Q Consensus       155 ~~~~~~~l~V--~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-----~g  227 (587)
                      ...++++|||  +||++++++++|+++|++||.|.+|.|+.+     +|||||+|.+.++|++|++.|||+.+     .+
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            4456789999  779999999999999999999999988753     78999999999999999999999998     68


Q ss_pred             eEEEEEEccCCC
Q psy1534         228 RRITVRMDRVAD  239 (587)
Q Consensus       228 ~~l~v~~a~~~~  239 (587)
                      ++|.|.++...+
T Consensus        96 ~~l~v~~a~~~p  107 (114)
T 2cq2_A           96 ITLYLNFVEKVQ  107 (114)
T ss_dssp             EECEEEEESCCC
T ss_pred             cEEEEEecccCc
Confidence            999999987554

>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=99.58  E-value=3.7e-15  Score=126.60  Aligned_cols=72  Identities=17%  Similarity=0.311  Sum_probs=68.9

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      ..++|||.|||+++|++||+++|.+||.|..+.+...+++|||+|.+.++|++||+.|||..|.|+.|+|.+
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   80 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            357999999999999999999999999999999988889999999999999999999999999999999976

>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=99.58  E-value=4.7e-16  Score=136.97  Aligned_cols=80  Identities=25%  Similarity=0.344  Sum_probs=74.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||++++|++|+++|++|| |++|.|+++++++++|||||+|.+.++|++|| .+|+..|.+|.|+|.++..
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~  122 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNST  122 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCC
Confidence            357999999999999999999999999 77999999988999999999999999999999 7899999999999998876


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      ..
T Consensus       123 ~~  124 (139)
T 2hgn_A          123 TG  124 (139)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

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

Probab=99.58  E-value=2.8e-15  Score=123.94  Aligned_cols=79  Identities=22%  Similarity=0.463  Sum_probs=71.6

Q ss_pred             CCCCcEEEEecCCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .++.++|||+|||+ ++++++|+++|++||.|.+|.|.       +|||||+|.+.++|++|++.||+..+.|++|.|++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            44578999999998 99999999999999999999984       68999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      ++.+.+.
T Consensus        80 a~~~~~~   86 (96)
T 2kvi_A           80 SSSNARP   86 (96)
T ss_dssp             EECCCC-
T ss_pred             cCcCCCC
Confidence            9877543

>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=99.58  E-value=5.2e-15  Score=126.65  Aligned_cols=82  Identities=17%  Similarity=0.339  Sum_probs=75.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .++.++|||+|||+++++++|+++|++||.|.+|.|+++  +.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            445789999999999999999999999999999999875  456899999999999999999999999999999999998


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      .+..
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            7654

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=4.3e-15  Score=126.20  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=71.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .++|||+|||+++++++|+++|++||.|..|.|++     ++|||||+|.+.++|++||+.||+..+.|++|.|.|+...
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            57999999999999999999999999999999875     4789999999999999999999999999999999998765


Q ss_pred             C
Q psy1534         239 D  239 (587)
Q Consensus       239 ~  239 (587)
                      .
T Consensus        85 ~   85 (111)
T 1whx_A           85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=99.58  E-value=1.4e-15  Score=125.89  Aligned_cols=80  Identities=18%  Similarity=0.232  Sum_probs=72.2

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-----HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-----SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-----~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      .+..++|||+|||+++++++|     ++|++||+|.+|+|++  ++.++|||||+|.+.++|++|++.||+..|.|++|+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            356789999999999999987     4799999999999874  577889999999999999999999999999999999


Q ss_pred             EEecccc
Q psy1534         104 IKEAVED  110 (587)
Q Consensus       104 V~~a~~~  110 (587)
                      |.++..+
T Consensus        83 v~~a~~~   89 (97)
T 1nu4_A           83 IQYAKTD   89 (97)
T ss_dssp             EEECSSC
T ss_pred             EEEccCC
Confidence            9999854

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=5.2e-16  Score=129.63  Aligned_cols=81  Identities=19%  Similarity=0.302  Sum_probs=73.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++++++|+++|++||.|.. .++.+. .++++|||||+|.+.++|++||+ ||+..|.|+.|+|+++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            34689999999999999999999999999877 555554 48899999999999999999998 9999999999999999


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      .++.
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8765

>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=99.57  E-value=1.4e-15  Score=131.39  Aligned_cols=80  Identities=16%  Similarity=0.216  Sum_probs=72.9

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCee--EEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVE--NVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ...++|||+|||+++++++|+++|++| .|+  +|+|++|++|+++|||||+|.+.++|++||+. ++..|.||.|.|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEE
Confidence            346799999999999999999999999 677  99999998899999999999999999999975 77999999999988


Q ss_pred             ccCC
Q psy1534         235 DRVA  238 (587)
Q Consensus       235 a~~~  238 (587)
                      +..+
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=3.2e-15  Score=123.57  Aligned_cols=80  Identities=23%  Similarity=0.391  Sum_probs=72.2

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+.++|||+|||+++++++|+++|++||.|..+    ...++++|||||+|.+.++|.+|++.||+..+.|++|.|+++.
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            346899999999999999999999999988666    3457889999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      ++.+
T Consensus        90 ~~~~   93 (96)
T 1fjc_A           90 EKGG   93 (96)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            7653

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1e-14  Score=120.05  Aligned_cols=78  Identities=29%  Similarity=0.367  Sum_probs=68.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|  +.++. ++   ||||+|.+.++|++||+ ||+..|.|+.|.|+++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            35799999999999999999999999999987  44443 44   99999999999999999 99999999999999887


Q ss_pred             CCCCC
Q psy1534         237 VADRL  241 (587)
Q Consensus       237 ~~~~~  241 (587)
                      .+...
T Consensus        81 ~~~~~   85 (94)
T 2e5g_A           81 QKEFQ   85 (94)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            66543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.57  E-value=6.9e-15  Score=126.86  Aligned_cols=77  Identities=12%  Similarity=0.103  Sum_probs=69.6

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceE-EEEEECCHHHHHHHHHHhCCceeCC--eEEEEEe
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGS-AIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKE  106 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~-aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~  106 (587)
                      .-.+|||+||++++|+++| ++|++||+|.+|+|+.+    ++|| |||+|.+.++|++|++.|||..|.+  ++|+|.+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            3457999999999999999 89999999999999874    3677 9999999999999999999999998  9999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      ++.+.
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            98543

>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=99.57  E-value=1.4e-15  Score=132.06  Aligned_cols=81  Identities=21%  Similarity=0.261  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEe-eCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIA-LDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~-~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++++++|+++|+.||.|.++.++ .+.+|+++|||||+|.+.++|++||+ ||+..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            345799999999999999999999999999885444 44569999999999999999999998 9999999999999998


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      ..+
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.57  E-value=4.4e-15  Score=137.00  Aligned_cols=85  Identities=21%  Similarity=0.402  Sum_probs=80.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ...+.++|||+|||+.+++++|+++|++||.|.+|.|+.+++++++|||||+|.+.++|++||+.||+..|.|++|+|++
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q psy1534         235 DRVAD  239 (587)
Q Consensus       235 a~~~~  239 (587)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            87654

>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=99.57  E-value=5.2e-15  Score=132.51  Aligned_cols=76  Identities=12%  Similarity=0.124  Sum_probs=69.2

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEecc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKEAV  108 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~a~  108 (587)
                      ..+|||+||++++|+++| ++|++||+|++|+|+.++   ++|||||+|.+.++|++|++.|||..|.+  ++|+|.++.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            347899999999999999 899999999999997653   57999999999999999999999999966  999999998


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus       123 ~~  124 (164)
T 1sjr_A          123 LT  124 (164)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.56  E-value=1.1e-14  Score=130.32  Aligned_cols=78  Identities=19%  Similarity=0.350  Sum_probs=71.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEcc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMDR  236 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a~  236 (587)
                      ..+|||+||++.+++++|+++|++||.|++|.|..++   ++|||||+|.+.++|++|++.|||..|.+  ++|+|+|++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            4678999999999999999999999999999997643   57899999999999999999999999976  999999998


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      .+.
T Consensus       123 ~~~  125 (164)
T 1sjr_A          123 LTS  125 (164)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            764

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.34  E-value=2.3e-16  Score=135.35  Aligned_cols=84  Identities=24%  Similarity=0.402  Sum_probs=78.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeE--------EEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVEN--------VEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE  227 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  227 (587)
                      .+.++|||+|||+++++++|+++|++||.|..        |.|++++. ++++|||||+|.+.++|++|++.||+..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34679999999999999999999999999998        89999865 8999999999999999999999999999999


Q ss_pred             eEEEEEEccCCCC
Q psy1534         228 RRITVRMDRVADR  240 (587)
Q Consensus       228 ~~l~v~~a~~~~~  240 (587)
                      ++|+|+++.++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999887653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.56  E-value=8.2e-15  Score=123.78  Aligned_cols=79  Identities=9%  Similarity=0.167  Sum_probs=71.5

Q ss_pred             cEEEEecC----CCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecC----HHH----HHHHHH--HhCCce
Q psy1534         160 NKVFVANL----DYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDH----PVE----AVQSIS--MLNNQN  224 (587)
Q Consensus       160 ~~l~V~nL----p~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~----~~~----A~~Al~--~l~g~~  224 (587)
                      ++|||+||    |+.+++++|+++|+.||+|.+|.++.|+. |+++|||||+|.+    +++    |.+|+.  .||+..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    99999999999999999999999999996 9999999999996    333    899998  789999


Q ss_pred             eCCeEEEEEEccCC
Q psy1534         225 LFERRITVRMDRVA  238 (587)
Q Consensus       225 ~~g~~l~v~~a~~~  238 (587)
                      |.|++|+|++.+..
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999987654

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

Probab=99.56  E-value=2.8e-14  Score=118.11  Aligned_cols=79  Identities=19%  Similarity=0.247  Sum_probs=71.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..+.++|||+||  ++++++|+++|++||.|.+|.|.     +++|||||+|.+.++|++||+.||+..|.|++|+|.++
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            345689999996  89999999999999999999985     35799999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      .++...
T Consensus        85 ~~~~~~   90 (97)
T 1x5p_A           85 RKQPML   90 (97)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            876543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.56  E-value=1.9e-14  Score=124.11  Aligned_cols=77  Identities=21%  Similarity=0.405  Sum_probs=70.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGF-GTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMD  235 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a  235 (587)
                      ...|||+||++.+|+++|+++|++||.|.+|.|+.+.    +|| |||+|.+.++|++|++.|||..|.+  ++|+|.|+
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            4578899999999999999999999999999988743    688 9999999999999999999999998  89999999


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      +.+.
T Consensus       104 k~~~  107 (130)
T 3zzy_A          104 KLTS  107 (130)
T ss_dssp             SCSS
T ss_pred             CCCc
Confidence            8764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.56  E-value=1.6e-14  Score=120.93  Aligned_cols=82  Identities=17%  Similarity=0.074  Sum_probs=72.0

Q ss_pred             CCCCcEEEcCCCC-----CCCHHHH-HhcccCCCeEEEEEeeCC--CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeE
Q psy1534          30 PLEVPVVMDLIQG-----DASLYQI-SHLSTVGDVTYVEILNDD--TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK  101 (587)
Q Consensus        30 ~~~~~vfV~nlp~-----~~t~~~l-~~F~~~G~V~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~  101 (587)
                      .+.+.|+|+|+..     +.++++| ++|++||+|++|+|++++  +++++|||||+|.+.++|++|++.|||..|.||+
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4567899999963     3477888 789999999999999986  4789999999999999999999999999999999


Q ss_pred             EEEEeccccc
Q psy1534         102 LVIKEAVEDK  111 (587)
Q Consensus       102 i~V~~a~~~~  111 (587)
                      |.|.++....
T Consensus        86 i~v~~a~~~~   95 (105)
T 2pe8_A           86 VKACFYNLDK   95 (105)
T ss_dssp             CEEEECCHHH
T ss_pred             EEEEEcCHHH
Confidence            9999998543

>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=99.56  E-value=8.2e-15  Score=118.96  Aligned_cols=76  Identities=11%  Similarity=0.187  Sum_probs=70.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||+++++++|+++|++| .|.+|+|.     +++|||||+|.+.++|++|++.||+..+.|++|+|+++..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            35789999999999999999999999 99999885     4689999999999999999999999999999999999865


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      ..
T Consensus        78 ~~   79 (88)
T 1wg1_A           78 DA   79 (88)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=5.7e-15  Score=122.02  Aligned_cols=79  Identities=18%  Similarity=0.193  Sum_probs=70.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEE-EEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYV-EILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v-~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....+|||+|||+++++++| ++|++||+|.+| .|++++.   .+.|||+|.+.++|++|++.||+..|.|++|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345689999999999999999 899999999999 4888752   23499999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9855

>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=99.55  E-value=6.8e-15  Score=131.18  Aligned_cols=85  Identities=24%  Similarity=0.341  Sum_probs=74.1

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE------EEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENV------EIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR  229 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v------~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  229 (587)
                      ..+.++|||+|||+++++++|+++|++||.|..|      .+....+++++|||||+|.+.++|.+||..||+..|.|++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            4567899999999999999999999999998764      1222235889999999999999999999999999999999


Q ss_pred             EEEEEccCCCC
Q psy1534         230 ITVRMDRVADR  240 (587)
Q Consensus       230 l~v~~a~~~~~  240 (587)
                      |.|.+++....
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999977643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=5.9e-15  Score=126.09  Aligned_cols=77  Identities=17%  Similarity=0.221  Sum_probs=65.7

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-C---CCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-T---GKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~---g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      ....++|||+|||+++++++| ++|++||+|. +.++.++ +   |++||||||+|.+.++|++|++.|+  .+.|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            346789999999999999999 8999999999 8888876 5   7999999999999999999999983  36666666


Q ss_pred             EEecc
Q psy1534         104 IKEAV  108 (587)
Q Consensus       104 V~~a~  108 (587)
                      +..+.
T Consensus        82 ~~~~~   86 (114)
T 2dnl_A           82 CVSSP   86 (114)
T ss_dssp             EECCS
T ss_pred             eccCC
Confidence            65443

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.8e-14  Score=118.94  Aligned_cols=79  Identities=19%  Similarity=0.184  Sum_probs=71.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE-EEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENV-EIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+|||+++++++|+++|++||.|.+| .|++++.   .+.|||+|.+.++|++|++.||+..|.|++|.|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            46799999999999999999999999999999 5888754   3449999999999999999999999999999999998


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ++.
T Consensus        91 ~~~   93 (96)
T 2e44_A           91 DEM   93 (96)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            764

>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=99.54  E-value=1.3e-14  Score=117.95  Aligned_cols=75  Identities=19%  Similarity=0.177  Sum_probs=62.2

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCce--eCCeEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE--TKGRKLVI  104 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~--l~gr~i~V  104 (587)
                      ..+...+|||+|||+++|+++| ++|++||+|.+|+|+++    +||||||+|.+.++|++    +++..  +.+++|.|
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            3467789999999999999999 89999999999999985    78999999999999984    35544  56999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++.++
T Consensus        79 ~~a~~k   84 (89)
T 3d2w_A           79 SNAEPK   84 (89)
T ss_dssp             EECC--
T ss_pred             EEcCCC
Confidence            999854

>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=99.54  E-value=1.9e-14  Score=116.88  Aligned_cols=77  Identities=22%  Similarity=0.230  Sum_probs=63.0

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--CCeEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL--FERRITV  232 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v  232 (587)
                      ..++.++|||+|||+++++++|+++|++||.|.+|.|+++    ++|||||+|.+.++|++    +++..+  .|++|.|
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            3455789999999999999999999999999999999985    68999999999999984    455554  5999999


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      .++.++.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9987764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.54  E-value=3.7e-14  Score=121.80  Aligned_cols=72  Identities=21%  Similarity=0.182  Sum_probs=65.7

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceE-EEEEECCHHHHHHHHHHhCCceeCC--eEEEEEeccc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGS-AIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKEAVE  109 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~-aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~a~~  109 (587)
                      .|||+||++++++++| ++|++||+|++|+|+..     .|| |||+|.+.++|++|++.|||..|.|  ++|+|.++..
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~  101 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP  101 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecC
Confidence            4789999999999999 89999999999999763     276 9999999999999999999999987  6999999985


Q ss_pred             c
Q psy1534         110 D  110 (587)
Q Consensus       110 ~  110 (587)
                      +
T Consensus       102 ~  102 (124)
T 2e5i_A          102 T  102 (124)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.54  E-value=2e-14  Score=116.35  Aligned_cols=70  Identities=20%  Similarity=0.310  Sum_probs=67.2

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhc----C-------CeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEE
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNC----G-------DIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIID  583 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~----G-------~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~  583 (587)
                      +.++|||.|||+++|++||+++|++|    |       .|..+.+..++++|||+|.+.++|++|| .||+..|.|++|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   83 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   83 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEE
Confidence            35799999999999999999999999    8       9999999988999999999999999999 9999999999999


Q ss_pred             EE
Q psy1534         584 VT  585 (587)
Q Consensus       584 v~  585 (587)
                      |.
T Consensus        84 V~   85 (87)
T 2hzc_A           84 IR   85 (87)
T ss_dssp             EE
T ss_pred             Ee
Confidence            96

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.7e-14  Score=115.15  Aligned_cols=74  Identities=23%  Similarity=0.281  Sum_probs=65.8

Q ss_pred             CCcE-EEEecCCCCCcHHH----HHHHHHhc-CCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         158 LINK-VFVANLDYKVDEKK----LREVFRLA-GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       158 ~~~~-l~V~nLp~~~te~~----l~~~F~~~-G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      +..+ |||+|||+++++++    |+++|++| |+|.+|      .   .|+|||+|.+.++|.+|++.|||..+.||+|+
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------t---gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------T---GCSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------C---TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------e---cCEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            3445 99999999999988    55899999 599998      2   29999999999999999999999999999999


Q ss_pred             EEEccCCCC
Q psy1534         232 VRMDRVADR  240 (587)
Q Consensus       232 v~~a~~~~~  240 (587)
                      |.+|+.+..
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999987763

>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=99.53  E-value=1.2e-14  Score=124.28  Aligned_cols=76  Identities=26%  Similarity=0.344  Sum_probs=66.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeE-----EEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR-----ITV  232 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~-----l~v  232 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+.+      |||||+|.+.++|++||+.||+..|.|+.     |+|
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v   88 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   88 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEe
Confidence            3579999999999999999999999999999999875      89999999999999999999999999988     777


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      ..+.+..
T Consensus        89 ~~~~~~~   95 (115)
T 3beg_B           89 KVDGPRS   95 (115)
T ss_dssp             EECC---
T ss_pred             ccCCCCC
Confidence            7766544

>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=99.53  E-value=6.5e-15  Score=131.31  Aligned_cols=82  Identities=12%  Similarity=0.159  Sum_probs=71.8

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEE------EeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVE------ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK  101 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~------i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~  101 (587)
                      .....+|||+|||+++++++| ++|++||.|.+|.      +....+++++|||||+|.+.++|++|++.||+..|.|++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            446679999999999999999 8999999998751      222247899999999999999999999999999999999


Q ss_pred             EEEEecccc
Q psy1534         102 LVIKEAVED  110 (587)
Q Consensus       102 i~V~~a~~~  110 (587)
                      |.|.++...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999999743

>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=99.53  E-value=1e-13  Score=129.78  Aligned_cols=79  Identities=15%  Similarity=0.146  Sum_probs=73.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .++|||+|||+++++++|+++|++||.|.+|+|+++.+++++|||||+|.+.++|++|+..++ ..+.|++|.|.++..-
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHH
Confidence            479999999999999999999999999999999999889999999999999999999997654 6999999999987553

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=1.3e-14  Score=115.91  Aligned_cols=71  Identities=17%  Similarity=0.227  Sum_probs=63.6

Q ss_pred             CCCc-EEEcCCCCCCCHHHH-----HhcccC-CCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          31 LEVP-VVMDLIQGDASLYQI-----SHLSTV-GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        31 ~~~~-vfV~nlp~~~t~~~l-----~~F~~~-G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      +..+ |||+|||+++++++|     ++|++| |+|.+|      ++   |+|||+|.+.++|++|++.|+|..|.||+|+
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            3444 999999999999884     589999 599998      33   9999999999999999999999999999999


Q ss_pred             EEecccc
Q psy1534         104 IKEAVED  110 (587)
Q Consensus       104 V~~a~~~  110 (587)
                      |.++..+
T Consensus        78 v~~A~~~   84 (96)
T 2diu_A           78 VSFTPKN   84 (96)
T ss_dssp             EESSCCS
T ss_pred             EEecCCC
Confidence            9999844

>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=99.52  E-value=1e-14  Score=118.33  Aligned_cols=76  Identities=22%  Similarity=0.229  Sum_probs=65.9

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++|||+|||+++++++| ++|++||+|.+|+|+++    +||||||+|.+.++|++|+..  ...+.+++|.|.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            35689999999999999999 89999999999999876    689999999999999875432  455689999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      ++.
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=7.3e-14  Score=116.90  Aligned_cols=81  Identities=17%  Similarity=0.070  Sum_probs=72.6

Q ss_pred             CCCcEEEEecCCC-----CCcHHHHHHHHHhcCCeeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCeE
Q psy1534         157 PLINKVFVANLDY-----KVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERR  229 (587)
Q Consensus       157 ~~~~~l~V~nLp~-----~~te~~l~~~F~~~G~i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  229 (587)
                      .++++|+|.||..     +-++++|+++|++||.|.+|.|++++.  ++++||+||+|.+.++|.+|++.|||+.+.||+
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4578999999963     237899999999999999999999864  688999999999999999999999999999999


Q ss_pred             EEEEEccC
Q psy1534         230 ITVRMDRV  237 (587)
Q Consensus       230 l~v~~a~~  237 (587)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>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=99.52  E-value=2.9e-14  Score=150.17  Aligned_cols=81  Identities=15%  Similarity=0.308  Sum_probs=76.3

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+|||+|||+++|+++| ++|++||+|+.|+|+.++ ++.++|||||+|.+.++|.+||+.||+..|.|++|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4579999999999999999 899999999999999996 99999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      .+.
T Consensus       181 ~~~  183 (437)
T 3pgw_S          181 GRT  183 (437)
T ss_pred             CCC
Confidence            443

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.51  E-value=6.2e-14  Score=120.41  Aligned_cols=75  Identities=21%  Similarity=0.303  Sum_probs=67.9

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEcc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGF-GTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMDR  236 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a~  236 (587)
                      ..|||+||++.+++++|+++|++||.|.+|.|+..     .|| |||+|.+.++|.+|++.|||..|.|  ++|+|.+++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            45789999999999999999999999999999763     386 9999999999999999999999987  689999988


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ++.
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            764

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

Probab=99.51  E-value=9.5e-14  Score=114.85  Aligned_cols=70  Identities=19%  Similarity=0.271  Sum_probs=66.5

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      +.++|||.||  ++|++||+++|++||.|..+.+...+++|||+|++.++|++||+.||+..|.|++|+|.+
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4679999996  999999999999999999999988889999999999999999999999999999999975

>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=99.51  E-value=4.2e-14  Score=132.43  Aligned_cols=75  Identities=24%  Similarity=0.204  Sum_probs=70.6

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ++|||+|||+++++++| ++|++||+|.+|+|+++.+++++|||||+|.+.++|++|++.+ +..|.|++|.|.+..
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            68999999999999999 8999999999999999989999999999999999999999765 569999999999876

>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=99.50  E-value=6e-14  Score=113.49  Aligned_cols=71  Identities=21%  Similarity=0.426  Sum_probs=66.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhc----C-------CeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLA----G-------KVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF  226 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~----G-------~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  226 (587)
                      +.++|||+|||+++++++|+++|++|    |       .|.++.+.++     +|||||+|.+.++|.+|+ .||+..+.
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            35799999999999999999999999    8       8999999875     799999999999999999 99999999


Q ss_pred             CeEEEEEE
Q psy1534         227 ERRITVRM  234 (587)
Q Consensus       227 g~~l~v~~  234 (587)
                      |++|+|+.
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999873

>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=99.48  E-value=3.6e-14  Score=115.14  Aligned_cols=77  Identities=22%  Similarity=0.187  Sum_probs=65.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +.++|||+|||+++++++|+++|++||.|.+|.|+++    ++|||||+|.+.++|++|+..  ...+.+++|.|.++.+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCC
Confidence            4689999999999999999999999999999999875    589999999999999765321  3445899999999877


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      +..
T Consensus        78 ~~~   80 (88)
T 1wf0_A           78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=1.2e-13  Score=117.91  Aligned_cols=76  Identities=18%  Similarity=0.188  Sum_probs=65.1

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC----CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ..++|||+|||+++++++|+++|++||.|. +.++.++.    |+++|||||+|.+.++|++||+.|+  .+.|+.+.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            457999999999999999999999999999 88887763    6899999999999999999999983  3666666665


Q ss_pred             Ecc
Q psy1534         234 MDR  236 (587)
Q Consensus       234 ~a~  236 (587)
                      .+.
T Consensus        84 ~~~   86 (114)
T 2dnl_A           84 SSP   86 (114)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            443

>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=99.46  E-value=2.7e-14  Score=119.42  Aligned_cols=72  Identities=17%  Similarity=0.220  Sum_probs=63.8

Q ss_pred             EEcCCCCCCCHHHH-Hhc------------ccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q psy1534          36 VMDLIQGDASLYQI-SHL------------STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL  102 (587)
Q Consensus        36 fV~nlp~~~t~~~l-~~F------------~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i  102 (587)
                      .+.+||+++++++| ++|            ++||+|++|+|+++.+++++|||||+|.++++|++|++.|||..|.||+|
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            35677777777766 455            99999999999998888999999999999999999999999999999999


Q ss_pred             EEEec
Q psy1534         103 VIKEA  107 (587)
Q Consensus       103 ~V~~a  107 (587)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.45  E-value=4.5e-13  Score=113.92  Aligned_cols=84  Identities=15%  Similarity=0.169  Sum_probs=69.9

Q ss_pred             cccCCCCCCCcEEEcCCCCCCC-----------HHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHH
Q psy1534          24 RIETGAPLEVPVVMDLIQGDAS-----------LYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNK   91 (587)
Q Consensus        24 ~~~~~~~~~~~vfV~nlp~~~t-----------~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~   91 (587)
                      +....+...+.|+|+||....+           +++| ++|++||+|.+|.| .++  .++|||||+|.+.++|++|++.
T Consensus         7 ~~~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~   83 (112)
T 2dit_A            7 GGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQT   83 (112)
T ss_dssp             SCCCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHH
T ss_pred             CCCCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHH
Confidence            3344556778899999944432           4677 78999999999965 554  3789999999999999999999


Q ss_pred             hCCceeCCeEEEEEecccc
Q psy1534          92 MHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        92 l~g~~l~gr~i~V~~a~~~  110 (587)
                      |||..|.|++|+|.++..+
T Consensus        84 lng~~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           84 LDGRWFGGRQITAQAWDGT  102 (112)
T ss_dssp             STTCEETTEECEEEECCSC
T ss_pred             cCCCEECCcEEEEEEeCCC
Confidence            9999999999999999854

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

Probab=99.42  E-value=2.6e-13  Score=129.84  Aligned_cols=80  Identities=19%  Similarity=0.260  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCCC---------cHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-
Q psy1534         156 CPLINKVFVANLDYKV---------DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL-  225 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~---------te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-  225 (587)
                      ....++|||+||+..+         +|++|+++|++||.|++|+|+.+     +|||||+|.+.++|+.|++.|+++.| 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            3457899999999998         79999999999999999999864     79999999999999999999999999 


Q ss_pred             -----------CCeEEEEEEccCCCC
Q psy1534         226 -----------FERRITVRMDRVADR  240 (587)
Q Consensus       226 -----------~g~~l~v~~a~~~~~  240 (587)
                                 .|+.|.|+||+....
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccccCCCCEEEEEEccCCCC
Confidence                       899999999987653

>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=99.42  E-value=3.1e-13  Score=113.12  Aligned_cols=82  Identities=20%  Similarity=0.108  Sum_probs=69.3

Q ss_pred             CCCCcEEEcCC--CCCCC--------HHHH-HhcccCCCeEEEEEeeCCC---CCcceEEEEEECCHHHHHHHHHHhCCc
Q psy1534          30 PLEVPVVMDLI--QGDAS--------LYQI-SHLSTVGDVTYVEILNDDT---GKPRGSAIVEFQSPDLVRKAVNKMHRF   95 (587)
Q Consensus        30 ~~~~~vfV~nl--p~~~t--------~~~l-~~F~~~G~V~~v~i~~d~~---g~skG~aFV~F~~~e~A~~Al~~l~g~   95 (587)
                      .+.+.|.+.|+  |.++.        +++| +.|++||+|++|+|++++.   ++++|+|||+|.+.++|++|++.|||+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            45677889998  33333        3466 7899999999999999863   468999999999999999999999999


Q ss_pred             eeCCeEEEEEeccccc
Q psy1534          96 ETKGRKLVIKEAVEDK  111 (587)
Q Consensus        96 ~l~gr~i~V~~a~~~~  111 (587)
                      .|.||+|+|.++....
T Consensus        83 ~f~GR~i~v~~~~~~~   98 (105)
T 3v4m_A           83 KFANRVVVTKYCDPDS   98 (105)
T ss_dssp             EETTEECEEEEECHHH
T ss_pred             EeCCCEEEEEEeCHHH
Confidence            9999999999988543

>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=99.41  E-value=1.4e-12  Score=110.75  Aligned_cols=82  Identities=22%  Similarity=0.272  Sum_probs=70.5

Q ss_pred             CCCCcEEEEecCCCCCc-----------HHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q psy1534         156 CPLINKVFVANLDYKVD-----------EKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQN  224 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~t-----------e~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~  224 (587)
                      ..++++|+|.||....+           +++|+++|++||.|.+|.| .++  .++|||||+|.+.++|++|++.|||+.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            34578999999954432           6899999999999999966 544  379999999999999999999999999


Q ss_pred             eCCeEEEEEEccCCCC
Q psy1534         225 LFERRITVRMDRVADR  240 (587)
Q Consensus       225 ~~g~~l~v~~a~~~~~  240 (587)
                      +.|++|+|.++.++..
T Consensus        89 ~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           89 FGGRQITAQAWDGTTD  104 (112)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCcEEEEEEeCCCCC
Confidence            9999999999887653

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

Probab=99.41  E-value=1.8e-13  Score=130.92  Aligned_cols=77  Identities=21%  Similarity=0.246  Sum_probs=69.6

Q ss_pred             CCCCCcEEEcCCCCCC---------CHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCcee-
Q psy1534          29 APLEVPVVMDLIQGDA---------SLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET-   97 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~---------t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l-   97 (587)
                      ....++|||+|||.++         ++++| ++|++||+|++|+|+.     +||||||+|.+.++|+.|++.|++..| 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            3466799999999998         68889 8999999999999996     489999999999999999999999999 


Q ss_pred             -----------CCeEEEEEecccc
Q psy1534          98 -----------KGRKLVIKEAVED  110 (587)
Q Consensus        98 -----------~gr~i~V~~a~~~  110 (587)
                                 .|+.|.|.|+..+
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC--
T ss_pred             ccccccccccCCCCEEEEEEccCC
Confidence                       8999999999844

>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=99.41  E-value=6.3e-13  Score=111.26  Aligned_cols=82  Identities=16%  Similarity=0.162  Sum_probs=71.3

Q ss_pred             CCCcEEEEecC--CCCCc--------HHHHHHHHHhcCCeeEEEEeeCCC---CCcceEEEEEecCHHHHHHHHHHhCCc
Q psy1534         157 PLINKVFVANL--DYKVD--------EKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQSISMLNNQ  223 (587)
Q Consensus       157 ~~~~~l~V~nL--p~~~t--------e~~l~~~F~~~G~i~~v~i~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~g~  223 (587)
                      .+++.|.|.|+  |.++.        ++||++.|++||.|.+|.|++++.   ++++|++||+|.+.++|.+|++.|||+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35789999998  43443        379999999999999999999875   368999999999999999999999999


Q ss_pred             eeCCeEEEEEEccCC
Q psy1534         224 NLFERRITVRMDRVA  238 (587)
Q Consensus       224 ~~~g~~l~v~~a~~~  238 (587)
                      .+.||+|+|.+....
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999997543

>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=99.39  E-value=6.4e-13  Score=113.38  Aligned_cols=81  Identities=19%  Similarity=0.187  Sum_probs=69.2

Q ss_pred             CCCcEEEcCCCC-----CCCHHHH-HhcccCCCeEEEEEeeCC-----CCCcceEEEEEECCHHHHHHHHHHhCCceeCC
Q psy1534          31 LEVPVVMDLIQG-----DASLYQI-SHLSTVGDVTYVEILNDD-----TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG   99 (587)
Q Consensus        31 ~~~~vfV~nlp~-----~~t~~~l-~~F~~~G~V~~v~i~~d~-----~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g   99 (587)
                      +.+.|+++|+-.     +..++|| +.|++||+|.+|+|++++     +++++|++||+|.+.++|.+|++.|||..|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            567899999843     2235667 789999999999999985     35678999999999999999999999999999


Q ss_pred             eEEEEEeccccc
Q psy1534         100 RKLVIKEAVEDK  111 (587)
Q Consensus       100 r~i~V~~a~~~~  111 (587)
                      |+|+|.++....
T Consensus        99 R~i~v~~~~~~~  110 (118)
T 3ue2_A           99 RKVVAEVYDQER  110 (118)
T ss_dssp             EECEEEEECHHH
T ss_pred             cEEEEEEcChHh
Confidence            999999987443

>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=99.39  E-value=2.5e-13  Score=113.54  Aligned_cols=72  Identities=19%  Similarity=0.266  Sum_probs=64.9

Q ss_pred             EecCCCCCcHHHHHHHH------------HhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         164 VANLDYKVDEKKLREVF------------RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       164 V~nLp~~~te~~l~~~F------------~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      +.+||+.+++++|++.|            ++||.|.+|.|+++..++++|||||+|.+.++|.+|++.|||+.+.||+|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56777778887776666            999999999999988889999999999999999999999999999999999


Q ss_pred             EEEc
Q psy1534         232 VRMD  235 (587)
Q Consensus       232 v~~a  235 (587)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.34  E-value=2.9e-12  Score=109.28  Aligned_cols=80  Identities=20%  Similarity=0.119  Sum_probs=70.4

Q ss_pred             CCcEEEEecCCC--C---CcHHHHHHHHHhcCCeeEEEEeeCCC-----CCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy1534         158 LINKVFVANLDY--K---VDEKKLREVFRLAGKVENVEIALDKD-----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE  227 (587)
Q Consensus       158 ~~~~l~V~nLp~--~---~te~~l~~~F~~~G~i~~v~i~~~~~-----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  227 (587)
                      ++++|+|.|+-.  +   -.++||++.|++||.|.+|.|++++.     ++++|++||+|.+.++|.+|++.|||+.+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            578999999832  2   24689999999999999999999863     4678999999999999999999999999999


Q ss_pred             eEEEEEEccC
Q psy1534         228 RRITVRMDRV  237 (587)
Q Consensus       228 ~~l~v~~a~~  237 (587)
                      |.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.28  E-value=1.5e-11  Score=101.44  Aligned_cols=75  Identities=20%  Similarity=0.141  Sum_probs=62.4

Q ss_pred             CCCcEEEcCCC-------CCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q psy1534          31 LEVPVVMDLIQ-------GDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL  102 (587)
Q Consensus        31 ~~~~vfV~nlp-------~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i  102 (587)
                      ...+|-|.-.+       .++++++| ++|++||+|.+|+|+.    ++||||||+|.+.++|++|++.++  .+.+++|
T Consensus         9 ~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~----~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A            9 GTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES----SSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             ccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc----CCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            35566666554       45799999 8999999999999983    678999999999999999998854  4689999


Q ss_pred             EEEeccccc
Q psy1534         103 VIKEAVEDK  111 (587)
Q Consensus       103 ~V~~a~~~~  111 (587)
                      +|.++..+.
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999988543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=4.3e-11  Score=98.74  Aligned_cols=75  Identities=16%  Similarity=0.105  Sum_probs=63.0

Q ss_pred             cEEEEecCC-------CCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         160 NKVFVANLD-------YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       160 ~~l~V~nLp-------~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      .+|.|.-..       ..+++++|+++|++||.|.+|.|+.    +++|||||+|.+.++|++||+.+++  +.+++|+|
T Consensus        11 ~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~----~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V   84 (100)
T 2d9o_A           11 PKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKI   84 (100)
T ss_dssp             CEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES----SSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEE
T ss_pred             ceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc----CCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEE
Confidence            456665443       4589999999999999999999983    5799999999999999999987544  67999999


Q ss_pred             EEccCCCC
Q psy1534         233 RMDRVADR  240 (587)
Q Consensus       233 ~~a~~~~~  240 (587)
                      +|++.+..
T Consensus        85 ~~a~~~~~   92 (100)
T 2d9o_A           85 SWLEGQPQ   92 (100)
T ss_dssp             ECSSCCCC
T ss_pred             EEccCCCC
Confidence            99877653

>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=99.22  E-value=4.3e-11  Score=101.25  Aligned_cols=80  Identities=13%  Similarity=0.065  Sum_probs=67.4

Q ss_pred             CCCCcEEEEecCCCCC----------cHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy1534         156 CPLINKVFVANLDYKV----------DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL  225 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~----------te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  225 (587)
                      ..+++.|.|.|+=..-          .++||++.|++||.|.+|.|.++.   ++||+||+|.+.++|.+|++.|||+.+
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            3457789999973221          136899999999999999997764   589999999999999999999999999


Q ss_pred             CCeEEEEEEccCC
Q psy1534         226 FERRITVRMDRVA  238 (587)
Q Consensus       226 ~g~~l~v~~a~~~  238 (587)
                      .||.|.|.++...
T Consensus        81 ~GR~i~v~~~~~~   93 (114)
T 3s6e_A           81 AGKMITAAYVPLP   93 (114)
T ss_dssp             TTEECEEEEECHH
T ss_pred             CCEEEEEEEEcHH
Confidence            9999999997543

>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=99.20  E-value=2e-11  Score=123.10  Aligned_cols=77  Identities=14%  Similarity=0.144  Sum_probs=66.0

Q ss_pred             CCCCCCCcEEEcC--CCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC---Ce
Q psy1534          27 TGAPLEVPVVMDL--IQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK---GR  100 (587)
Q Consensus        27 ~~~~~~~~vfV~n--lp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~---gr  100 (587)
                      ...++.++|||+|  |++++|+++| ++|++||+|++|++.+     +||||||+|.+.++|++|++.|||..+.   |+
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            3446778999999  6899999999 8999999999987754     4799999999999999999999998883   45


Q ss_pred             --EEEEEecc
Q psy1534         101 --KLVIKEAV  108 (587)
Q Consensus       101 --~i~V~~a~  108 (587)
                        +|.|.++.
T Consensus        88 ~~~ly~~~~~   97 (345)
T 3tht_A           88 KITLYLNFVE   97 (345)
T ss_dssp             EEECEEEECS
T ss_pred             ceEEEEEEee
Confidence              67777775

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=7.2e-11  Score=99.93  Aligned_cols=73  Identities=14%  Similarity=0.142  Sum_probs=67.9

Q ss_pred             CCCeEEEeCCCCC-CChHHHHHHHhhcCCeeEEEeecCCCeEEEEECC-HHHHHHHHHHhC--CCcccCceEEEEEC
Q psy1534         515 ERDTVVVKNLPPT-ITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDS-EWTAKRAIDMMD--RTRIDGKIIDVTFF  587 (587)
Q Consensus       515 ~~~~v~V~~Lp~~-~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~-~~~a~~Ai~~l~--g~~~~g~~i~v~~~  587 (587)
                      +++.|+|.||+++ ++++||+++|++||+|.+|++..+..+|||+|.+ .++|..|++.||  +.+|++..++|+++
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            4679999999999 9999999999999999999999988899999999 899999999995  77899999998864

>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=99.18  E-value=5.4e-11  Score=100.67  Aligned_cols=77  Identities=13%  Similarity=0.079  Sum_probs=63.4

Q ss_pred             CCCcEEEcCCCCCCC----------HHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC
Q psy1534          31 LEVPVVMDLIQGDAS----------LYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG   99 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t----------~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g   99 (587)
                      ..+.|.+.|+-....          ++|| +.|++||+|++|+|.++.   ++|++||+|.+.++|++|++.|||..|.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            445688888744322          2244 679999999999997653   58999999999999999999999999999


Q ss_pred             eEEEEEecccc
Q psy1534         100 RKLVIKEAVED  110 (587)
Q Consensus       100 r~i~V~~a~~~  110 (587)
                      |+|+|.++...
T Consensus        83 R~i~v~~~~~~   93 (114)
T 3s6e_A           83 KMITAAYVPLP   93 (114)
T ss_dssp             EECEEEEECHH
T ss_pred             EEEEEEEEcHH
Confidence            99999999743

>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=99.17  E-value=5e-11  Score=120.25  Aligned_cols=77  Identities=16%  Similarity=0.243  Sum_probs=66.5

Q ss_pred             CCCCCcEEEEec--CCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---Ce-
Q psy1534         155 NCPLINKVFVAN--LDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF---ER-  228 (587)
Q Consensus       155 ~~~~~~~l~V~n--Lp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~-  228 (587)
                      ...++++|||+|  |++.+||++|+++|++||+|.+|.+..     +||||||+|.+.++|++||+.|||+.+.   |+ 
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            456788999999  578999999999999999999987764     3799999999999999999999999883   45 


Q ss_pred             -EEEEEEcc
Q psy1534         229 -RITVRMDR  236 (587)
Q Consensus       229 -~l~v~~a~  236 (587)
                       +|.|.+..
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             56777753

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=8.2e-11  Score=93.09  Aligned_cols=71  Identities=15%  Similarity=0.200  Sum_probs=62.0

Q ss_pred             CCCCCeEEEeCCCC----CCCh----HHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEE
Q psy1534         513 NIERDTVVVKNLPP----TITW----QELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV  584 (587)
Q Consensus       513 ~~~~~~v~V~~Lp~----~~~~----~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v  584 (587)
                      ++++.||+|..+|.    ...+    .+|.+.|.+||+|..+++..+  .+||+|++.++|.+||+ |||.+++||+|+|
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d--~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV   80 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED--KMWVTFLEGSSALNVLS-LNGKELLNRTITI   80 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS--SEEEEESSHHHHHHGGG-GTTCEETTEEEEE
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC--CEEEEECChHHHHHHHh-cCCeEeCCeEEEE
Confidence            44567999998772    3333    789999999999999999887  49999999999999999 9999999999999


Q ss_pred             EE
Q psy1534         585 TF  586 (587)
Q Consensus       585 ~~  586 (587)
                      .+
T Consensus        81 ~l   82 (91)
T 2dnr_A           81 AL   82 (91)
T ss_dssp             EE
T ss_pred             Ee
Confidence            86

>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=99.08  E-value=1.8e-10  Score=91.51  Aligned_cols=72  Identities=25%  Similarity=0.328  Sum_probs=63.1

Q ss_pred             CCCCCCeEEEeCCCCC---CCh------HHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceE
Q psy1534         512 SNIERDTVVVKNLPPT---ITW------QELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKII  582 (587)
Q Consensus       512 ~~~~~~~v~V~~Lp~~---~~~------~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i  582 (587)
                      .++++.||+|..++..   .+|      .+|.+.|.+||+|+.+++..+  .+||+|++.++|.+||+ |||.+++||.|
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d--~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L   87 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--QMLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--EEEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC--cEEEEEcChHHHHHHHh-cCCeeeCCeEE
Confidence            4556779999988743   233      679999999999999999988  59999999999999999 99999999999


Q ss_pred             EEEE
Q psy1534         583 DVTF  586 (587)
Q Consensus       583 ~v~~  586 (587)
                      +|.+
T Consensus        88 ~V~~   91 (95)
T 1ufw_A           88 KISG   91 (95)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9985

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=8.8e-10  Score=87.18  Aligned_cols=76  Identities=24%  Similarity=0.246  Sum_probs=65.4

Q ss_pred             CCCCcEEEEecCCC----CCcH----HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy1534         156 CPLINKVFVANLDY----KVDE----KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE  227 (587)
Q Consensus       156 ~~~~~~l~V~nLp~----~~te----~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  227 (587)
                      .|+..+|+|.-.+.    .+..    .+|.+.|++||.|..++|..++       +||+|.+.++|.+||+ |||..+.|
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            45667899988762    3333    6799999999999999999874       8999999999999997 99999999


Q ss_pred             eEEEEEEccCCC
Q psy1534         228 RRITVRMDRVAD  239 (587)
Q Consensus       228 ~~l~v~~a~~~~  239 (587)
                      |.|+|+++.+..
T Consensus        76 r~LkV~lkt~dW   87 (91)
T 2dnr_A           76 RTITIALKSPSG   87 (91)
T ss_dssp             EEEEEEECCCSS
T ss_pred             eEEEEEeCCCCc
Confidence            999999988765

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.97  E-value=1.3e-09  Score=92.29  Aligned_cols=77  Identities=14%  Similarity=0.107  Sum_probs=68.4

Q ss_pred             CCCCCcEEEEecCCCC-CcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecC-HHHHHHHHHHhC--CceeCCeEE
Q psy1534         155 NCPLINKVFVANLDYK-VDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDH-PVEAVQSISMLN--NQNLFERRI  230 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~-~~~A~~Al~~l~--g~~~~g~~l  230 (587)
                      ..++++.|||+||+++ +++++|+++|++||+|.+|.+.++..     .|||+|.+ .++|..|++.||  +..|.+..+
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            3567899999999999 99999999999999999999998753     69999999 899999999995  678889888


Q ss_pred             EEEEcc
Q psy1534         231 TVRMDR  236 (587)
Q Consensus       231 ~v~~a~  236 (587)
                      ++++..
T Consensus        89 ~~evL~   94 (121)
T 1owx_A           89 TWEVLE   94 (121)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            887743

>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=98.85  E-value=6e-09  Score=82.76  Aligned_cols=74  Identities=16%  Similarity=0.146  Sum_probs=63.7

Q ss_pred             CCCCCcEEEEecCCCC-----CcH----HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy1534         155 NCPLINKVFVANLDYK-----VDE----KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL  225 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~-----~te----~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  225 (587)
                      ..|+..+|+|.-++.+     +..    .+|.+.|+.||+|..++|..|+       +||+|.+.++|.+||+ |||..+
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeee
Confidence            4567789999988743     222    5689999999999999999874       9999999999999998 999999


Q ss_pred             CCeEEEEEEcc
Q psy1534         226 FERRITVRMDR  236 (587)
Q Consensus       226 ~g~~l~v~~a~  236 (587)
                      .||.|+|++..
T Consensus        83 ~Gr~L~V~~k~   93 (95)
T 1ufw_A           83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             CCeEEEEeccC
Confidence            99999998754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.73  E-value=1.2e-08  Score=97.62  Aligned_cols=67  Identities=19%  Similarity=0.198  Sum_probs=59.2

Q ss_pred             CHHHH-HhcccCCCeEEEEEeeCC-----CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccccc
Q psy1534          45 SLYQI-SHLSTVGDVTYVEILNDD-----TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK  111 (587)
Q Consensus        45 t~~~l-~~F~~~G~V~~v~i~~d~-----~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~~  111 (587)
                      .+++| +.|++||+|.+|+|+++.     +++++|++||+|.+.++|++|++.|||..+.||+|.|.++....
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~  214 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQER  214 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHH
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHHH
Confidence            44566 789999999999998663     45899999999999999999999999999999999999988443

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.62  E-value=4.5e-08  Score=93.58  Aligned_cols=68  Identities=22%  Similarity=0.149  Sum_probs=61.2

Q ss_pred             CCcHHHHHHHHHhcCCeeEEEEeeCCC-----CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         170 KVDEKKLREVFRLAGKVENVEIALDKD-----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       170 ~~te~~l~~~F~~~G~i~~v~i~~~~~-----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +-.+++|++.|++||.|.++.|+++..     ++++|++||+|.+.++|.+|++.|||+.+.||.|.|.+...
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            345689999999999999999987653     48999999999999999999999999999999999999653

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.60  E-value=2e-07  Score=75.35  Aligned_cols=70  Identities=11%  Similarity=0.162  Sum_probs=67.1

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhc-----CCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNC-----GDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT  585 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~-----G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~  585 (587)
                      ..+|-+.|||+.+++..++.|+.++     |.|+.+-+.++-+-|+|+|++...|.+|.-.|||.+|.||+|+|-
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            5689999999999999999999999     999999999999999999999999999999999999999999983

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.20  E-value=7e-06  Score=66.38  Aligned_cols=70  Identities=13%  Similarity=0.127  Sum_probs=65.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhc-----CCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLA-----GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~-----G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      .++|-+-|||..+++..|+.+.+++     |.|..|.+..|.     +=|+|+|.+...|-+|.-.|+|.+|.||+|+|.
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-----~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-----NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-----TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-----CceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            5789999999999999999999999     999999999885     459999999999999999999999999999985

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.99  E-value=2.5e-05  Score=62.78  Aligned_cols=74  Identities=15%  Similarity=0.179  Sum_probs=61.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHHHh-ccc-----CCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQISH-LST-----VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL  102 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l~~-F~~-----~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i  102 (587)
                      ....++|.|.|||.++.++.|++ |+.     =|+|++|....       +-|+|+|.+.+.|++.++. ..+.|.+.+|
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            34568999999999999998864 765     35999998764       4699999999999999965 5788999999


Q ss_pred             EEEecccc
Q psy1534         103 VIKEAVED  110 (587)
Q Consensus       103 ~V~~a~~~  110 (587)
                      .|......
T Consensus        77 sV~P~~~~   84 (104)
T 2dhx_A           77 SLRPAPPR   84 (104)
T ss_dssp             EEEECCCC
T ss_pred             EEEcCCCC
Confidence            99887633

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.81  E-value=0.00018  Score=57.79  Aligned_cols=69  Identities=22%  Similarity=0.259  Sum_probs=59.9

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhc-----CCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEEC
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNC-----GDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF  587 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~-----G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~  587 (587)
                      ..+|.|.|||.+++++.|.-+|+.-     |+|..++...  +.|+|+|.+.+.|++.+++ ..+.|++..|.|+.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~   81 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPA   81 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEEC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcC
Confidence            4699999999999999999999982     3788888876  6999999999999999886 677888888888754

>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=97.66  E-value=9e-05  Score=59.88  Aligned_cols=70  Identities=13%  Similarity=0.087  Sum_probs=59.8

Q ss_pred             CeEEEeCCCCCC-Ch----HHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         517 DTVVVKNLPPTI-TW----QELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       517 ~~v~V~~Lp~~~-~~----~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .+|+|.||+.++ +.    +.++++|+.|+++..-...+.=+.-.|.|.++++|.+|-..||+..|.|++|+|.+
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YF   80 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYF   80 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEEC
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEe
Confidence            499999998866 33    46689999999887766666546789999999999999999999999999999864

>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=97.63  E-value=0.00022  Score=57.66  Aligned_cols=76  Identities=12%  Similarity=0.167  Sum_probs=64.4

Q ss_pred             CcEEEEecCCCCCcH-----HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         159 INKVFVANLDYKVDE-----KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       159 ~~~l~V~nLp~~~te-----~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      .++|+|.||+.++-.     +.++++|..|+++....+++.-     .-..|.|.+.++|.+|-..||+..+.|+.|+|-
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF-----RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----KRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----TEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc-----eEEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            368999999886522     5789999999998888777653     247899999999999999999999999999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      ++.+..
T Consensus        80 Fgq~~~   85 (104)
T 1wey_A           80 FAQTLH   85 (104)
T ss_dssp             CCCCSS
T ss_pred             ecCCCC
Confidence            988554

>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=97.13  E-value=0.0009  Score=55.65  Aligned_cols=72  Identities=14%  Similarity=0.071  Sum_probs=61.0

Q ss_pred             CCCcEEEcCCCCCCCHHHHHhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCC-eEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG-RKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g-r~i~V~~a~  108 (587)
                      .+.-|-|-++|.+.....|+.|++||+|.+....   ++  ..+-.|+|.++.+|++||.+ ||..|.+ -.|-|.+..
T Consensus        23 ~~~wVtVFGFp~~~~~~VL~~F~~~G~Iv~~~~~---~~--~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQASASYILLQFAQYGNILKHVMS---NT--GNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGGGHHHHHHHHHTTSCEEEEEEC---SS--SSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHhhCcEEEeccC---CC--CCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEECC
Confidence            4667999999999988888999999999998762   12  36899999999999999965 9999984 788888865

>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=97.07  E-value=0.003  Score=50.13  Aligned_cols=67  Identities=10%  Similarity=0.151  Sum_probs=55.9

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQSISMLNNQNLF  226 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  226 (587)
                      ++|.|++||+.+||+++.+.++.+..+........+.   -....-|+|.|.+.+++..-.+.++|+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            5899999999999999999999988877666665542   223356999999999999999999999875

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.93  E-value=0.0033  Score=52.25  Aligned_cols=69  Identities=20%  Similarity=0.277  Sum_probs=58.3

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccC-ceEEEE
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDG-KIIDVT  585 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g-~~i~v~  585 (587)
                      ..+-|.|.+.|... -..+.++|+.||.|+..........-.|.|+++.+|++|+.+ ||..|.+ -.|=|.
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~   92 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVK   92 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEE
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEE
Confidence            46799999999886 577889999999998777754557899999999999999998 9999985 455554

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.83  E-value=0.0038  Score=49.52  Aligned_cols=55  Identities=13%  Similarity=0.160  Sum_probs=46.8

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN  221 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  221 (587)
                      ...++| .+|.++...||.++|+.||. ..|+++.|-      -|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            456667 99999999999999999995 457777763      69999999999999998764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.72  E-value=0.0015  Score=54.94  Aligned_cols=78  Identities=12%  Similarity=0.087  Sum_probs=60.0

Q ss_pred             CCCcEEEcCCCCCCCHHHHHhcccCCCeEE-EEEeeCCC---------C-----CcceEEEEEECCHHHHHHHHHHhCCc
Q psy1534          31 LEVPVVMDLIQGDASLYQISHLSTVGDVTY-VEILNDDT---------G-----KPRGSAIVEFQSPDLVRKAVNKMHRF   95 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l~~F~~~G~V~~-v~i~~d~~---------g-----~skG~aFV~F~~~e~A~~Al~~l~g~   95 (587)
                      .+.-|.|=+.|.+.+...|+.|++||.|.+ +.+.++..         .     ....+-.|+|.++.+|++||.. ||.
T Consensus         6 ~e~~VtVFGFp~~~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~   84 (132)
T 3p3d_A            6 GELAILVFGYPETMANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGA   84 (132)
T ss_dssp             --CEEEEECCCGGGHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTC
T ss_pred             CceEEEEEecCHHHHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCe
Confidence            455688889999999999999999999877 22211000         0     0135779999999999999966 999


Q ss_pred             eeCCeEEEEEeccc
Q psy1534          96 ETKGRKLVIKEAVE  109 (587)
Q Consensus        96 ~l~gr~i~V~~a~~  109 (587)
                      .|.|..|-|.+..+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999999999873

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.66  E-value=0.0054  Score=48.64  Aligned_cols=64  Identities=19%  Similarity=0.268  Sum_probs=54.8

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC--------CCeEEEEECCHHHHHHHHHHhCCCcccCc
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK--------GDIGLVRFDSEWTAKRAIDMMDRTRIDGK  580 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~--------~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~  580 (587)
                      .+|.|++||...|++++.+.+.+...+.+..-...        ...|.|.|.+.+++..=.+.++|+.|...
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            48999999999999999999999988766555332        15699999999999999999999988644

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.55  E-value=0.0017  Score=54.64  Aligned_cols=70  Identities=19%  Similarity=0.241  Sum_probs=55.2

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeE-EEee-------------------cCCCeEEEEECCHHHHHHHHHHhCCC
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKF-AEIK-------------------GKGDIGLVRFDSEWTAKRAIDMMDRT  575 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~-~~~~-------------------~~~g~g~v~f~~~~~a~~Ai~~l~g~  575 (587)
                      ..-|+|.+.|.+.+|. +.++|++||.|+. ..+.                   .....-.|.|+++.+|.+|+.. ||.
T Consensus         7 e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGA   84 (132)
T ss_dssp             -CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTC
T ss_pred             ceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCe
Confidence            5689999999888765 6688999999854 2111                   1235668999999999999998 999


Q ss_pred             cccCceEEEEEC
Q psy1534         576 RIDGKIIDVTFF  587 (587)
Q Consensus       576 ~~~g~~i~v~~~  587 (587)
                      .|.|..|=|..|
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999988877764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.42  E-value=0.012  Score=46.59  Aligned_cols=54  Identities=17%  Similarity=0.244  Sum_probs=44.1

Q ss_pred             eEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhC
Q psy1534         518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMD  573 (587)
Q Consensus       518 ~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~  573 (587)
                      -||+-+.|.++.-.||.++|++||.|.-.=|. + ..|+|.|.+++.|..|++.++
T Consensus        17 HVf~l~FP~ewKt~DI~~lFs~fggv~I~Wid-D-TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHVTFPKEWKTSDLYQLFSAFGNIQISWID-D-TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE-T-TEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEEeCChhhhhHHHHHHhhccCCEEEEEEc-C-CeEEEEecCHHHHHHHHHhcc
Confidence            45544999999999999999999965433333 3 699999999999999999874

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.29  E-value=0.0066  Score=48.30  Aligned_cols=54  Identities=13%  Similarity=0.167  Sum_probs=46.5

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN  221 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  221 (587)
                      ..++| ++|.++...||.++|+.|| -..|.++.|-      -|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            45666 9999999999999999998 4567777763      69999999999999998765

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.24  E-value=0.0057  Score=48.65  Aligned_cols=53  Identities=23%  Similarity=0.322  Sum_probs=44.4

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhC
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH   93 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~   93 (587)
                      -||+=.+|.++...|| ++|+.||. ..|+-+-|      ..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fgg-v~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSEE-EEEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEEeCChhhhhHHHHHHHhccCC-EEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            3454499999999999 89999995 46666666      579999999999999998764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.49  E-value=0.025  Score=45.10  Aligned_cols=69  Identities=16%  Similarity=0.185  Sum_probs=47.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC--CCCc-ceEEEEEECCHHHHHHHHHHhCCceeCC
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD--TGKP-RGSAIVEFQSPDLVRKAVNKMHRFETKG   99 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~--~g~s-kG~aFV~F~~~e~A~~Al~~l~g~~l~g   99 (587)
                      ..-+|.|+.||..+||+++ +.++.+=++.....+.-+  .+.+ -.-|||.|.+.|+...-.+..+|..|.+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            3468999999999999976 444443333222222111  1111 1468999999999999999999988864

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.01  E-value=0.019  Score=45.79  Aligned_cols=65  Identities=18%  Similarity=0.210  Sum_probs=52.2

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecC--------CCeEEEEECCHHHHHHHHHHhCCCcccCc
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK--------GDIGLVRFDSEWTAKRAIDMMDRTRIDGK  580 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~--------~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~  580 (587)
                      .-+|.||.||+..||+++.+.+.+.-++.+..-...        ...|.|.|.+.++...=.+.++|+.|-..
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            358999999999999999988888766544332221        15699999999999999999999987644

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.94  E-value=0.023  Score=59.07  Aligned_cols=56  Identities=20%  Similarity=0.188  Sum_probs=41.8

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHH
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNK   91 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~   91 (587)
                      ..+.|||. .|.+.++.+| ++|++||+|.++...++ .|   -||.|||.+.+++..++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~-~g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES-FG---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS-SS---EEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc-CC---eEEEEEeCCHHHHHHHHhc
Confidence            45689997 7999999999 99999999999977654 22   6999999999999988754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.41  E-value=0.044  Score=56.98  Aligned_cols=56  Identities=16%  Similarity=0.085  Sum_probs=42.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHH
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM  219 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~  219 (587)
                      .+.|+|. .|..+++.+|.++|++||.|.++...+++    .-|+.|+|.+.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHhc
Confidence            3689998 79999999999999999999999887654    36999999999998877643

---

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	587
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-05
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-04
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-04
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	0.003
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	0.003
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	7e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	0.001
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	9e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	9e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	8e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-04
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.002
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-09
d1go4a_	196	d.135.1.1 (A:) The spindle assembly checkpoint pro	3e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.003
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	9e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	7e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-04
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 7e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-05
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
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	8e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	8e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	9e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	4e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	9e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	8e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.002
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	6e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	0.003
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	9e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	6e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	9e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.004
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	9e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	9e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	4e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04

>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 = 65.3 bits (159), Expect = 7e-14
 Identities = 19/78 (24%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSI 217
           +K+ V N+ ++ +++++RE+F   G+++ V +       G  RGFG V+F    +A ++ 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 218 -SMLNNQNLFERRITVRM 234
            ++ ++ +L+ RR+ +  
Sbjct: 69  NALCHSTHLYGRRLVLEW 86

>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 = 54.6 bits (131), Expect = 4e-10
 Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-------GLVRFDSEWTAKRAID 570
            ++V+N+P     +E+R+ F   G++K   +  K          G V F ++  AK+A +
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 571 -MMDRTRIDGKIIDVTF 586
            +   T + G+ + + +
Sbjct: 70  ALCHSTHLYGRRLVLEW 86

>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 = 41.5 bits (97), Expect = 2e-05
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 50  SHLSTVGDVTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIKE 106
              ST G++  V +      TG  RG   V+F +    +KA N + H     GR+LV++ 
Sbjct: 27  ELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW 86

Query: 107 AVEDK 111
           A  + 
Sbjct: 87  ADSEV 91

>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 = 61.1 bits (148), Expect = 1e-12
 Identities = 19/74 (25%), Positives = 41/74 (55%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           K+ V+NLD+ V +  ++E+F   G ++   +  D+ G+S G   V F+   +A++++   
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 221 NNQNLFERRITVRM 234
           N   L  R + +++
Sbjct: 62  NGVPLDGRPMNIQL 75

>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 = 56.5 bits (136), Expect = 6e-11
 Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 5/71 (7%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIK-----GKGDIGLVRFDSEWTAKRAIDMMDRT 575
           V NL   ++  ++++ F   G +K A +             V F+ +  A +A+   +  
Sbjct: 5   VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGV 64

Query: 576 RIDGKIIDVTF 586
            +DG+ +++  
Sbjct: 65  PLDGRPMNIQL 75

>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 = 38.4 bits (89), Expect = 1e-04
 Identities = 12/58 (20%), Positives = 24/58 (41%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
              +  G +    +  D +G+  G+A V F+      KA+ + +     GR + I+  
Sbjct: 19  ELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 76

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.1 bits (148), Expect = 1e-12
 Identities = 22/72 (30%), Positives = 33/72 (45%)

Query: 515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDR 574
           +R  + V NLPP IT +E+R  F   G      I      G +R ++   A+ A   +D 
Sbjct: 7   QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDN 66

Query: 575 TRIDGKIIDVTF 586
             + GK + V F
Sbjct: 67  MPLRGKQLRVRF 78

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.8 bits (129), Expect = 6e-10
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +++FV NL   + E+++R++F   GK   V        K +GFG +  +    A  +   
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEV-----FIHKDKGFGFIRLETRTLAEIAKVE 63

Query: 220 LNNQNLFERRITVRM 234
           L+N  L  +++ VR 
Sbjct: 64  LDNMPLRGKQLRVRF 78

>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 = 59.3 bits (143), Expect = 6e-12
 Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 4/82 (4%)

Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKD----GKSRGFGTVEFDHPVEAVQSIS 218
           F+ NL++   E+ L+ VF   G +++  I+  K+      S GFG VE+  P +A +++ 
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 219 MLNNQNLFERRITVRMDRVADR 240
            L    +   ++ VR+   A +
Sbjct: 62  QLQGHTVDGHKLEVRISERATK 83

>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 = 56.2 bits (135), Expect = 8e-11
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI---------GLVRFDSEWTAKRAIDM 571
           +KNL  + T + L+  F   G IK   I  K +          G V +     A++A+  
Sbjct: 3   IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 62

Query: 572 MDRTRIDGKIIDVTF 586
           +    +DG  ++V  
Sbjct: 63  LQGHTVDGHKLEVRI 77

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 9/43 (20%), Positives = 19/43 (44%)

Query: 65  NDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
                   G   VE++ P+  +KA+ ++      G KL ++ +
Sbjct: 36  KAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS 78

>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 = 59.6 bits (144), Expect = 8e-12
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSIS 218
             ++V NL +   E+++ E+F  +G ++ + + LDK    + GF  VE+    +A  ++ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 219 MLNNQNLFERRITVRMDR 236
            +N   L +R I    D 
Sbjct: 68  YINGTRLDDRIIRTDWDA 85

>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 = 55.0 bits (132), Expect = 3e-10
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG------KGDIGLVRFDSEWTAKRAIDM 571
           T+ V NL    T +++ + F   GDIK   +              V + S   A+ A+  
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 572 MDRTRIDGKIIDVTF 586
           ++ TR+D +II   +
Sbjct: 69  INGTRLDDRIIRTDW 83

>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 = 38.4 bits (89), Expect = 2e-04
 Identities = 13/67 (19%), Positives = 22/67 (32%), Gaps = 1/67 (1%)

Query: 50  SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
              S  GD+  + +  D       G   VE+ S      A+  ++      R +      
Sbjct: 26  ELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 85

Query: 109 EDKGGRR 115
             K GR+
Sbjct: 86  GFKEGRQ 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (143), Expect = 1e-11
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 502 LDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDS 561
           L     +NQSS  +  TV    +   +T Q +R  F   G I    +  +     VRF +
Sbjct: 5   LRFEDVVNQSSP-KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFST 63

Query: 562 EWTAKRAIDMMDRTRIDGKIIDVTF 586
             +A  AI  ++ T I+G ++   +
Sbjct: 64  HESAAHAIVSVNGTTIEGHVVKCYW 88

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.7 bits (121), Expect = 1e-08
 Identities = 10/76 (13%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            V+   +   + ++ +R+ F   G++  + +        +G+  V F     A  +I  +
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSV 74

Query: 221 NNQNLFERRITVRMDR 236
           N   +    +     +
Sbjct: 75  NGTTIEGHVVKCYWGK 90

>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 = 59.3 bits (143), Expect = 1e-11
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI---GLVRFDSEWTAKRAIDMMDR 574
            + ++NLP  IT +E+ D F   G I+   +    +      V ++  + AK A D +  
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 575 TRIDGKIIDVTF 586
             +  + + V +
Sbjct: 69  FNVCNRYLVVLY 80

>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 = 59.3 bits (143), Expect = 2e-11
 Identities = 22/108 (20%), Positives = 48/108 (44%), Gaps = 6/108 (5%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +++ NL YK+  +++ ++F   G +  + +      ++RG   V ++   +A  +   
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 220 LNNQNLFERRITVRM---DRVADRLDGPVRLPEGLKSIGMGLGANGAP 264
           L+  N+  R + V     +R   ++D   +  E LK +    G N  P
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKKK-EEQLKLLKEKYGINTDP 112

>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 = 41.5 bits (97), Expect = 2e-05
 Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
                 G +   +I   +T + RG+A V ++     + A + +  F    R LV+     
Sbjct: 26  DIFGKYGPI--RQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA 83

Query: 110 DKGGRR 115
           ++  ++
Sbjct: 84  NRAFQK 89

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  L ++  ++ LRE F   G+V+   +  D    +SRGFG V F       + ++ 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 220 LNNQNLFERRITVRM 234
            +   L  + I  ++
Sbjct: 62  -SRHELDSKTIDPKV 75

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 7/72 (9%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIG------LVRFDSEWTAKRAIDMM 572
           + +  L    T + LR+ F   G++K   +              V F  +    + +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 573 DRTRIDGKIIDV 584
            R  +D K ID 
Sbjct: 62  SRHELDSKTIDP 73

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 1/40 (2%)

Query: 68  TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           T + RG   V F     V K +    R E   + +  K A
Sbjct: 38  TKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVA 76

>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 = 57.2 bits (138), Expect = 3e-11
 Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIA-LDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++V +L   V E  L E F  AG + ++ +       +S G+  V F  P +A +++  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 220 LNNQNLFERRITVR 233
           +N   +  + + + 
Sbjct: 62  MNFDVIKGKPVRIM 75

>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 = 55.3 bits (133), Expect = 2e-10
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
           V +L P +T   L +KF   G I    +      +       V F     A+RA+D M+ 
Sbjct: 5   VGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF 64

Query: 575 TRIDGKIIDVTF 586
             I GK + + +
Sbjct: 65  DVIKGKPVRIMW 76

>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 = 38.4 bits (89), Expect = 1e-04
 Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 50  SHLSTVGDVTYVEIL-NDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
              S  G +  + +  +  T +  G A V FQ P    +A++ M+    KG+ + I  + 
Sbjct: 19  EKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ 78

Query: 109 ED 110
            D
Sbjct: 79  RD 80

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 6e-11
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSIS 218
             VF   L  ++  + L + F   GKV +V I  D++  +S+G   VEF    ++V    
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI-QSVPLAI 77

Query: 219 MLNNQNLFERRITVR 233
            L  Q L    I V+
Sbjct: 78  GLTGQRLLGVPIIVQ 92

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 7e-07
 Identities = 22/90 (24%), Positives = 32/90 (35%), Gaps = 9/90 (10%)

Query: 505 NRSMNQSSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGL 556
              ++  S  ERD  TV    L   I  ++L D F   G ++   I    +      I  
Sbjct: 5   REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 64

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           V F    +   AI  +   R+ G  I V  
Sbjct: 65  VEFCEIQSVPLAI-GLTGQRLLGVPIIVQA 93

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 56.5 bits (136), Expect = 7e-11
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIG------LVRFDSEWTAKRAIDM 571
            ++V  LP  +T +EL   FR  G I    I      G       V F SE  ++RAI +
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 572 MDRTRIDGKIIDVTF 586
           ++   +  K + V++
Sbjct: 64  LNGITVRNKRLKVSY 78

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 54.6 bits (131), Expect = 3e-10
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENV-EIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            + V  L   + +++L  +FR  G +     +   K G S G+  V+F   +++ ++I +
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 220 LNNQNLFERRITVRMDR 236
           LN   +  +R+ V   R
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 11/59 (18%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 50  SHLSTVGDVTYVE-ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           +    +G +     + +  TG   G A V+F S    ++A+  ++    + ++L +  A
Sbjct: 21  ALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 7e-11
 Identities = 16/69 (23%), Positives = 30/69 (43%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
            + V+NL  + + + +  +F N        +K   D   V F +   A  A+  ++   +
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVL 69

Query: 578 DGKIIDVTF 586
           DG  I+VT 
Sbjct: 70  DGSPIEVTL 78

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 8e-08
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 5/80 (6%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            ++V NL     E+ + + F          +      K R +  V F +  +AV+++  L
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKAL 64

Query: 221 NNQNLFERRITVRMDRVADR 240
           N + L    I V + +  D+
Sbjct: 65  NGKVLDGSPIEVTLAKPVDK 84

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 2e-10
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           + ++ V NL Y V    L ++F   G V  +         ++    +++  PV A  +  
Sbjct: 7   VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT---FTKNNQFQALLQYADPVSAQHAKL 63

Query: 219 MLNNQNLFERRITVRMD 235
            L+ QN++    T+R+D
Sbjct: 64  SLDGQNIYNACCTLRID 80

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 6e-07
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 508 MNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI--KGKGDIGLVRFDSEWTA 565
           M   S + R  ++V+NL   +T   L   F   G +       K      L+++    +A
Sbjct: 1   MAGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSA 58

Query: 566 KRAIDMMDRTRI--DGKIIDVTF 586
           + A   +D   I      + + F
Sbjct: 59  QHAKLSLDGQNIYNACCTLRIDF 81

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 2e-10
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIK----GKGDIGLVRFDSEWTAKRAIDMMD 573
            + +KNL  +I  + L D F   G+I   ++     G    G V F+++  A+RAI+ M+
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 69

Query: 574 RTRIDGKIIDVTF 586
              ++ + + V  
Sbjct: 70  GMLLNDRKVFVGR 82

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 6e-10
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +F+ NLD  +D K L + F   G + + ++ +  +  S+G+G V F+    A ++I  
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKV-VCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 220 LNNQNLFERRITVR 233
           +N   L +R++ V 
Sbjct: 68  MNGMLLNDRKVFVG 81

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
              S  G++   +++ D+ G  +G   V F++ +   +A+ KM+      RK+ +     
Sbjct: 27  DTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 85

Query: 110 DK 111
            K
Sbjct: 86  RK 87

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  L ++  E+ LR  +   GK+ +  +  D    +SRGFG V F    E   +++ 
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 81

Query: 220 LNNQNLFERRITVR 233
               ++  R +  +
Sbjct: 82  -RPHSIDGRVVEPK 94

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 7e-08
 Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDI---KFAEIKGKGDI---GLVRFDSEWTAKRAIDM 571
            + +  L    T + LR+ +   G +                 G V F S      A+  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 81

Query: 572 MDRTRIDGKIIDV 584
              + IDG++++ 
Sbjct: 82  RPHS-IDGRVVEP 93

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 16/76 (21%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           +K+F+  L   +++ +++E+    G ++   +  D   G S+G+   E+       Q+I+
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 219 MLNNQNLFERRITVRM 234
            LN   L ++++ V+ 
Sbjct: 62  GLNGMQLGDKKLLVQR 77

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 6e-08
 Identities = 8/74 (10%), Positives = 23/74 (31%), Gaps = 6/74 (8%)

Query: 519 VVVKNLPPTITWQELRD---KFRNCGDIKFAEIKGKG---DIGLVRFDSEWTAKRAIDMM 572
           + +  LP  +   ++++    F         +    G         +       +AI  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 573 DRTRIDGKIIDVTF 586
           +  ++  K + V  
Sbjct: 64  NGMQLGDKKLLVQR 77

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 68  TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRN 116
           TG  +G A  E+   ++  +A+  ++  +   +KL+++ A     G +N
Sbjct: 39  TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA---SVGAKN 84

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 2e-10
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLVRFDSEWTAKRAI 569
           +  ++V  LP  +T +E R  F + G+I+  ++            G V +     A++AI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 570 DMMDRTRIDGKIIDVTF 586
           + ++  R+  K I V++
Sbjct: 62  NTLNGLRLQTKTIKVSY 78

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKV-ENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            + V  L   + +++ R +F   G++     +     G+S G+G V +  P +A ++I+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 220 LNNQNLFERRITVRMDR 236
           LN   L  + I V   R
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 9/43 (20%), Positives = 19/43 (44%)

Query: 65  NDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           +  TG+  G   V +  P    KA+N ++    + + + +  A
Sbjct: 37  DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
            ++V NL   + + +L  +F   G +    I  DK  G+ RG   V ++   EA ++IS 
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 220 LNNQNLF--ERRITVR 233
           LNN       + ++VR
Sbjct: 68  LNNVIPEGGSQPLSVR 83

>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 = 54.6 bits (131), Expect = 4e-10
 Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 8/77 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLVRFDSEWTAKRAIDM 571
            + V NLP TIT  +L   F   G I    I           +  VR++    A+ AI  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 572 MDRTRIDG--KIIDVTF 586
           ++    +G  + + V  
Sbjct: 68  LNNVIPEGGSQPLSVRL 84

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 2e-10
 Identities = 11/82 (13%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIAL------DKDGKSRGFGTVEFDHPVEAV 214
           +++V N+ + + E+ + + F    ++  +  A        +  + + F  +EF    E  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 215 QSISMLNNQNLFERRITVRMDR 236
           Q++   +      + + +R   
Sbjct: 63  QAM-AFDGIIFQGQSLKIRRPH 83

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 1e-06
 Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 12/78 (15%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-----------GLVRFDSEWTAK 566
            + V N+P  IT + + D F     +          +             + F S     
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 567 RAIDMMDRTRIDGKIIDV 584
           +A+   D     G+ + +
Sbjct: 63  QAM-AFDGIIFQGQSLKI 79

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 54.7 bits (131), Expect = 5e-10
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 510 QSSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-IGLVRFDSEWTAK 566
            +S   R   T++ KNL   IT  EL++ F +  +I+     GK   I  + F SE  A+
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 567 RAIDMMDRTRIDGKIIDVTF 586
           + ++      IDG+ + + +
Sbjct: 68  KNLEEKQGAEIDGRSVSLYY 87

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +   NL + + E +L+EVF  A ++  V      DGKS+G   +EF    +A +++  
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEE 72

Query: 220 LNNQNLFERRITVR 233
                +  R +++ 
Sbjct: 73  KQGAEIDGRSVSLY 86

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 39.6 bits (92), Expect = 9e-05
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 67  DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
             GK +G A +EF+S     K + +    E  GR + +     +KGG R
Sbjct: 48  QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT-GEKGGTR 95

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 5e-10
 Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLVRFDSEWTAKRAIDM 571
            + V  L   +  + L   F   GDI   +I    +         V F+    A  AID 
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 572 MDRTRIDGKIIDVTF 586
           M+ + + G+ I V  
Sbjct: 67  MNESELFGRTIRVNL 81

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 3e-09
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSIS 218
             ++V  L  +VD+K L   F   G + +++I LD +  K RGF  VEF+   +A  +I 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 219 MLNNQNLFERRITVRM 234
            +N   LF R I V +
Sbjct: 66  NMNESELFGRTIRVNL 81

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 8e-04
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 50  SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           +     GD+T ++I  D  T K RG A VEF+  +    A++ M+  E  GR + +  A
Sbjct: 24  AAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 5e-10
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSISM 219
           K+F+  L +   +K L++ F   G+V +  + LD     SRGFG V F       + +  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 220 LNNQNLFERRITVR 233
                L  + I  +
Sbjct: 61  -KEHKLNGKVIDPK 73

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.2 bits (117), Expect = 2e-08
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLVRFDSEWTAKRAIDMM 572
           + +  L    T ++L+D F   G++    +K           G V F    +  + +D  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 573 DRTRIDGKIIDV 584
           +   ++GK+ID 
Sbjct: 62  EHK-LNGKVIDP 72

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 6e-10
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVF-RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  L ++  ++ LR  F +     + V +      +SRGFG V +    E   +++ 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 220 LNNQNLFERRITVR 233
                +  R +  +
Sbjct: 68  -RPHKVDGRVVEPK 80

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 9e-08
 Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKG------DIGLVRFDSEWTAKRAIDM 571
            + +  L    T + LR  F   G +    +            G V + +      A++ 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 572 MDRTRIDGKIIDV 584
                +DG++++ 
Sbjct: 68  RPHK-VDGRVVEP 79

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 6e-04
 Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 68  TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
           T + RG   V + + + V  A+N     +  GR +  K AV
Sbjct: 44  TKRSRGFGFVTYATVEEVDAAMNARP-HKVDGRVVEPKRAV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 7e-10
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 509 NQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLVRFDSE 562
           N+++      + V  L    T ++LR+ F   G I    I              V F++ 
Sbjct: 2   NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61

Query: 563 WTAKRAIDMMDRTRIDGKIIDV 584
             AK A +  +   +DG+ I V
Sbjct: 62  DDAKEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 9e-10
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSIS 218
             + V  L     E+ LREVF   G + +V I  D+   +SRGF  V F++  +A ++  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 219 MLNNQNLFERRITV 232
             N   L  RRI V
Sbjct: 70  RANGMELDGRRIRV 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.5 bits (128), Expect = 8e-10
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQ 215
           P    + V N+ + V   ++ + F     +   V +  ++ G   G   V F+   EA  
Sbjct: 7   PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 66

Query: 216 SISMLNNQNLFERRITVRM 234
           ++  LN++ +  R++ + +
Sbjct: 67  AVIDLNDRPIGSRKVKLVL 85

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
            + V+N+P T++  E+ D F     I  +            G   +V F+S   A  A+ 
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG-EAMVAFESRDEATAAVI 69

Query: 571 MMDRTRIDGKIIDVTF 586
            ++   I  + + +  
Sbjct: 70  DLNDRPIGSRKVKLVL 85

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 13/47 (27%), Positives = 22/47 (46%)

Query: 61  VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
           V +  ++ G P G A+V F+S D    AV  ++      RK+ +   
Sbjct: 40  VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 514 IERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG------KGDIGLVRFDSEWTAKR 567
           +E   + V ++       E+++KF + G+IK   +             LV +++   A  
Sbjct: 5   VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 64

Query: 568 AIDMMDRTRIDGKIIDVTF 586
           A + ++   I G+ I V +
Sbjct: 65  AKEALNGAEIMGQTIQVDW 83

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 48.2 bits (114), Expect = 7e-08
 Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSIS 218
             +FV ++  +  E +++E F   G+++N+ + LD+    S+G+  VE++   +A+ +  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 219 MLNNQNLFERRITV 232
            LN   +  + I V
Sbjct: 68  ALNGAEIMGQTIQV 81

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.6 bits (128), Expect = 1e-09
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSIS 218
            ++FV NL Y   E+ L ++F   G +  +   +D   K  +GF  V F  P  AV++ +
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 219 MLNNQNLFERRITVRM 234
            ++ Q    R + V  
Sbjct: 69  EVDGQVFQGRMLHVLP 84

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFA------EIKGKGDIGLVRFDSEWTAKRAIDM 571
            + V+NL  T + ++L   F   G +           K       V F     A +A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 572 MDRTRIDGKIIDVTF 586
           +D     G+++ V  
Sbjct: 70  VDGQVFQGRMLHVLP 84

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 13/51 (25%), Positives = 22/51 (43%)

Query: 71  PRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGG 121
           P+G A V F  P+   KA  ++     +GR L +  +   K   ++    G
Sbjct: 49  PKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.9 bits (127), Expect = 1e-09
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 3/84 (3%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPP-TITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSE 562
           S  S           V + NL    +   ++   F   G I             V++ +E
Sbjct: 3   SGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIV--GCSVHKGFAFVQYVNE 60

Query: 563 WTAKRAIDMMDRTRIDGKIIDVTF 586
             A+ A+   D   I G+++D+  
Sbjct: 61  RNARAAVAGEDGRMIAGQVLDINL 84

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.8 bits (124), Expect = 4e-09
 Identities = 12/78 (15%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 160 NKVFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           ++VF+ NL+   V +  +  +F   GK+    +        +GF  V++ +   A  +++
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVA 68

Query: 219 MLNNQNLFERRITVRMDR 236
             + + +  + + + +  
Sbjct: 69  GEDGRMIAGQVLDINLAA 86

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 7/70 (10%)

Query: 51  HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED 110
             S  G +    +        +G A V++ +    R AV         G+ L I  A E 
Sbjct: 36  IFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP 88

Query: 111 KGGRRNMGGG 120
           K  R     G
Sbjct: 89  KVNRSGPSSG 98

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 2e-09
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIK---GKGDIGLVRFDSEWTAKRAIDMMDR 574
            + V NLPP I  +++ D F   G I+  ++K   G      V F+    A+ A+   D 
Sbjct: 16  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 75

Query: 575 TRIDGKIIDVTF 586
              DG  + V F
Sbjct: 76  YDYDGYRLRVEF 87

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            +++V NL   +  K + +VF   G + ++++          F  VEF+ P +A  ++  
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK--NRRGGPPFAFVEFEDPRDAEDAVYG 72

Query: 220 LNNQNLFERRITVRMDR 236
            +  +    R+ V   R
Sbjct: 73  RDGYDYDGYRLRVEFPR 89

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 7e-05
 Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 2/63 (3%)

Query: 50  SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
                 G +  +++ N         A VEF+ P     AV     ++  G +L ++    
Sbjct: 33  DVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 90

Query: 110 DKG 112
            +G
Sbjct: 91  GRG 93

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.9 bits (126), Expect = 2e-09
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 14/88 (15%)

Query: 513 NIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVR-------------- 558
           + +   + V+ L  ++T  +L D F+ CG +K  +  G+  I +                
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           ++   TAK A++  D     G  + V+ 
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQGSKLKVSL 92

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD---------KDGKSRGFGTVEFDHP 210
           + ++V  L+  V    L + F+  G V+  +             + GK +G  TV ++ P
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 211 VEAVQSISMLNNQNLFERRITVRMDR 236
             A  ++   + ++    ++ V + R
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLAR 94

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 0.002
 Identities = 18/70 (25%), Positives = 28/70 (40%)

Query: 38  DLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET 97
           DL         +      G       L+ +TGKP+G A V ++ P   + AV      + 
Sbjct: 24  DLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF 83

Query: 98  KGRKLVIKEA 107
           +G KL +  A
Sbjct: 84  QGSKLKVSLA 93

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L     E+K+RE F   G+VE++E+ +D    K RGF  + F       + +  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 220 LNNQNLFERRITVRM 234
               N+   +  +++
Sbjct: 61  -KYHNVGLSKCEIKV 74

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.1 bits (122), Expect = 5e-09
 Identities = 10/72 (13%), Positives = 26/72 (36%), Gaps = 7/72 (9%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK------GDIGLVRFDSEWTAKRAIDMM 572
           + V  L P    +++R+ F   G+++  E+              + F  E   K+ ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 573 DRTRIDGKIIDV 584
               +     ++
Sbjct: 62  YHN-VGLSKCEI 72

>d1go4a_ d.135.1.1 (A:) The spindle assembly checkpoint protein mad2 {Human (Homo sapiens) [TaxId: 9606]} Length = 196

class: Alpha and beta proteins (a+b)
fold: The spindle assembly checkpoint protein mad2
superfamily: The spindle assembly checkpoint protein mad2
family: The spindle assembly checkpoint protein mad2
domain: The spindle assembly checkpoint protein mad2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (132), Expect = 3e-09
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKT 320
           ++ + +WL +  VQKL ++ISN  + EVLERW F ++ DK++ ++ A    +    
Sbjct: 62  VEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAI 117

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 3e-09
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 9/85 (10%)

Query: 155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK---SRGFGTVEFDHPV 211
           NC    ++F+  +      +++ E      +     I          +RGF  VE++   
Sbjct: 1   NC----RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 56

Query: 212 EAVQSISMLNNQN--LFERRITVRM 234
            A  +   L      L+  +I V  
Sbjct: 57  AAAMARRKLMPGRIQLWGHQIAVDW 81

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 4e-06
 Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 10/79 (12%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI--------GLVRFDSEWTAKRAI 569
            + +  +P     +E+ ++     +     I                V ++S   A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 570 DMMD--RTRIDGKIIDVTF 586
             +   R ++ G  I V +
Sbjct: 63  RKLMPGRIQLWGHQIAVDW 81

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 2/42 (4%)

Query: 68  TGKPRGSAIVEFQSPDLVRKAVNKM--HRFETKGRKLVIKEA 107
             K RG A VE++S      A  K+   R +  G ++ +  A
Sbjct: 41  KMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWA 82

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISM 219
            ++V+ L   + +K+L ++F   G++    I +D+    SRG G + FD  +EA ++I  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 220 LNNQNLF--ERRITVR 233
           LN Q        ITV+
Sbjct: 68  LNGQKPSGATEPITVK 83

>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 = 50.4 bits (120), Expect = 9e-09
 Identities = 24/84 (28%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 511 SSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI------GLVRFDSEWT 564
           S++I    + V  LP T+T +EL   F   G I  + I            G +RFD    
Sbjct: 1   SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 60

Query: 565 AKRAIDMMDRTRIDGKI--IDVTF 586
           A+ AI  ++  +  G    I V F
Sbjct: 61  AEEAIKGLNGQKPSGATEPITVKF 84

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 4e-09
 Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 7/73 (9%)

Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-------IGLVRFDSEWTAKRAIDMMD 573
           + NL P I  + L D F   G I       +            + F S   +  AI+ M+
Sbjct: 3   IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 62

Query: 574 RTRIDGKIIDVTF 586
              +  + I V++
Sbjct: 63  GQYLCNRPITVSY 75

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIA--LDKDGKSRGFGTVEFDHPVEAVQSISM 219
           +F+ NLD ++DEK L + F   G +            G S+G+  + F     +  +I  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 220 LNNQNLFERRITVRM 234
           +N Q L  R ITV  
Sbjct: 61  MNGQYLCNRPITVSY 75

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 6e-04
 Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 4/67 (5%)

Query: 50  SHLSTVGDVTYVEILN--DDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
              S  G +     +    DTG  +G A + F S D    A+  M+      R + +  A
Sbjct: 17  DTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA 76

Query: 108 V--EDKG 112
              + KG
Sbjct: 77  FKKDSKG 83

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 5e-09
 Identities = 22/75 (29%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDI------KFAEIKGKGDIGLVRFDSEWTAKRAIDM 571
           TV V  L   ++   L + F   G +      K          G V F SE  A  AI +
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 572 MDRTRIDGKIIDVTF 586
           MD  ++ GK I V  
Sbjct: 71  MDMIKLYGKPIRVNK 85

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 5e-08
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKV-ENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
             V+V  LD KV E  L E+F  AG V           G+ +G+G VEF    +A  +I 
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 219 MLNNQNLFERRITVRM 234
           +++   L+ + I V  
Sbjct: 70  IMDMIKLYGKPIRVNK 85

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 5e-09
 Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            ++ V+N+ ++  +  LR++F   GK+ +VEI  ++   S+GFG V F++  +A ++   
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREK 70

Query: 220 LNNQNLFERRITVRM 234
           L+   +  R+I V  
Sbjct: 71  LHGTVVEGRKIEVNN 85

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 22/84 (26%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 507 SMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIG----LVRFDSE 562
           S N  S      + V N+P      +LR  F   G I   EI            V F++ 
Sbjct: 2   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENS 61

Query: 563 WTAKRAIDMMDRTRIDGKIIDVTF 586
             A RA + +  T ++G+ I+V  
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNN 85

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 7e-09
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           NK+++ NL   V    LR++F         ++         G+  V++     A+++I  
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIET 56

Query: 220 LNNQ-NLFERRITVR 233
           L+ +  L  + + V 
Sbjct: 57  LSGKVELHGKIMEVD 71

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 3e-07
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMD-RTR 576
            + + NL P +T  +LR  F +       ++  K     V +  +  A RAI+ +  +  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 577 IDGKIIDVTF 586
           + GKI++V +
Sbjct: 63  LHGKIMEVDY 72

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 7e-09
 Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFR------NCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDM 571
           T+ V NL       +L++ FR           K            + F     A RAI  
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 572 MDRTRIDGKIIDVTF 586
           +     D  I++V +
Sbjct: 70  VSGFGYDHLILNVEW 84

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 4e-08
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             + V NL     E  L+E+FR  G +  + +A DK  G+S+GF  + F    +A ++I+
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 219 MLNNQNLFERRITVRMDR 236
            ++        + V   +
Sbjct: 69  GVSGFGYDHLILNVEWAK 86

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.6 bits (120), Expect = 7e-09
 Identities = 11/75 (14%), Positives = 30/75 (40%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG------KGDIGLVRFDSEWTAKRAIDM 571
           T+ + N PP+ T + +RD  ++   +  +                +   S+  A+  ++ 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 572 MDRTRIDGKIIDVTF 586
           ++  +I+G  +    
Sbjct: 63  LNGLKIEGYTLVTKV 77

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.6 bits (120), Expect = 9e-09
 Identities = 9/77 (11%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVE-NVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            +++ N      ++ +R++ +    V  ++ +   +   SR F  ++     +A   +  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 220 LNNQNLFERRITVRMDR 236
           LN   +    +  ++  
Sbjct: 63  LNGLKIEGYTLVTKVSN 79

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 7/76 (9%)

Query: 518 TVVVKNLPPTITWQELRD-------KFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAID 570
           T+ + NL   I   EL+        +F    DI  +          V F    +A  A+ 
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 571 MMDRTRIDGKIIDVTF 586
            M       K + + +
Sbjct: 65  SMQGFPFYDKPMRIQY 80

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 9e-08
 Identities = 13/86 (15%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRL--AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
           + +++ NL+ K+ + +L++      +   + ++I + +  K RG   V F     A  ++
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 218 SMLNNQNLFERRITVRM-----DRVA 238
             +     +++ + ++      D +A
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDIIA 89

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 4/73 (5%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI----KGKGDIGLVRFDSEWTAKRAIDMMD 573
           T+ V NL   +T   +   F   G  K  ++            V F     A  A+  M+
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 574 RTRIDGKIIDVTF 586
             +I GK + V +
Sbjct: 70  GRKILGKEVKVNW 82

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 5e-08
 Identities = 13/75 (17%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             ++V NL   V E  + ++F   G  ++ ++  +    +  +  VEF    +A  +++ 
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT-SNDPYCFVEFYEHRDAAAALAA 67

Query: 220 LNNQNLFERRITVRM 234
           +N + +  + + V  
Sbjct: 68  MNGRKILGKEVKVNW 82

>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 = 50.1 bits (119), Expect = 2e-08
 Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 2/91 (2%)

Query: 499 RAGLDSNRSMNQSSNIERDTVVVK-NLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLV 557
           +  L  +  +   S   +  VV    L   ++  +L      CG +    +         
Sbjct: 2   KHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFA 61

Query: 558 RFDSEWTAKRAIDMMDRTRI-DGKIIDVTFF 587
           R+ +   +KRA   ++   + D     +T +
Sbjct: 62  RYRTTEESKRAYVTLNGKEVVDDLGQKITLY 92

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 8/75 (10%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
           V    L   V   +L  V    G V+ +         ++ +    +    E+ ++   LN
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDAL-----LMPPNKPYSFARYRTTEESKRAYVTLN 77

Query: 222 NQNLFE---RRITVR 233
            + + +   ++IT+ 
Sbjct: 78  GKEVVDDLGQKITLY 92

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
           + + V  L +K  E+ L+E F   G+V  V++  D   G S+GFG V F      V+ +S
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 219 MLNNQNLFERRITVRM 234
                 +  R    ++
Sbjct: 69  --QRHMIDGRWCDCKL 82

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 2e-07
 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 13/87 (14%)

Query: 506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLVRF 559
           R++ ++S++     +V  LP   T Q+L++ F   G++   ++K           G VRF
Sbjct: 3   RAVQKTSDL-----IVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 57

Query: 560 DSEWTAKRAIDMMDRTRIDGKIIDVTF 586
               T  + +       IDG+  D   
Sbjct: 58  TEYETQVKVMSQRH--MIDGRWCDCKL 82

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 7e-04
 Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 2/45 (4%)

Query: 67  DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
            TG  +G   V F   +   K +++ H  +  GR    K     +
Sbjct: 45  KTGHSKGFGFVRFTEYETQVKVMSQRHMID--GRWCDCKLPNSKQ 87

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAG-KVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L      + ++  F   G   + + +      + RGFG V F+   + V+ +  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE-DIVEKVCE 59

Query: 220 LNNQNLFERRITVRM 234
           ++   +  + +  + 
Sbjct: 60  IHFHEINNKMVECKK 74

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.2 bits (114), Expect = 5e-08
 Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 7/72 (9%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIK------FAEIKGKGDIGLVRFDSEWTAKRAIDMM 572
           + V  L    T ++++  F   G +                 G V F+SE   ++  + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 573 DRTRIDGKIIDV 584
               I+ K+++ 
Sbjct: 61  HFHEINNKMVEC 72

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSI 217
           + K+FV  +    +E  LR+ F   GK+E +EI  D+     RGF  V FD   ++V  I
Sbjct: 2   VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 60

Query: 218 SMLNNQNLFERRITVR 233
            +     +      VR
Sbjct: 61  VIQKYHTVNGHNCEVR 76

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 15/73 (20%), Positives = 23/73 (31%), Gaps = 7/73 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK------GDIGLVRFDSEWTAKRAIDM 571
            + V  +        LRD F   G I+  EI              V FD    +   I +
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVI 62

Query: 572 MDRTRIDGKIIDV 584
                ++G   +V
Sbjct: 63  QKYHTVNGHNCEV 75

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 5e-08
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVF-RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
             +F+ +L  +  ++ L ++F      V        +   S+ FG V +D+PV A  +I 
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 219 MLNNQNLFERRITVRMDR 236
            +N   +  +R+ V++ R
Sbjct: 79  SMNGFQIGMKRLKVQLKR 96

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 6e-08
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGL------ 556
               + +Q    E   + + +LP     Q+L   F   G++  A++       L      
Sbjct: 5   SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 64

Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
           V +D+  +A+ AI  M+  +I  K + V  
Sbjct: 65  VSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 94

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 7e-08
 Identities = 14/76 (18%), Positives = 32/76 (42%)

Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           ++ V +     +  E+   E+    G+VE + +  +      G   V+F    +A +++ 
Sbjct: 27  VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVI 86

Query: 219 MLNNQNLFERRITVRM 234
            LNN+    + I   +
Sbjct: 87  DLNNRWFNGQPIHAEL 102

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 14/97 (14%), Positives = 31/97 (31%), Gaps = 9/97 (9%)

Query: 495 YGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIK-FAEIKGKGD 553
           Y NP     ++             V ++        +   +     G+++        GD
Sbjct: 10  YRNP----QNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGD 65

Query: 554 ----IGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
                  V+F  E  A++A+  ++    +G+ I    
Sbjct: 66  HLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 9/55 (16%), Positives = 23/55 (41%)

Query: 51  HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK 105
                G+V  + + ++      G+  V+F+  +   KAV  ++     G+ +  +
Sbjct: 47  MEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 8e-08
 Identities = 12/74 (16%), Positives = 25/74 (33%), Gaps = 1/74 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            V++           ++E     G+V N+++        +G   V FD    A + +   
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET- 66

Query: 221 NNQNLFERRITVRM 234
             Q   E  + +  
Sbjct: 67  PGQKYKETDLLILF 80

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 13/80 (16%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 512 SNIERDTVVVKNLPPTITWQELRDKFRNCGD-----IKFAEIKGKGDIGLVRFDSEWTAK 566
           ++++  +V +K  P   T  ++++   + G      ++    K       V FDS  +AK
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 567 RAIDMMDRTRIDGKIIDVTF 586
           + ++   +       + + F
Sbjct: 62  KFVETPGQK-YKETDLLILF 80

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 9e-08
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
            K+FV  L +  +E+ L +VF   G++   V +   +  +SRGFG V F++  +A  ++ 
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 219 MLNNQNLFERRITVRM 234
            +N +++  R+I V  
Sbjct: 66  AMNGKSVDGRQIRVDQ 81

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD------IGLVRFDSEWTAKRAIDM 571
            + V  L      Q L   F   G I    +    +       G V F++   AK A+  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 572 MDRTRIDGKIIDVTF 586
           M+   +DG+ I V  
Sbjct: 67  MNGKSVDGRQIRVDQ 81

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 5e-05
 Identities = 13/55 (23%), Positives = 27/55 (49%)

Query: 60  YVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
            V + + +T + RG   V F++ D  + A+  M+     GR++ + +A +    R
Sbjct: 35  VVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 89

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 9e-08
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 1/69 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
            ++VKNLP     QE+ D  ++         + K     V   +   A+ AI M  +   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAF-VTLLNGEQAQNAIQMFHQYSF 65

Query: 578 DGKIIDVTF 586
            GK + V  
Sbjct: 66  RGKDLIVQL 74

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 8/77 (10%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + + V NL    + +++ ++ +                +++    V   +  +A  +I M
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD------RNKRTAFVTLLNGEQAQNAIQM 59

Query: 220 LNNQNLFERRITVRMDR 236
            +  +   + + V++  
Sbjct: 60  FHQYSFRGKDLIVQLQP 76

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 1e-07
 Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 6/70 (8%)

Query: 519 VVVKNLPPTITWQELRDKFR------NCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMM 572
           + ++ L P  T Q+L    +      +   I           G V FDS   A++A+  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 573 DRTRIDGKII 582
             + +  ++ 
Sbjct: 61  KASGVQAQMA 70

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 5e-05
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 162 VFVANLDYKVDEKKLREVF-RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
           +++  L     ++ L ++       V    I      K +G+G V+FD P  A ++++ L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 221 NNQNLFERRI 230
               +  +  
Sbjct: 61  KASGVQAQMA 70

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 1e-07
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N ++V   D  +    LR  F   G + ++          R    V ++    A Q+++ 
Sbjct: 6   NTLYVYGED--MTPTLLRGAFSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAE 58

Query: 220 LNNQNLFERRITVRMDR 236
           LN   +   ++ V + R
Sbjct: 59  LNGTQVESVQLKVNIAR 75

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (106), Expect = 7e-07
 Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
           T+ V      +T   LR  F   G+I    +    +   V ++   +A +A+  ++ T++
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 64

Query: 578 DGKIIDVTF 586
           +   + V  
Sbjct: 65  ESVQLKVNI 73

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.5 bits (112), Expect = 2e-07
 Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 13/95 (13%)

Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGK 551
           SG  G P       R            V+V  LPP+ +WQ+L+D  R  GD+ +     K
Sbjct: 3   SGSSGGPPTRRSDFR------------VLVSGLPPSGSWQDLKDHMREAGDVCY-ADVQK 49

Query: 552 GDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
             +G+V +  +   + A+  +D T+      + ++
Sbjct: 50  DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY 84

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.5 bits (107), Expect = 8e-07
 Identities = 16/88 (18%), Positives = 29/88 (32%), Gaps = 7/88 (7%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            +V V+ L      + L++  R              D +  G G VE+    +   ++  
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMR------EAGDVCYADVQKDGMGMVEYLRKEDMEYALRK 69

Query: 220 LNNQNLFERRITVRMDRVA-DRLDGPVR 246
           L++             RV  +R  GP  
Sbjct: 70  LDDTKFRSHEGETSYIRVYPERSSGPSS 97

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 2e-07
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 10/100 (10%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG-KSRGFGTVEFDHPVEAVQSISM 219
           K+FV  L Y   +  LR+ F   G +E   +  D+   KSRG+G V       A ++   
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMGLG 259
             N  +  R+  V +  +  +       P  L++ G  +G
Sbjct: 72  P-NPIIDGRKANVNLAYLGAK-------PRSLQT-GFAIG 102

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 22/82 (26%), Positives = 31/82 (37%), Gaps = 11/82 (13%)

Query: 515 ERDT----VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI------GLVRFDSEWT 564
           ++DT    + V  LP   T   LR  F   GDI+ A +            G V       
Sbjct: 5   QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 64

Query: 565 AKRAIDMMDRTRIDGKIIDVTF 586
           A+RA    +   IDG+  +V  
Sbjct: 65  AERACKDPNPI-IDGRKANVNL 85

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 3e-07
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
            + V  L P  +   L  +F   G I+  +         ++++S   A+ A   M    +
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPL 78

Query: 578 DG--KIIDVTF 586
            G  + + V F
Sbjct: 79  GGPDRRLRVDF 89

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.7 bits (92), Expect = 9e-05
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 5/76 (6%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            +++V  L        L   F   G +  +        K   F  ++++    A  + + 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTI-----DHVKGDSFAYIQYESLDAAQAACAK 72

Query: 220 LNNQNLFERRITVRMD 235
           +    L      +R+D
Sbjct: 73  MRGFPLGGPDRRLRVD 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.4 bits (109), Expect = 3e-07
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLA---GKVENVEIALDKDGK----SRGFGTVEFDHPVE 212
           N VFV  L  ++ + ++ +        GK+  V I                 V +    +
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 213 AVQSISMLNNQNLFERRITV 232
           A+++I  +NN  +  R +  
Sbjct: 69  ALRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.7 bits (102), Expect = 2e-06
 Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 12/83 (14%)

Query: 514 IERDTVVVKNLPPTITWQELRDKFRNCG------------DIKFAEIKGKGDIGLVRFDS 561
           ++++ V V  L   +   E+  +    G               +A  +G      V +  
Sbjct: 6   VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 65

Query: 562 EWTAKRAIDMMDRTRIDGKIIDV 584
              A RAI  ++   +DG+ +  
Sbjct: 66  SEDALRAIQCVNNVVVDGRTLKA 88

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 46.1 bits (108), Expect = 4e-07
 Identities = 13/77 (16%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             +F+ NL+      +L+          ++ +   + G +R FG V+F+   +  +++  
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-E 72

Query: 220 LNNQNLFERRITVRMDR 236
           L    +F   I +   +
Sbjct: 73  LTGLKVFGNEIKLEKPK 89

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 8e-07
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
            VFV N+ Y+  E++L+++F   G V +   +   + GK +G+G  E+     A+ ++  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRLPEGLKSIGMG 257
           LN +    R + V             +  E LKS+G G
Sbjct: 70  LNGREFSGRALRVDNAA-------SEKNKEELKSLGTG 100

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 8e-07
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 513 NIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI------GLVRFDSEWT 564
            ++R   +V V N+P   T ++L+D F   G +    +    +       G   +  + T
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 565 AKRAIDMMDRTRIDGKIIDVTF 586
           A  A+  ++     G+ + V  
Sbjct: 63  ALSAMRNLNGREFSGRALRVDN 84

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 2e-04
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 71  PRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV--EDKGGRRNMGGG 120
           P+G    E+Q  +    A+  ++  E  GR L +  A   ++K   +++G G
Sbjct: 49  PKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (107), Expect = 1e-06
 Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 1/71 (1%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW-TAKRAIDMMDRTR 576
                +L      ++L   F N G+IK+ +       G++ F  +   A       +   
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 577 IDGKIIDVTFF 587
           +  +  +VT+ 
Sbjct: 73  LQLRNKEVTWE 83

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 9e-05
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVE-AVQSISML 220
            F  +LD +   + L  +F   G+++ ++       +    G + F    + A+      
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFV-----RGAKEGIILFKEKAKEALGKAKDA 68

Query: 221 NNQNLFERRITVRMDRV 237
           NN NL  R   V  + +
Sbjct: 69  NNGNLQLRNKEVTWEVL 85

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 46.1 bits (108), Expect = 1e-06
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 518 TVVVKNLPPTITWQELRD------KFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDM 571
            ++V  +P T+   +LR          +   +   E +     G V+F S  +A++AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 572 MDRTRIDGKIIDVTF 586
           ++   I  K + V  
Sbjct: 104 LNGFNILNKRLKVAL 118

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 41.4 bits (96), Expect = 5e-05
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 159 INKVFVANLDYKVDEKKLREVFRL-AGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
           +  + V  +   VDE +LR++F           +   +  +SRG+G V+F     A Q+I
Sbjct: 42  LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101

Query: 218 SMLNNQNLFERRITVRM 234
           + LN  N+  +R+ V +
Sbjct: 102 AGLNGFNILNKRLKVAL 118

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.1 bits (103), Expect = 1e-06
 Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKG----DIGLVRFDSEWTAKRAIDMMD 573
           TV+VKNLP +    ++   F++CG I   ++            + F     A  AI    
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 61

Query: 574 RTRIDGKIIDVT 585
           +  +    I V+
Sbjct: 62  KV-VGQNEIIVS 72

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.8 bits (97), Expect = 8e-06
 Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
            V V NL    ++ K+ + F+  G + +V++  D   K+  F  +EF     A+ +I+  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDV-ADSLKKNFRFARIEFARYDGALAAITK- 59

Query: 221 NNQNLFERRITVRM 234
            ++ + +  I V  
Sbjct: 60  THKVVGQNEIIVSH 73

>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 = 45.2 bits (106), Expect = 1e-06
 Identities = 14/99 (14%), Positives = 29/99 (29%), Gaps = 10/99 (10%)

Query: 160 NKVFVANLDYKV-----DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
           + +     +  V        K   +FR   K    +       KS     + F +P+ A 
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPLSAA 60

Query: 215 QSISMLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKS 253
            +   L+      + + +   +        +  P   KS
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKS 99

>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 = 44.0 bits (103), Expect = 2e-06
 Identities = 10/75 (13%), Positives = 22/75 (29%), Gaps = 5/75 (6%)

Query: 517 DTVVVKNLPPTI-----TWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDM 571
             ++       +     T  +    FR        +         + F +  +A  A   
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR 65

Query: 572 MDRTRIDGKIIDVTF 586
           + +T   GK + + F
Sbjct: 66  LHKTEFLGKEMKLYF 80

>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 = 44.9 bits (106), Expect = 1e-06
 Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 162 VFVANL----DYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
           V + N+    D++ D   L E    +     K   +   L  D    G  +V F  P EA
Sbjct: 11  VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEA 70

Query: 214 VQSISMLNNQNLFERRITVRMDR 236
              I  L+ +    R+IT +   
Sbjct: 71  DYCIQTLDGRWFGGRQITAQAWD 93

>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 = 41.8 bits (98), Expect = 1e-05
 Identities = 15/84 (17%), Positives = 26/84 (30%), Gaps = 15/84 (17%)

Query: 518 TVVVKNL--PPTI-----TWQELRDKFRNCG-------DIKFAEIKGKGDIGLVRFDSEW 563
            V++KN+  P           E+R+  R           +   +    G +  V F    
Sbjct: 10  VVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDG-VASVSFRDPE 68

Query: 564 TAKRAIDMMDRTRIDGKIIDVTFF 587
            A   I  +D     G+ I    +
Sbjct: 69  EADYCIQTLDGRWFGGRQITAQAW 92

>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 = 35.7 bits (82), Expect = 0.002
 Identities = 9/51 (17%), Positives = 17/51 (33%)

Query: 55  VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK 105
                 +  L      P G A V F+ P+     +  +      GR++  +
Sbjct: 40  CSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 90

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 4/78 (5%)

Query: 160 NKVFVANLDYKV-DEKKLREVF--RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
            ++ + NL  ++ DE  LRE F    + +  N+     +   +     + F++   A ++
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 217 ISMLNNQNLFERRITVRM 234
           + M N   L  R I+V +
Sbjct: 65  LQM-NRSLLGNREISVSL 81

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.7 bits (92), Expect = 6e-05
 Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 9/81 (11%)

Query: 514 IERDTVVVKNLPPTITWQE-LRDKFRNCGDIKFAEIKGKGD-------IGLVRFDSEWTA 565
           +E   ++++NL   +  +  LR+ F   G I+   I               + F+++ +A
Sbjct: 2   LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 61

Query: 566 KRAIDMMDRTRIDGKIIDVTF 586
           +RA+  M+R+ +  + I V+ 
Sbjct: 62  ERALQ-MNRSLLGNREISVSL 81

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (101), Expect = 2e-06
 Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRID 578
           ++++ LP  +T QE+ D   +  ++K+  +        V   +   A+ AI+   ++R+ 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLR 59

Query: 579 GKIIDVTF 586
            + + V  
Sbjct: 60  ERELSVQL 67

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 14/72 (19%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT 575
           T+ + N+PP+++ ++L+  F + G +   F   +    + L++  S   A +A+  +   
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 71

Query: 576 RI-DGKIIDVTF 586
            + +   + V+F
Sbjct: 72  DLGENHHLRVSF 83

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
           P    + ++N+   V E+ L+ +F   G V           K R    ++     EAVQ+
Sbjct: 8   PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF---KFFQKDRKMALIQMGSVEEAVQA 64

Query: 217 ISMLNNQNLFE-RRITV 232
           +  L+N +L E   + V
Sbjct: 65  LIDLHNHDLGENHHLRV 81

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 3e-06
 Identities = 16/77 (20%), Positives = 31/77 (40%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             ++++NL   +DE++L  + +  G+V +  I  D  G SRG G    +   +    I  
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 220 LNNQNLFERRITVRMDR 236
            N + +           
Sbjct: 79  FNGKFIKTPPGVSAPTE 95

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 5/83 (6%)

Query: 507 SMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGD-----IKFAEIKGKGDIGLVRFDS 561
            M +    +   + + NLP ++  QEL +  +  G      I          +G  R +S
Sbjct: 9   QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 68

Query: 562 EWTAKRAIDMMDRTRIDGKIIDV 584
               +  I   +   I       
Sbjct: 69  TEKCEAVIGHFNGKFIKTPPGVS 91

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 3e-06
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 2/85 (2%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
           S  S +         V V+ L  ++   +L +     G I +  +       LV F++  
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENID 62

Query: 564 TAKRAIDMMD--RTRIDGKIIDVTF 586
           +AK  +         I G+     +
Sbjct: 63  SAKECVTFAADVPVYIAGQQAFFNY 87

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.9 bits (82), Expect = 0.002
 Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 5/76 (6%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
             V V  L   V E  L E     G +  V +   K         VEF++   A + ++ 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFENIDSAKECVTF 70

Query: 220 LNNQNLFERRITVRMD 235
             +  ++        +
Sbjct: 71  AADVPVYIAGQQAFFN 86

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 3e-06
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
              F+ NL Y V E+ ++E FR              +  + +GFG  EF+   +++ S  
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDL-DSLLSAL 74

Query: 219 MLNNQNLFERRITVR 233
            LN ++L  +RI V 
Sbjct: 75  SLNEESLGNKRIRVD 89

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 9e-06
 Identities = 10/74 (13%), Positives = 25/74 (33%), Gaps = 5/74 (6%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAK-----RAIDMM 572
           T  + NLP  +T + +++ FR          +   +   ++       +      +   +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 573 DRTRIDGKIIDVTF 586
           +   +  K I V  
Sbjct: 77  NEESLGNKRIRVDV 90

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 19/91 (20%), Positives = 40/91 (43%), Gaps = 10/91 (10%)

Query: 506 RSMNQSSNIERD----TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDS 561
           R +   S+         + +KNL P +T ++L   F    + K   I+ +   G +R  +
Sbjct: 4   RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 63

Query: 562 EWTA------KRAIDMMDRTRIDGKIIDVTF 586
             T        +A+ +++  ++ GKI+ + F
Sbjct: 64  FITFPNKEIAWQALHLVNGYKLYGKILVIEF 94

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
             +++ NL  +V E+ L  +F    + +   I      G+ RG   + F +   A Q++ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 219 MLNNQNLFERRITVRM 234
           ++N   L+ + + +  
Sbjct: 79  LVNGYKLYGKILVIEF 94

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.3 bits (101), Expect = 5e-06
 Identities = 11/84 (13%), Positives = 29/84 (34%), Gaps = 12/84 (14%)

Query: 515 ERDTVVVKNLPPTITWQELRDKFR------NCGDIKFAEIKGKGDIGLVRFDSEWTAKRA 568
           E  TV ++NL      + L +  +          +   + +        +F ++  A++ 
Sbjct: 7   EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 66

Query: 569 IDMM------DRTRIDGKIIDVTF 586
           +            ++DG+ + V  
Sbjct: 67  LAAASLEAEGGGLKLDGRQLKVDL 90

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.0 bits (95), Expect = 3e-05
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK-SRGFGTVEFDHPVEAVQSIS 218
             VF+ NL +  +E+ L EV +  G ++ V + L  D + S+G    +F     A + ++
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 219 MLNNQN------LFERRITVRM 234
             + +       L  R++ V +
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDL 90

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 6e-06
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 518 TVVVKNLPP-TITWQELRDKFRNCGDIKFAEIKGKGD-IGLVRFDSEWTAKRAIDMMDRT 575
            ++V NL P  +T Q L   F   GD++  +I        LV+      A+ A+  ++  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 63

Query: 576 RIDGKIIDVTF 586
           ++ GK I +T 
Sbjct: 64  KLHGKPIRITL 74

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 5e-04
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 160 NKVFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
           + + V+NL+  +V  + L  +F + G V+ V+I        +    V+     +A  ++S
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI----LFNKKENALVQMADGNQAQLAMS 58

Query: 219 MLNNQNLFERRITVRMDR 236
            LN   L  + I + + +
Sbjct: 59  HLNGHKLHGKPIRITLSK 76

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (99), Expect = 6e-06
 Identities = 8/71 (11%), Positives = 24/71 (33%), Gaps = 2/71 (2%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMM--DRT 575
            + ++ LP  +T  E+       G +    +    +   +   +E  A   ++       
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTP 69

Query: 576 RIDGKIIDVTF 586
            +  + I + +
Sbjct: 70  HLRNQPIYIQY 80

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 9e-06
 Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 3/70 (4%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-GLVRFDSEWTAKRAIDMMDRTR 576
            V V      +T  ELR+ F   GD+    I         V F  +  A+      +   
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC--GEDLI 64

Query: 577 IDGKIIDVTF 586
           I G  + ++ 
Sbjct: 65  IKGISVHISN 74

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 4e-05
 Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 6/74 (8%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + VFV      + E +LRE F   G V +V          R F  V F     A      
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDV----FIPKPFRAFAFVTFADDQIAQSLCG- 60

Query: 220 LNNQNLFERRITVR 233
             +  +    + + 
Sbjct: 61  -EDLIIKGISVHIS 73

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 8/48 (16%), Positives = 12/48 (25%), Gaps = 2/48 (4%)

Query: 73  GSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
             A V F    + +    +      KG  + I  A            G
Sbjct: 43  AFAFVTFADDQIAQSLCGEDLII--KGISVHISNAEPKHNSNSGPSSG 88

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (98), Expect = 9e-06
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRID 578
           VVV  LPP+ +WQ+L+D  R  GD+ +A++   G    V F  +     A+  +D T+  
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGV-VEFVRKEDMTYAVRKLDNTKFR 61

Query: 579 GKIIDVTF 586
               +  +
Sbjct: 62  SHEGETAY 69

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (90), Expect = 9e-05
 Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 8/85 (9%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           N+V V+ L      + L++  R              D    G G VEF    +   ++  
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMR------EAGDVCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 220 LNNQNLFERRITVRMDRVADRLDGP 244
           L+N             RV  ++DGP
Sbjct: 55  LDNTKFRSHEGETAYIRV--KVDGP 77

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.2 bits (103), Expect = 1e-05
 Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENV-EIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           K+F+  L ++  ++ LR  F   G + +   +      +SRGFG V +    E   +++ 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 220 LNNQNLFERRITVRM 234
             ++         R 
Sbjct: 68  RPHKVDGRVVEPKRA 82

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (99), Expect = 3e-05
 Identities = 8/62 (12%), Positives = 18/62 (29%), Gaps = 6/62 (9%)

Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVR------FDSEWTAKRAIDM 571
            + +  L    T + LR  F   G +    +    +    R      + +      A++ 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 572 MD 573
             
Sbjct: 68  RP 69

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

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]

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 513 NIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMM 572
           +++   V V   P       +  +F   G+I    +   G+   +R+ S+  A++A+   
Sbjct: 1   HLDDTWVTVFGFPQASA-SYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-K 58

Query: 573 DRTRIDGKII 582
           D       I+
Sbjct: 59  DGRIFGESIM 68

>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 = 41.9 bits (98), Expect = 1e-05
 Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 164 VANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKS---RGFGTVEFDHPVEAVQSISML 220
           + + +Y+   + +R+     G V+++EI    DG      G   VEF    +  +++  L
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 221 NNQNLFERRITV 232
             +    R +  
Sbjct: 79  TGRKFANRVVVT 90

>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 = 38.4 bits (89), Expect = 3e-04
 Identities = 18/96 (18%), Positives = 33/96 (34%), Gaps = 5/96 (5%)

Query: 21  MFQRIETGAPLEVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQ 80
           M    E     E   +++ ++      + S    V  +     ++       G   VEF 
Sbjct: 12  MVLPEELLDDEEYEEIVEDVR-----DECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFT 66

Query: 81  SPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRN 116
           S    +KA+  +   +   R +V K    D   RR+
Sbjct: 67  SVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRD 102

>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 = 37.3 bits (86), Expect = 7e-04
 Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 8/84 (9%)

Query: 512 SNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD--------IGLVRFDSEW 563
            N+     ++ +       +++RD+    G +K  EI    D           V F S +
Sbjct: 10  MNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVF 69

Query: 564 TAKRAIDMMDRTRIDGKIIDVTFF 587
             ++A+  +   +   +++   + 
Sbjct: 70  DCQKAMQGLTGRKFANRVVVTKYC 93

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.9 bits (97), Expect = 2e-05
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 4/83 (4%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
           S+ S  +S       ++ KNLP      E+++ F   G +    +   G   +V F    
Sbjct: 2   SSGSSGRSKT----VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPL 57

Query: 564 TAKRAIDMMDRTRIDGKIIDVTF 586
            A++A   +  ++     + + +
Sbjct: 58  EARKAFRHLAYSKFHHVPLYLEW 80

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (97), Expect = 2e-05
 Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
              + N+ + + +  + +        EN    L  + G+  G   V+F +  +A +S  +
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 69

Query: 220 LNNQNLFERRITVRM 234
            + + L  R   V +
Sbjct: 70  -HRKKLNGREAFVHV 83

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 4e-04
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 513 NIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIG------LVRFDSEWTAK 566
           N  +    + N+P +IT  ++          + A      + G      LV+F +E  A+
Sbjct: 5   NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR 64

Query: 567 RAIDMMDRTRIDGKIIDV 584
           ++   + R +++G+   V
Sbjct: 65  KSER-LHRKKLNGREAFV 81

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.2 bits (93), Expect = 4e-05
 Identities = 16/79 (20%), Positives = 28/79 (35%), Gaps = 2/79 (2%)

Query: 510 QSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIK-FAEIKGKGDIGLVRFDSEWTAKRA 568
           Q+       + + NLP       L   F      K    +  + DI  V F +E  +  A
Sbjct: 2   QTEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAA 61

Query: 569 IDMMDRTRID-GKIIDVTF 586
            + +   +I     + +TF
Sbjct: 62  KEALQGFKITPTHAMKITF 80

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 7e-05
 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 2/81 (2%)

Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
           + V +  L Y+  E  +   F     +      +  DG+  G   VEF    E   +   
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLNPMRVHIE-IGPDGRVTGEADVEFATH-EDAVAAMA 73

Query: 220 LNNQNLFERRITVRMDRVADR 240
            +  N+  R + + ++  A  
Sbjct: 74  KDKANMQHRYVELFLNSTAGT 94

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 13/85 (15%), Positives = 30/85 (35%), Gaps = 5/85 (5%)

Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKG----DIGLVRF 559
           S  S +   +     V ++ LP   T  ++ + F     ++     G          V F
Sbjct: 3   SGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEF 62

Query: 560 DSEWTAKRAIDMMDRTRIDGKIIDV 584
            +   A  A+   D+  +  + +++
Sbjct: 63  ATHEDAVAAMA-KDKANMQHRYVEL 86

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	587
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.91
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.79
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.79
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.79
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.78
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.78
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.78
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.78
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.78
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.77
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.76
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.76
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.76
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.75
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.75
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.75
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.74
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.74
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.74
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.73
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.73
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.72
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.72
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.72
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.72
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.72
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.72
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.71
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.71
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.71
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.7
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.7
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.69
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.69
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.69
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.69
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.69
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.68
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.68
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.68
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.68
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.67
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.67
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.67
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.67
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.67
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.67
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.67
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.66
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.66
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.66
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.65
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.65
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.65
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.64
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.64
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.63
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.63
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.63
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.62
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.62
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.62
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.62
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.62
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.62
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.62
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.61
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.61
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.61
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.61
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.56
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.56
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	99.55
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.53
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.51
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.5
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.49
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	99.48
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.42
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.41
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.4
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.39
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.38
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.35
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.31
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.31
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.29
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.26
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.65
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.47
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.35
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.32
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.16
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.7
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.64
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.46

>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=99.97  E-value=1e-29  Score=235.87  Aligned_cols=168  Identities=24%  Similarity=0.349  Sum_probs=147.6

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      .++|||+|||+++|+++| ++|++||+|++|+++++. ++.++|||||+|.+.++|++|++. ++..+..+.+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            378999999999999999 899999999999999997 999999999999999999999975 67888999998887763


Q ss_pred             ccCCCCCCCCCCCCCCchhhhhccCCcccCCCCCCChhhhhccCCCCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE
Q psy1534         110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENV  189 (587)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v  189 (587)
                      ......                                     .......++|||+|||+.+++++|+++|+.||.|..+
T Consensus        85 ~~~~~~-------------------------------------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~  127 (183)
T d1u1qa_          85 REDSQR-------------------------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI  127 (183)
T ss_dssp             TTGGGS-------------------------------------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEE
T ss_pred             cccccc-------------------------------------cccccccceeEEccCCCcCCHHHHhhhhccCCceeee
Confidence            321000                                     0123345799999999999999999999999999999


Q ss_pred             EEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         190 EIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       190 ~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .|+.+.. ++++|||||+|.+.++|.+||+ ++++.+.|++|+|++|.++
T Consensus       128 ~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             EEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             eeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            9999886 8999999999999999999996 6889999999999998654

>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=99.91  E-value=2e-23  Score=192.96  Aligned_cols=76  Identities=21%  Similarity=0.421  Sum_probs=67.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .++|||+|||+++|+++|+++|++||.|.++.++++.. +.++|||||+|.+.++|.+|+.. ++..+..+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~   82 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   82 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhh
Confidence            36999999999999999999999999999999999875 99999999999999999999965 566777777766553

>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=99.80  E-value=1e-19  Score=149.40  Aligned_cols=83  Identities=22%  Similarity=0.221  Sum_probs=77.8

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .....+|||+|||+++++++| ++|++||+|.+|+|++|+ +++++|||||+|.+.++|++||+.||+..|.|++|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345678999999999999999 899999999999999997 999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +..++
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98654

>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=99.80  E-value=7e-20  Score=144.06  Aligned_cols=75  Identities=21%  Similarity=0.283  Sum_probs=72.7

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .|||+|||+++|+++| ++|++||+|.+|+|++|+ +|+++|||||+|.++++|++|++.|||..+.||+|+|.++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            5999999999999999 899999999999999997 89999999999999999999999999999999999999986

>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=99.80  E-value=1.2e-19  Score=145.52  Aligned_cols=80  Identities=18%  Similarity=0.255  Sum_probs=75.2

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ....|||+|||.++++++| ++|++||+|++|+|++|+ +|++||||||+|.+.++|++|++.|||..|.|++|+|.|+.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            4568999999999999999 899999999999999996 89999999999999999999999999999999999999987


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            43

>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=99.79  E-value=2.1e-19  Score=145.51  Aligned_cols=81  Identities=15%  Similarity=0.073  Sum_probs=76.4

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....+|||+|||+++|+++| ++|++||+|++|+|++++ ++++||||||+|.+.++|++|++.||+..|.|++|+|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45679999999999999999 899999999999999997 8999999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            733

>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=99.79  E-value=7.5e-20  Score=147.05  Aligned_cols=81  Identities=23%  Similarity=0.262  Sum_probs=76.8

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++|||+|||+++++++| ++|++||+|.+|+|++|+ +|++||||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45689999999999999999 899999999999999997 8999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      .++
T Consensus        83 ~p~   85 (89)
T d2cqba1          83 KPM   85 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.79  E-value=7.6e-20  Score=143.04  Aligned_cols=75  Identities=19%  Similarity=0.256  Sum_probs=72.9

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +|||+|||+++++++| ++|++||+|.+|+|+++++++++|||||+|.+.++|++|++.||+..+.|++|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            6999999999999999 89999999999999999999999999999999999999999999999999999999875

>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=99.79  E-value=7.7e-20  Score=144.78  Aligned_cols=77  Identities=18%  Similarity=0.352  Sum_probs=73.8

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..+|||+|||.++++++| ++|++||+|++|+|++|+ +|+++|||||+|.++++|++|++.||+..+.|++|+|.++.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357999999999999999 899999999999999986 89999999999999999999999999999999999999986

>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=99.79  E-value=1.6e-19  Score=148.96  Aligned_cols=84  Identities=13%  Similarity=0.238  Sum_probs=78.2

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..|+..+|||+|||+++++++| ++|++||+|.+|+++.++ +|++||||||+|.+.++|++||+.||+..|.|++|+|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456678999999999999999 899999999999999996 89999999999999999999999999999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++.++.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            998553

>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=99.79  E-value=2.3e-19  Score=142.00  Aligned_cols=77  Identities=16%  Similarity=0.393  Sum_probs=73.6

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..+|||+|||+++++++| ++|++||+|.+|+|++|. +++++|||||+|.++++|++|++.||+..|.|++|+|.++.
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            357999999999999999 899999999999999996 89999999999999999999999999999999999999986

>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=99.79  E-value=2.9e-19  Score=143.90  Aligned_cols=80  Identities=15%  Similarity=0.250  Sum_probs=75.8

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...+|||+|||.++++++| ++|++||+|.+|+|++|+ +|.+||||||+|.+.++|++|++.||+..|.|++|+|.++.
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            4568999999999999999 899999999999999997 89999999999999999999999999999999999999997


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      ++
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.78  E-value=2.6e-19  Score=141.64  Aligned_cols=79  Identities=24%  Similarity=0.439  Sum_probs=75.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|.+|+|++++. |+++|||||+|.+.++|++||+.||+..+.|++|+|+++++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999875 99999999999999999999999999999999999999875

>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=99.78  E-value=1.4e-19  Score=146.66  Aligned_cols=81  Identities=20%  Similarity=0.261  Sum_probs=76.5

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....+|||+|||.++|+++| ++|++||+|.+|+|++|+ +|++||||||+|.+.++|++|++.||+..|.|++|+|+++
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34578999999999999999 899999999999999997 9999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      ..+
T Consensus        87 ~~~   89 (93)
T d1x5ua1          87 SAH   89 (93)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            854

>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=99.78  E-value=2.5e-19  Score=142.11  Aligned_cols=78  Identities=22%  Similarity=0.281  Sum_probs=73.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +..++|||+|||+++++++| ++|++||+|.+|+|++|+ +|++||||||+|.++++|++|++ +++..|.||.|+|+.|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            45578999999999999999 899999999999999997 89999999999999999999996 5999999999999987


Q ss_pred             c
Q psy1534         108 V  108 (587)
Q Consensus       108 ~  108 (587)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.78  E-value=2.9e-19  Score=141.63  Aligned_cols=75  Identities=20%  Similarity=0.267  Sum_probs=71.4

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ++.++|||+|||+++|+++| ++|++||+|.+|+|++|+ +++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34578999999999999999 899999999999999997 8999999999999999999999999999999999987

>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=99.78  E-value=1.1e-19  Score=144.69  Aligned_cols=78  Identities=17%  Similarity=0.309  Sum_probs=74.5

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      .+|||+|||.++|+++| ++|++||+|++|+|++|+ +|++||||||+|.++++|++|++.||+..|.|++|.|.++...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999 899999999999999997 8999999999999999999999999999999999999999843

>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=99.78  E-value=5.9e-19  Score=141.60  Aligned_cols=82  Identities=20%  Similarity=0.227  Sum_probs=74.8

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ......+|||+|||+++|+++| ++|++||+|.+|+|++|+ +|++||||||+|.++++|++||+.  ...|.|+.|.|+
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~   81 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEE
Confidence            3456789999999999999999 899999999999999997 899999999999999999999985  558999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..++
T Consensus        82 ~a~~k~   87 (90)
T d2cqga1          82 LPNSKQ   87 (90)
T ss_dssp             CCCTTC
T ss_pred             eCCCCC
Confidence            998553

>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=99.78  E-value=3.2e-19  Score=142.02  Aligned_cols=77  Identities=21%  Similarity=0.397  Sum_probs=72.9

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEe
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKE  106 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~  106 (587)
                      ...+|||+|||+++++++| ++|++||+|.+|+|++|+ +|++||||||+|.+.++|++|++.||+..+.|  ++|+|++
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            5578999999999999999 899999999999999997 89999999999999999999999999999976  8999998


Q ss_pred             c
Q psy1534         107 A  107 (587)
Q Consensus       107 a  107 (587)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.78  E-value=8.1e-19  Score=138.81  Aligned_cols=78  Identities=28%  Similarity=0.487  Sum_probs=74.9

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ++|||+|||+++++++|+++|++||.|.+|+|+++.. ++++|||||+|.+.++|++|++.||+..+.|++|+|++|+|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999875 89999999999999999999999999999999999999875

>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=99.78  E-value=1e-18  Score=141.38  Aligned_cols=82  Identities=24%  Similarity=0.389  Sum_probs=77.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+++|||+|||+++++++|+++|++||.|.+|.|++++. +.++|||||+|.+.++|.+|++.||+..+.|++|+|+|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999999985 9999999999999999999999999999999999999986


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ...
T Consensus        86 ~~~   88 (93)
T d1h2vz_          86 GFK   88 (93)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.78  E-value=3.4e-19  Score=143.18  Aligned_cols=81  Identities=32%  Similarity=0.541  Sum_probs=77.2

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|.+|.|++|+. ++++|||||+|.+.++|++|++.||+..+.|++|+|+++++
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            57999999999999999999999999999999999986 99999999999999999999999999999999999999976


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        85 ~~   86 (89)
T d2cqba1          85 MR   86 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.77  E-value=7.1e-19  Score=145.01  Aligned_cols=85  Identities=26%  Similarity=0.448  Sum_probs=79.6

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      .+++++|||+|||+++++++|+++|+.||.|.++.++.++. |+++|||||+|.+.++|++||+.||+..|.|++|+|++
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999875 99999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      ++++..
T Consensus        95 a~~k~~  100 (102)
T d2cpza1          95 KRSKND  100 (102)
T ss_dssp             CCCSCC
T ss_pred             eCCCCC
Confidence            988763

>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=99.77  E-value=6.8e-19  Score=137.55  Aligned_cols=76  Identities=25%  Similarity=0.514  Sum_probs=74.1

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      +|||+|||+++++++|+++|++||.|.+|+|.++++++++|||||+|.+.++|++|++.||+..+.|++|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.77  E-value=9.1e-19  Score=140.22  Aligned_cols=81  Identities=25%  Similarity=0.404  Sum_probs=76.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .+++|||+|||+++++++|+++|++||.|.+|+|++|+. |+++|||||+|.+.++|++|++.|||..+.|++|+|+|+.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            357999999999999999999999999999999999875 9999999999999999999999999999999999999987


Q ss_pred             CC
Q psy1534         237 VA  238 (587)
Q Consensus       237 ~~  238 (587)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>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=99.77  E-value=4.1e-19  Score=141.28  Aligned_cols=77  Identities=18%  Similarity=0.290  Sum_probs=72.1

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCC--eEEEEEe
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG--RKLVIKE  106 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~g--r~i~V~~  106 (587)
                      ...+|||+|||.++|+++| ++|++||+|.+|+|++|+ +|++||||||+|.++++|++|++.||+..+.|  ++|+|.+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            4568999999999999999 899999999999999997 89999999999999999999999999999987  6699988


Q ss_pred             c
Q psy1534         107 A  107 (587)
Q Consensus       107 a  107 (587)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.77  E-value=4.4e-19  Score=143.95  Aligned_cols=82  Identities=27%  Similarity=0.350  Sum_probs=76.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC--CCCcceEEEEEECCHHHHHHHHHHh-CCceeCCeEEEEE
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD--TGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIK  105 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Al~~l-~g~~l~gr~i~V~  105 (587)
                      ....+|||+|||+++++++| ++|++||+|.+|+|+++.  +|++||||||+|.+.++|.+|++.| |+..|.|++|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            35678999999999999999 899999999999999884  7999999999999999999999998 8999999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..+.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998553

>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=99.77  E-value=2.4e-19  Score=144.57  Aligned_cols=82  Identities=21%  Similarity=0.295  Sum_probs=77.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ...++|||+|||+++++++| ++|++||+|..|.++++. ++.++|||||+|.++++|++|++.||+..|.|++|+|+++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            46788999999999999999 899999999999999986 8999999999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      .++.
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8553

>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=99.77  E-value=2.2e-19  Score=139.22  Aligned_cols=73  Identities=22%  Similarity=0.335  Sum_probs=69.2

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +|||+|||+++++++| ++|++||+|.+|+|++|+ ++++||||||+|.++++|++|++ +++..|.|++|.|++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            6999999999999999 899999999999999997 89999999999999999999996 6999999999999764

>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=99.76  E-value=1.1e-18  Score=140.47  Aligned_cols=82  Identities=24%  Similarity=0.365  Sum_probs=77.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+|||.++++++|+++|++||.|.+|+|++++. +.++|||||+|.+.++|++||+.||+..+.|++|+|++++
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            457999999999999999999999999999999999985 9999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ++.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.76  E-value=1.4e-19  Score=140.84  Aligned_cols=73  Identities=19%  Similarity=0.251  Sum_probs=70.1

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +|||+|||+++|+++| ++|++||+|++|+|++|+ +|++||||||+|.++++|++|++ ++++.|.||+|.|+.|
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            7999999999999999 899999999999999997 89999999999999999999996 6999999999999986

>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=99.76  E-value=8e-19  Score=142.07  Aligned_cols=82  Identities=32%  Similarity=0.454  Sum_probs=77.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++. +.++|||||+|.+.++|++|++.||+..|.|++|+|++|.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            357999999999999999999999999999999999875 9999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            765

>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=99.76  E-value=7.2e-19  Score=145.23  Aligned_cols=81  Identities=17%  Similarity=0.213  Sum_probs=74.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .+..++|||+|||+++++++| ++|++||+|.+|+|++|+ +|++||||||+|.+.++|++|++.+++ .|.||+|+|++
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            345578999999999999999 899999999999999997 899999999999999999999998876 79999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +..+
T Consensus        86 a~~~   89 (103)
T d2cqda1          86 AYLG   89 (103)
T ss_dssp             STTT
T ss_pred             cCCC
Confidence            8744

>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=99.76  E-value=1.6e-18  Score=142.23  Aligned_cols=83  Identities=25%  Similarity=0.417  Sum_probs=78.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|++||+.||+..|.|++|+|+++.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            357899999999999999999999999999999999875 9999999999999999999999999999999999999988


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      .+..
T Consensus        87 ~~~~   90 (99)
T d1whwa_          87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCCc
Confidence            7653

>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=99.76  E-value=1.2e-18  Score=136.82  Aligned_cols=76  Identities=22%  Similarity=0.406  Sum_probs=73.7

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .|||+|||+++|+++|+++|++||+|.+|+|++|+. ++++|||||+|.++++|.+|++.|||..+.|++|+|.|++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            699999999999999999999999999999999986 9999999999999999999999999999999999999985

>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=99.76  E-value=2.3e-18  Score=139.43  Aligned_cols=81  Identities=20%  Similarity=0.281  Sum_probs=75.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....++|||+|||+++++++| ++|++||+|.+|+|++++.+ ++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            346778999999999999999 89999999999999998744 6899999999999999999999999999999999999


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      .++
T Consensus        87 ~~r   89 (93)
T d2cq3a1          87 TAR   89 (93)
T ss_dssp             CSS
T ss_pred             CcC
Confidence            854

>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=99.75  E-value=2.4e-18  Score=136.22  Aligned_cols=76  Identities=33%  Similarity=0.393  Sum_probs=72.4

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      .+.++|||+|||+++|+++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|++|++.||+..|.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4467999999999999999999999999999999999986 999999999999999999999999999999999987

>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=99.75  E-value=1.8e-18  Score=151.42  Aligned_cols=80  Identities=21%  Similarity=0.340  Sum_probs=75.5

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|++||+|++|+|++|+ +|++||||||+|.+.++|++||+.||+..|.||+|+|.++.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4467999999999999999 899999999999999997 89999999999999999999999999999999999999997


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus       121 ~~  122 (139)
T d1u6fa1         121 SG  122 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.75  E-value=7.8e-19  Score=144.14  Aligned_cols=78  Identities=21%  Similarity=0.298  Sum_probs=73.2

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      .++|||+|||+++++++| ++|+.||+|.+|+|++|+ +|++||||||+|.+.++|++|++ ||+..|.|++|.|+++..
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            357999999999999999 899999999999999996 89999999999999999999995 999999999999999874


Q ss_pred             c
Q psy1534         110 D  110 (587)
Q Consensus       110 ~  110 (587)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.75  E-value=4.6e-18  Score=136.29  Aligned_cols=82  Identities=26%  Similarity=0.385  Sum_probs=75.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++|+. |+++|||||+|.+.++|++||+.  .+.|.|+.|.|+++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            3467899999999999999999999999999999999986 99999999999999999999974  45899999999998


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87653

>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=99.75  E-value=2.1e-18  Score=139.81  Aligned_cols=83  Identities=24%  Similarity=0.518  Sum_probs=77.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC--CCCcceEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSISML-NNQNLFERRITVRM  234 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~  234 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|+|+++.  +|+++|||||+|.+.++|.+||+.| |+..+.|++|.|+|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            45789999999999999999999999999999999875  3899999999999999999999998 89999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      |..+..
T Consensus        87 A~~~~~   92 (94)
T d2cpha1          87 ADSEVT   92 (94)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987653

>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=99.75  E-value=6.7e-19  Score=139.58  Aligned_cols=76  Identities=20%  Similarity=0.309  Sum_probs=71.4

Q ss_pred             EEEcCCCCCCCHHHH-HhcccCCCeEEE-EEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          35 VVMDLIQGDASLYQI-SHLSTVGDVTYV-EILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        35 vfV~nlp~~~t~~~l-~~F~~~G~V~~v-~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      |||+|||+++++++| ++|++||+|.++ +|++|+ +|+++|||||+|.+.++|++|++.|++..|.|++|+|.++.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            899999999999999 899999999775 788886 8999999999999999999999999999999999999999854

>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=99.75  E-value=2.6e-18  Score=138.20  Aligned_cols=81  Identities=15%  Similarity=0.173  Sum_probs=74.0

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++|||+|||.++++++| ++|++||+|.+|+|++|+.. .+|||||+|.+.++|++|++.||+..|.|++|+|.++.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45679999999999999999 89999999999999998633 37999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      ++.
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.75  E-value=6.2e-19  Score=146.15  Aligned_cols=80  Identities=28%  Similarity=0.387  Sum_probs=75.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|++||+|.+|+|++++ +|++||||||+|.+.++|++|++.||+..|.|++|+|.++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3468999999999999999 899999999999999997 89999999999999999999999999999999999999987


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.75  E-value=1.8e-18  Score=136.32  Aligned_cols=78  Identities=12%  Similarity=0.167  Sum_probs=69.1

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+.. ++++|||||+|.+.++|++|++.||+..+.|++|.|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999998888777664 99999999999999999999999999999999999999876

>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=99.75  E-value=1.2e-18  Score=138.41  Aligned_cols=80  Identities=21%  Similarity=0.387  Sum_probs=76.4

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .+|||+|||+++|+++|+++|++||+|.+|+|++|+. |+++|||||+|.++++|.+|++.||+..|.|++|.|+++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            3799999999999999999999999999999999986 999999999999999999999999999999999999999766


Q ss_pred             C
Q psy1534         239 D  239 (587)
Q Consensus       239 ~  239 (587)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.6e-18  Score=136.52  Aligned_cols=77  Identities=31%  Similarity=0.492  Sum_probs=72.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEEc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRMD  235 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~a  235 (587)
                      .++|||+|||+++++++|+++|++||.|.+|+|++|+. ++++|||||+|.+.++|++|++.|||..+.|  ++|+|+||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            56899999999999999999999999999999999985 9999999999999999999999999999987  56888875

>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=99.75  E-value=1.3e-18  Score=138.53  Aligned_cols=76  Identities=17%  Similarity=0.316  Sum_probs=70.6

Q ss_pred             EEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CC---CcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          35 VVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TG---KPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        35 vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g---~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      |||+|||+++|+++| ++|++||+|.+|+|++++ ++   ++||||||+|.+.++|++|++.||+..|.|++|.|+++.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            799999999999999 899999999999999985 33   5799999999999999999999999999999999999864


Q ss_pred             c
Q psy1534         110 D  110 (587)
Q Consensus       110 ~  110 (587)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.74  E-value=4.6e-18  Score=140.33  Aligned_cols=82  Identities=27%  Similarity=0.453  Sum_probs=75.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++. |+++|||||+|.+.++|++||+.+|+ .|.|++|.|+++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            346899999999999999999999999999999999986 99999999999999999999998875 7999999999998


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      .+.+
T Consensus        88 ~~~~   91 (103)
T d2cqda1          88 LGAK   91 (103)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7653

>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=99.74  E-value=3e-18  Score=136.32  Aligned_cols=78  Identities=28%  Similarity=0.416  Sum_probs=73.5

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRM  234 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~  234 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|.+||+.||+..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            356899999999999999999999999999999999875 9999999999999999999999999999976  8899998


Q ss_pred             c
Q psy1534         235 D  235 (587)
Q Consensus       235 a  235 (587)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.74  E-value=3.7e-18  Score=133.88  Aligned_cols=75  Identities=25%  Similarity=0.386  Sum_probs=71.2

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .++|||+|||+++|+++| ++|++||+|..++++.++ ++.++|||||+|.++++|++|++ +++..|.||+|+|++|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            478999999999999999 899999999999999997 89999999999999999999995 7999999999999976

>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=99.74  E-value=1.2e-18  Score=137.38  Aligned_cols=77  Identities=21%  Similarity=0.185  Sum_probs=67.7

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +.+|||+|||+++|+++| ++|++||+|..++++.+. +|+++|||||+|.+.++|++|++.||+..|.|++|+|+++.
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            358999999999999999 899999999999888775 89999999999999999999999999999999999999986

>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=99.74  E-value=1.2e-17  Score=134.28  Aligned_cols=81  Identities=16%  Similarity=0.328  Sum_probs=74.8

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|++++.. .+|||||+|.+.++|.+|++.||+..+.|++|+|.|+++
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            4579999999999999999999999999999999998753 378999999999999999999999999999999999976


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        86 ~~   87 (90)
T d2cqia1          86 PS   87 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.74  E-value=4.5e-19  Score=136.97  Aligned_cols=73  Identities=25%  Similarity=0.327  Sum_probs=68.7

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +|||+|||+++|+++| ++|++||+|.+|+|++|+ ++++||||||+|.+.++|++||+. ++..|.|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            6999999999999999 899999999999999997 899999999999999999999965 778899999999865

>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=99.74  E-value=9e-18  Score=146.88  Aligned_cols=84  Identities=31%  Similarity=0.553  Sum_probs=78.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ...++|||+|||+++++++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|.+||+.||+..|.|++|+|+++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3457899999999999999999999999999999999985 899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy1534         236 RVADR  240 (587)
Q Consensus       236 ~~~~~  240 (587)
                      +.+..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.74  E-value=1e-17  Score=135.43  Aligned_cols=81  Identities=27%  Similarity=0.488  Sum_probs=75.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||+++++++|+++|++||.|.+|++++++.+ ++|||||+|.+.++|.+||+.||+..|.|++|+|++|++
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            4578999999999999999999999999999999988754 689999999999999999999999999999999999987


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        89 r~   90 (93)
T d2cq3a1          89 RV   90 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.73  E-value=8.5e-18  Score=133.09  Aligned_cols=77  Identities=21%  Similarity=0.405  Sum_probs=72.8

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .++|||+|||+++++++|+++|++||.|.+|.|++|+. |+++|||||+|.+.++|++||+ ++++.|.|+.|+|+.|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            46999999999999999999999999999999999986 9999999999999999999996 59999999999998874

>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=99.73  E-value=4.3e-18  Score=135.47  Aligned_cols=78  Identities=28%  Similarity=0.535  Sum_probs=72.4

Q ss_pred             EEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC----CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       162 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      |||+|||+++++++|+++|++||.|.+|.|++++.    +.++|||||+|.+.++|.+|++.||+..+.|++|.|+++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            79999999999999999999999999999998864    25789999999999999999999999999999999999865


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.73  E-value=1e-18  Score=135.82  Aligned_cols=75  Identities=25%  Similarity=0.423  Sum_probs=71.8

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      |+|||+|||+++++++|+++|++||.|.+++|++|+. ++++|||||+|.+.++|++||+ +|++.+.|++|.|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            6899999999999999999999999999999999986 9999999999999999999996 6999999999999987

>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=99.73  E-value=3e-18  Score=141.01  Aligned_cols=79  Identities=19%  Similarity=0.202  Sum_probs=73.8

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..++|||+|||+++++++| ++|++||+|.+|.|++|+ ++.+||||||+|.+.++|++|++ +++..|.|++|.|+++.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            3478999999999999999 899999999999999997 88999999999999999999995 69999999999999988


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      ++
T Consensus        98 ~k   99 (103)
T d1x4ba1          98 AR   99 (103)
T ss_dssp             SC
T ss_pred             cc
Confidence            54

>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=99.73  E-value=1.8e-18  Score=138.84  Aligned_cols=78  Identities=15%  Similarity=0.336  Sum_probs=72.6

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      ..+|||+|||+++++++| ++|++||+|.+|+|+.++.+ ++|||||+|.+.++|++|++.|||..|.|++|.|.++.++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~-~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB-CCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            457999999999999999 89999999999999998643 7899999999999999999999999999999999999854

>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=99.73  E-value=6.3e-18  Score=134.17  Aligned_cols=76  Identities=24%  Similarity=0.208  Sum_probs=71.9

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      .++|||+|||.++|+++| ++|++||+|.+|+|++++++++||||||+|.++++|++||+ +++..+.|++|.|++..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            478999999999999999 89999999999999999999999999999999999999995 69999999999999864

>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=99.73  E-value=5.3e-18  Score=136.50  Aligned_cols=81  Identities=28%  Similarity=0.520  Sum_probs=76.5

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..+|||+|||+++++++|+++|++||.|..|.++++.. +.++|||||+|.++++|++||+.||+..|.|++|+|+++.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999988775 99999999999999999999999999999999999999876


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        85 ~~   86 (90)
T d1x5sa1          85 SS   86 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.73  E-value=2.4e-18  Score=137.07  Aligned_cols=79  Identities=13%  Similarity=0.172  Sum_probs=69.6

Q ss_pred             CCCcEEEcCCCCCCC-HHHH-HhcccCCCeEEEEEeeC-C-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          31 LEVPVVMDLIQGDAS-LYQI-SHLSTVGDVTYVEILND-D-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t-~~~l-~~F~~~G~V~~v~i~~d-~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ..++|||+|||++++ +++| ++|++||+|++|+|+++ . +++++|||||+|.+.++|++|++ ||+..|.|++|+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            467999999999986 5568 89999999999999876 3 89999999999999999999995 999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9754

>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=99.72  E-value=5.3e-18  Score=134.26  Aligned_cols=78  Identities=33%  Similarity=0.494  Sum_probs=72.8

Q ss_pred             EEEecCCCCCcHHHHHHHHHhcCCeeEE-EEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q psy1534         162 VFVANLDYKVDEKKLREVFRLAGKVENV-EIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVAD  239 (587)
Q Consensus       162 l~V~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~~  239 (587)
                      |||+|||+++++++|+++|++||.|.++ .|++++. ++++|||||+|.+.++|++||+.||+..+.|++|+|+++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998664 7888875 8999999999999999999999999999999999999988765

>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=99.72  E-value=6.2e-18  Score=135.66  Aligned_cols=80  Identities=26%  Similarity=0.486  Sum_probs=74.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      ..+|||+|||+++++++|+++|++||.|.+|+|+.++. .++|||||+|.+.++|++||+.|||..|.|++|.|++++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            35899999999999999999999999999999998864 46899999999999999999999999999999999999866


Q ss_pred             C
Q psy1534         239 D  239 (587)
Q Consensus       239 ~  239 (587)
                      .
T Consensus        87 ~   87 (89)
T d1cvja2          87 K   87 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=2.3e-18  Score=133.68  Aligned_cols=73  Identities=22%  Similarity=0.368  Sum_probs=69.8

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +|||+|||+++|+++| ++|++||.|..+.+++++ ++.++|||||+|.+.++|++|++ +|++.|.||+|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            6999999999999999 899999999999999987 89999999999999999999996 8999999999999875

>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=99.72  E-value=3.5e-18  Score=140.53  Aligned_cols=79  Identities=15%  Similarity=0.174  Sum_probs=74.0

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ..+++|||+|||+++++++| ++|++||+|..++++.+.++.++|||||+|.+.++|++|++.|||..|.||++.|.++.
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            35678999999999999999 89999999999999999999999999999999999999999999999999998887665

>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=99.72  E-value=1e-17  Score=137.30  Aligned_cols=83  Identities=20%  Similarity=0.330  Sum_probs=76.0

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhC------CceeCC
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMH------RFETKG   99 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~------g~~l~g   99 (587)
                      .....++|||+|||+++|+++| ++|++||+|.++.++.++ +++++|||||+|.+.++|++|++.|+      +..+.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            3456789999999999999999 899999999999999987 88999999999999999999999886      678999


Q ss_pred             eEEEEEecccc
Q psy1534         100 RKLVIKEAVED  110 (587)
Q Consensus       100 r~i~V~~a~~~  110 (587)
                      |+|+|.++.++
T Consensus        84 r~l~v~~a~~k   94 (98)
T d1x4ha1          84 RQLKVDLAVTR   94 (98)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEEECCCC
Confidence            99999999854

>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=99.72  E-value=1e-17  Score=141.20  Aligned_cols=79  Identities=14%  Similarity=0.189  Sum_probs=72.5

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +..++|||+|||+++++++| ++|++||+|++|++..+  +.+||||||+|.+.++|.+|++.|||..|.|++|.|.++.
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45678999999999999999 89999999999999764  5678999999999999999999999999999999999987


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            43

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=7.3e-18  Score=139.58  Aligned_cols=81  Identities=26%  Similarity=0.556  Sum_probs=76.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|.+|+|++++. |+++|||||+|.+.++|++|++.||+..|.|++|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            35899999999999999999999999999999999885 99999999999999999999999999999999999999876


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.71  E-value=6.2e-19  Score=141.94  Aligned_cols=80  Identities=14%  Similarity=0.253  Sum_probs=74.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +....+|||+|||+++++++| ++|++||.|.+|+|+.+.+|++||||||+|.+.++|++||+ ||+..|.|++|+|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            445668999999999999999 89999999999999877799999999999999999999995 8999999999999998


Q ss_pred             cc
Q psy1534         108 VE  109 (587)
Q Consensus       108 ~~  109 (587)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.71  E-value=7.6e-18  Score=130.33  Aligned_cols=74  Identities=27%  Similarity=0.481  Sum_probs=69.5

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +|||+|||++++|++|+++|++||.|.+|.|++++. ++++|||||+|.+.++|++||+ +++..|.|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            489999999999999999999999999999999986 9999999999999999999996 6999999999998653

>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=99.71  E-value=1.7e-17  Score=136.42  Aligned_cols=80  Identities=23%  Similarity=0.419  Sum_probs=74.9

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|..+.|++|+. +.++|||||+|.+.++|++||+ ++++.|.|+.|.|+++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            36899999999999999999999999999999999985 8899999999999999999995 799999999999999887


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>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=99.70  E-value=1.4e-17  Score=132.59  Aligned_cols=79  Identities=22%  Similarity=0.306  Sum_probs=70.4

Q ss_pred             CcEEEEecCCCCCc-HHHHHHHHHhcCCeeEEEEeeCC--CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         159 INKVFVANLDYKVD-EKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       159 ~~~l~V~nLp~~~t-e~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .++|||+|||++++ +++|+++|++||.|.+|+|+++.  +++++|||||+|.+.++|++||+ ||+..+.|++|+|+++
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            57999999999976 56699999999999999988754  48999999999999999999995 9999999999999998


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.70  E-value=3.8e-17  Score=128.00  Aligned_cols=76  Identities=30%  Similarity=0.521  Sum_probs=71.4

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++. ++++|||||+|.++++|++|+ .+|++.|.||+|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            36999999999999999999999999999999999885 899999999999999999998 57999999999999876

>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=99.70  E-value=1.1e-17  Score=137.24  Aligned_cols=79  Identities=28%  Similarity=0.445  Sum_probs=74.3

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|+.||.|.+|+|++++. |+++|||||+|.+.++|.+|+. ||+..|.|++|.|+++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            36899999999999999999999999999999999985 9999999999999999999995 999999999999999865


Q ss_pred             C
Q psy1534         238 A  238 (587)
Q Consensus       238 ~  238 (587)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.70  E-value=1.5e-17  Score=132.61  Aligned_cols=80  Identities=21%  Similarity=0.246  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEE-EEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTY-VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~  105 (587)
                      ..|....|||+|||++++++|| ++|+.||.|.. +.+..+++++++|||||+|.+.++|++|++.||+..|.||+|+|.
T Consensus         5 g~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~   84 (86)
T d2cqpa1           5 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   84 (86)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456667999999999999999 89999999976 567777799999999999999999999999999999999999998


Q ss_pred             ec
Q psy1534         106 EA  107 (587)
Q Consensus       106 ~a  107 (587)
                      .+
T Consensus        85 l~   86 (86)
T d2cqpa1          85 LG   86 (86)
T ss_dssp             ES
T ss_pred             EC
Confidence            64

>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=99.70  E-value=6.3e-18  Score=130.43  Aligned_cols=74  Identities=27%  Similarity=0.460  Sum_probs=69.5

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +|||+|||+++|+++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|++||+. +++.+.|+.|.|++|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            599999999999999999999999999999999985 99999999999999999999964 778999999999875

>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=99.70  E-value=1.7e-17  Score=136.77  Aligned_cols=83  Identities=23%  Similarity=0.375  Sum_probs=75.4

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeE--------EEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCcee
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVT--------YVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFET   97 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~--------~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l   97 (587)
                      ..+...+|||+|||+++|+++| ++|++||+|.        .+.+.+++ +++++|||||+|.++++|++|++.||+..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            3456789999999999999999 8999999984        57777886 899999999999999999999999999999


Q ss_pred             CCeEEEEEecccc
Q psy1534          98 KGRKLVIKEAVED  110 (587)
Q Consensus        98 ~gr~i~V~~a~~~  110 (587)
                      .||+|+|.++.++
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999999854

>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=99.70  E-value=3.3e-17  Score=133.06  Aligned_cols=79  Identities=14%  Similarity=0.306  Sum_probs=73.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      .+..++|||+|||.++++++|+++|++||.|.+|+|+++     +|||||+|.+.++|.+|+..||+..|.|++|+|.|+
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            344679999999999999999999999999999999976     689999999999999999999999999999999998


Q ss_pred             cCCC
Q psy1534         236 RVAD  239 (587)
Q Consensus       236 ~~~~  239 (587)
                      +.++
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.70  E-value=1.3e-17  Score=135.62  Aligned_cols=76  Identities=14%  Similarity=0.228  Sum_probs=71.0

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +...+|||+|||.++++++| ++|++||+|.+|+|+++     ||||||+|.+.++|++|++.||+..|.|++|+|.|+.
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45578999999999999999 89999999999999986     7999999999999999999999999999999999987


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      ++
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.69  E-value=2.5e-17  Score=131.89  Aligned_cols=75  Identities=17%  Similarity=0.184  Sum_probs=67.9

Q ss_pred             CCCcEEEcCCCCCCCHHHH----HhcccCCCeEEEEEeeCC-CCC---cceEEEEEECCHHHHHHHHHHhCCceeCCeEE
Q psy1534          31 LEVPVVMDLIQGDASLYQI----SHLSTVGDVTYVEILNDD-TGK---PRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL  102 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l----~~F~~~G~V~~v~i~~d~-~g~---skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i  102 (587)
                      ..++|||+|||+++++++|    ++|++||+|.+|+|++|+ ++.   ++|||||+|.++++|++|++.|||..|.||+|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4578999999999999988    479999999999999996 544   45999999999999999999999999999999


Q ss_pred             EEE
Q psy1534         103 VIK  105 (587)
Q Consensus       103 ~V~  105 (587)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.69  E-value=3.2e-18  Score=137.68  Aligned_cols=80  Identities=16%  Similarity=0.284  Sum_probs=74.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ...+|||+|||+++++++|+++|+.||.|..+.|+.+.+|+++|||||+|.+.++|++||+ ||+..+.|++|+|++++.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            4568999999999999999999999999999988877779999999999999999999995 899999999999999875


Q ss_pred             C
Q psy1534         238 A  238 (587)
Q Consensus       238 ~  238 (587)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.69  E-value=5.7e-17  Score=132.69  Aligned_cols=82  Identities=24%  Similarity=0.379  Sum_probs=75.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhC------CceeCCeEE
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLN------NQNLFERRI  230 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~------g~~~~g~~l  230 (587)
                      ..++|||+|||+++++++|+++|++||.|.++.++.++. +.++|||||+|.+.++|.+||+.||      +..+.|++|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            457999999999999999999999999999999998885 8899999999999999999999886      677899999


Q ss_pred             EEEEccCCC
Q psy1534         231 TVRMDRVAD  239 (587)
Q Consensus       231 ~v~~a~~~~  239 (587)
                      +|.++.++.
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999988764

>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=99.69  E-value=7e-18  Score=129.68  Aligned_cols=69  Identities=19%  Similarity=0.274  Sum_probs=66.0

Q ss_pred             EEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          35 VVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        35 vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      |||+|||+++|+++| ++|++||+|..+++++++ ++.++|||||+|.+.++|++|++.|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999 899999999999999997 899999999999999999999999999999998764

>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=99.69  E-value=2e-17  Score=131.52  Aligned_cols=75  Identities=15%  Similarity=0.244  Sum_probs=70.3

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ...+|||+|||.++++++| ++|++||+|.+|+++++     ||||||+|.+.++|++|++.||+..|.|++|+|+++..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4568999999999999999 89999999999999876     68999999999999999999999999999999999985


Q ss_pred             c
Q psy1534         110 D  110 (587)
Q Consensus       110 ~  110 (587)
                      +
T Consensus        82 ~   82 (86)
T d2cpja1          82 S   82 (86)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=7.6e-17  Score=130.87  Aligned_cols=81  Identities=20%  Similarity=0.322  Sum_probs=73.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ....++|||+|||+++++++|+++|+.||.|..+.+.++  ..+++||||+|.+.++|++||+.||+..|.|++|+|+++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            345679999999999999999999999999999887654  356899999999999999999999999999999999998


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.69  E-value=5.7e-17  Score=132.12  Aligned_cols=75  Identities=20%  Similarity=0.203  Sum_probs=67.6

Q ss_pred             CCCCcEEEcCCC-CCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQ-GDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp-~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ....+|||+||| ..+++++| ++|++||+|++|+|.       ||||||+|.+.++|++||+.||++.|.|++|+|.++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            455689999996 57888889 789999999999983       699999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      ..++
T Consensus        86 ~~~~   89 (98)
T d1wf2a_          86 AEPK   89 (98)
T ss_dssp             TSCC
T ss_pred             CCCC
Confidence            7543

>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=99.69  E-value=4.6e-17  Score=134.70  Aligned_cols=79  Identities=11%  Similarity=0.188  Sum_probs=71.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC--CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD--TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ++.+|||+|||+++++++| ++|++|| |.++++++++  ++++||||||+|.+.++|++|+ .||+..|.||+|+|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            4579999999999999999 8999999 7788888874  7899999999999999998777 58999999999999999


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      .+++
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8554

>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=99.69  E-value=7.7e-17  Score=127.79  Aligned_cols=77  Identities=16%  Similarity=0.174  Sum_probs=72.9

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      .++|||+|||+++|+++|+++|+.||.|..|.|.++++++++|||||+|.+.++|++||+ +++..+.|+.|.|.++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            469999999999999999999999999999999999889999999999999999999995 69999999999999864

>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=99.68  E-value=8.8e-17  Score=135.41  Aligned_cols=81  Identities=17%  Similarity=0.335  Sum_probs=74.2

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ++.+++|||+|||.++++++|+++|++||.|.+|++..+  +.++|||||+|.+.++|..||+.|||+.|.|++|.|.++
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345689999999999999999999999999999999765  467899999999999999999999999999999999998


Q ss_pred             cCC
Q psy1534         236 RVA  238 (587)
Q Consensus       236 ~~~  238 (587)
                      ...
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            654

>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=99.68  E-value=5.7e-17  Score=128.83  Aligned_cols=71  Identities=31%  Similarity=0.466  Sum_probs=68.9

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .++|||.|||.+++++||+++|++||.|..+++.+++++|||+|+++++|++||+.|||..|.|++|+|.+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~   78 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   78 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            56899999999999999999999999999999999999999999999999999999999999999999986

>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=99.68  E-value=6.6e-17  Score=131.73  Aligned_cols=71  Identities=25%  Similarity=0.560  Sum_probs=67.6

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      +.++|||.|||++++++||+++|++||.|.++++..+ ++|||+|.+.++|++||+.|||..|.|+.|+|.+
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-GMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT-TEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc-ceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3679999999999999999999999999999999875 9999999999999999999999999999999875

>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=99.68  E-value=2.8e-17  Score=127.40  Aligned_cols=74  Identities=22%  Similarity=0.433  Sum_probs=70.3

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +|||+|||+++|+++|+++|+.||.|..+.+++++. +.+++||||+|.+.++|++|++ +|++.|.|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            489999999999999999999999999999998885 8999999999999999999996 8999999999999875

>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=99.68  E-value=6.8e-17  Score=131.17  Aligned_cols=79  Identities=16%  Similarity=0.213  Sum_probs=71.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .....+|||+|||+++++++| ++|++||+|..|.+..+  ..+++||||+|.+.++|++||+.||+..|.|++|+|+++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            345668999999999999999 89999999999987654  446899999999999999999999999999999999998


Q ss_pred             cc
Q psy1534         108 VE  109 (587)
Q Consensus       108 ~~  109 (587)
                      ..
T Consensus        89 ~~   90 (95)
T d1x4aa1          89 RS   90 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>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=99.68  E-value=9e-17  Score=132.26  Aligned_cols=83  Identities=24%  Similarity=0.452  Sum_probs=75.1

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCee--------EEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVE--------NVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE  227 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  227 (587)
                      ...++|||+|||+.+++++|+++|+.||.|.        .+.+.+++. ++++|||||+|.+.++|.+||+.||+..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            4467999999999999999999999999874        566677765 8999999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q psy1534         228 RRITVRMDRVAD  239 (587)
Q Consensus       228 ~~l~v~~a~~~~  239 (587)
                      ++|+|++++++.
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999998764

>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=99.67  E-value=4.8e-17  Score=128.54  Aligned_cols=77  Identities=13%  Similarity=0.157  Sum_probs=70.1

Q ss_pred             CCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeC-CeEEEEE
Q psy1534          28 GAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK-GRKLVIK  105 (587)
Q Consensus        28 ~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~-gr~i~V~  105 (587)
                      ..|+.++|||+|||.++++++| ++|++||+|.+|+++++    .+|||||+|.+.++|.+|++.|+|..|. +++|+|.
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            4456789999999999999999 89999999999999876    3689999999999999999999999885 6999999


Q ss_pred             ecc
Q psy1534         106 EAV  108 (587)
Q Consensus       106 ~a~  108 (587)
                      |+.
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.67  E-value=6.8e-17  Score=127.63  Aligned_cols=78  Identities=15%  Similarity=0.268  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF-ERRITVR  233 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~  233 (587)
                      ..+++++|||+|||.++++++|+++|++||.|.+|++++++    +|||||+|.+.++|.+|++.|||..+. +++|+|+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            45668899999999999999999999999999999998754    689999999999999999999999885 7899999


Q ss_pred             Ecc
Q psy1534         234 MDR  236 (587)
Q Consensus       234 ~a~  236 (587)
                      |++
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.67  E-value=2.5e-17  Score=135.39  Aligned_cols=79  Identities=20%  Similarity=0.314  Sum_probs=73.9

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .++|||+|||+++++++|+++|++||.|..+.+..+..++++|||||+|.+.++|++||+.|||..|.|+++.|.++.+
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            4789999999999999999999999999999999988899999999999999999999999999999999988866543

>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=99.67  E-value=9.5e-18  Score=138.47  Aligned_cols=82  Identities=17%  Similarity=0.236  Sum_probs=76.6

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ++.++|||+|||.++++++| ++|++||.|..+.++.+. +|+++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45678999999999999999 899999999999999886 8999999999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      .+++
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            8553

>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=99.67  E-value=6.2e-17  Score=133.20  Aligned_cols=81  Identities=19%  Similarity=0.113  Sum_probs=73.4

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      ......|||+|||+++|++|| ++|+.||. .+|.++++.+++++|||||+|.+.++|++|++ +|+..|.||.|+|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            345678999999999999999 89999985 58899999899999999999999999999995 8999999999999998


Q ss_pred             cccc
Q psy1534         108 VEDK  111 (587)
Q Consensus       108 ~~~~  111 (587)
                      .++.
T Consensus        90 ~~~~   93 (102)
T d1weza_          90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8554

>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=99.67  E-value=2.4e-17  Score=129.17  Aligned_cols=74  Identities=12%  Similarity=0.170  Sum_probs=67.9

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCc-eeCCeEEEEEecccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRF-ETKGRKLVIKEAVED  110 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~-~l~gr~i~V~~a~~~  110 (587)
                      .+|||+|||.++|+++| ++|++||.|.++++++.     ||||||+|.+.++|++|++.|||. .|.|++|+|+++.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            68999999999999999 89999999988887764     799999999999999999999985 699999999999855


Q ss_pred             c
Q psy1534         111 K  111 (587)
Q Consensus       111 ~  111 (587)
                      +
T Consensus        77 ~   77 (80)
T d2cqha1          77 K   77 (80)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.67  E-value=1.4e-17  Score=137.43  Aligned_cols=85  Identities=18%  Similarity=0.310  Sum_probs=78.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  234 (587)
                      ..++++|||+|||.++++++|+++|+.||.|..+.+..+. .++++|||||+|.+.++|.+||+.||+..|.|++|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3457899999999999999999999999999999888876 489999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q psy1534         235 DRVADR  240 (587)
Q Consensus       235 a~~~~~  240 (587)
                      ++++..
T Consensus        95 ak~k~~  100 (102)
T d2cpxa1          95 GKNKKQ  100 (102)
T ss_dssp             CCCCSC
T ss_pred             CCCccc
Confidence            987653

>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=99.67  E-value=2.4e-16  Score=125.45  Aligned_cols=78  Identities=21%  Similarity=0.294  Sum_probs=71.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||+++++++|+++|++||.|..+.+.+     ++|||||+|.+.++|.+|+..||+..|.|+.|.|+|+++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            357999999999999999999999999998887765     378999999999999999999999999999999999987


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      +.+
T Consensus        82 ~~~   84 (86)
T d2cpda1          82 VDK   84 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.67  E-value=1.2e-16  Score=132.05  Aligned_cols=82  Identities=27%  Similarity=0.449  Sum_probs=72.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCC--CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +.++|||+|||+++++++|+++|+.|| |+++.++.+.  .++++|||||+|.+.++|++|+ .||+..|.|+.|+|+++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            457999999999999999999999998 8888888775  3889999999999999998776 69999999999999998


Q ss_pred             cCCCCC
Q psy1534         236 RVADRL  241 (587)
Q Consensus       236 ~~~~~~  241 (587)
                      ..+...
T Consensus        92 ~~~~~~   97 (104)
T d1wi8a_          92 DQAQDK   97 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            776543

>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=99.66  E-value=5.2e-17  Score=127.24  Aligned_cols=76  Identities=21%  Similarity=0.328  Sum_probs=69.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCc-eeCCeEEEEEEccCC
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQ-NLFERRITVRMDRVA  238 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~-~~~g~~l~v~~a~~~  238 (587)
                      ++|||+|||+++++++|+++|++||.|.++.+.+.     +|||||+|.+.++|++|++.|||. .+.|++|+|+++.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            47999999999999999999999999988777764     789999999999999999999996 699999999999876


Q ss_pred             CC
Q psy1534         239 DR  240 (587)
Q Consensus       239 ~~  240 (587)
                      ..
T Consensus        77 ~~   78 (80)
T d2cqha1          77 KL   78 (80)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>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=99.66  E-value=1e-16  Score=130.40  Aligned_cols=82  Identities=18%  Similarity=0.234  Sum_probs=73.8

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCC-eeEEEEeeCCC--CCcceEEEEEecCHHHHHHHHHHhCCc--eeCCeEEEEEE
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGK-VENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQ--NLFERRITVRM  234 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~v~~  234 (587)
                      |+|||+|||.++++++|+++|++||+ |.++.++++..  ++++|||||+|.++++|.+|++.|++.  .+.|++|+|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 89999998863  889999999999999999999999654  45799999999


Q ss_pred             ccCCCCC
Q psy1534         235 DRVADRL  241 (587)
Q Consensus       235 a~~~~~~  241 (587)
                      |+++..+
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9876644

>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=99.66  E-value=1.2e-16  Score=127.29  Aligned_cols=78  Identities=18%  Similarity=0.264  Sum_probs=71.7

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeE-EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ..++|||+|||++++++||+++|+.||.|.. +.+..+.+++++|+|||+|.+.++|++||+.||++.+.||+|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3568999999999999999999999999865 56677777999999999999999999999999999999999999875

>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=99.66  E-value=2.1e-17  Score=131.85  Aligned_cols=72  Identities=22%  Similarity=0.328  Sum_probs=67.1

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      ++|||+|||+++++++| ++|++||+|.+|+|++|      |||||+|.+.++|++||+.||+..|.|+.|+|.++..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            47999999999999999 89999999999999765      89999999999999999999999999999999887643

>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=99.65  E-value=1.5e-16  Score=131.38  Aligned_cols=82  Identities=21%  Similarity=0.156  Sum_probs=72.4

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeC-CCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .....|||+|||+++|++|| ++|+.||.|..+.++.+ .+++++|||||+|.++++|++|++ +|+..|.||.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            35557999999999999999 89999999988555555 599999999999999999999995 8999999999999999


Q ss_pred             ccccC
Q psy1534         108 VEDKG  112 (587)
Q Consensus       108 ~~~~~  112 (587)
                      .+++.
T Consensus        92 ~~~~~   96 (104)
T d1wg5a_          92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHh
Confidence            86543

>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=99.65  E-value=1.7e-16  Score=126.95  Aligned_cols=80  Identities=23%  Similarity=0.318  Sum_probs=71.4

Q ss_pred             CCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCeEEEEEE
Q psy1534         156 CPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL-FERRITVRM  234 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~v~~  234 (587)
                      .+++++|||+|||+++++++|+++|++||.|..+.+..+   +.++||||+|.+.++|.+|+..||+..+ .|++|+|+|
T Consensus         7 ~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            356789999999999999999999999999988877654   3478999999999999999999999988 589999999


Q ss_pred             ccCC
Q psy1534         235 DRVA  238 (587)
Q Consensus       235 a~~~  238 (587)
                      ++..
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8753

>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=99.65  E-value=1.6e-16  Score=129.35  Aligned_cols=75  Identities=16%  Similarity=0.366  Sum_probs=68.5

Q ss_pred             CCcEEEEecCC-CCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp-~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+||| ..+++++|+++|++||.|.+|.|.       +|||||+|.+.++|++||+.||++.|.|++|+|++++
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45689999997 578899999999999999999983       6899999999999999999999999999999999987


Q ss_pred             CCC
Q psy1534         237 VAD  239 (587)
Q Consensus       237 ~~~  239 (587)
                      .+.
T Consensus        87 ~~~   89 (98)
T d1wf2a_          87 EPK   89 (98)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.65  E-value=1.3e-16  Score=124.67  Aligned_cols=75  Identities=20%  Similarity=0.274  Sum_probs=69.3

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .+++|||+||+  +|+++|+++|++||.|.+|.+.++     ++||||+|.+.++|.+|++.||+..+.|++|+|+|+++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            46899999996  899999999999999999999865     68999999999999999999999999999999999976


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      ++
T Consensus        77 ~P   78 (79)
T d2bz2a1          77 QP   78 (79)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.65  E-value=2.2e-16  Score=126.01  Aligned_cols=76  Identities=13%  Similarity=0.312  Sum_probs=66.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ....+|||+|||++++++|| ++|++|| +..+.+.     ++||||||+|.+.++|++|++.||+..|.|++|+|+++.
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            35678999999999999999 8999999 3334443     358999999999999999999999999999999999997


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.65  E-value=1.8e-16  Score=122.33  Aligned_cols=73  Identities=11%  Similarity=0.126  Sum_probs=67.2

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .+|||+|||+++++++| ++|+.||+|.+|+|++++.+. ++||||+|.++++|++|+ .+|++.|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            37999999999999999 899999999999999997654 579999999999999999 57999999999999875

>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=99.65  E-value=9.8e-17  Score=125.36  Aligned_cols=75  Identities=12%  Similarity=0.142  Sum_probs=68.6

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      +...++|||+||+  +|+++| ++|++||+|.+|++.++     +|||||+|.+.++|.+|++.||+..+.|++|+|.++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            3466899999986  899999 89999999999999865     689999999999999999999999999999999999


Q ss_pred             ccc
Q psy1534         108 VED  110 (587)
Q Consensus       108 ~~~  110 (587)
                      .++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            754

>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=99.65  E-value=6.8e-17  Score=131.49  Aligned_cols=79  Identities=20%  Similarity=0.205  Sum_probs=71.3

Q ss_pred             CcEEEcCCCCCCCHHHH-HhcccCCC-eEEEEEeeCC--CCCcceEEEEEECCHHHHHHHHHHhCC--ceeCCeEEEEEe
Q psy1534          33 VPVVMDLIQGDASLYQI-SHLSTVGD-VTYVEILNDD--TGKPRGSAIVEFQSPDLVRKAVNKMHR--FETKGRKLVIKE  106 (587)
Q Consensus        33 ~~vfV~nlp~~~t~~~l-~~F~~~G~-V~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Al~~l~g--~~l~gr~i~V~~  106 (587)
                      .+|||+|||.++++++| ++|++||+ |++|+|++|.  ++++||||||+|.+.++|.+|++.|++  ..+.|++|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            37999999999999999 89999996 9999999985  689999999999999999999999864  556799999999


Q ss_pred             ccccc
Q psy1534         107 AVEDK  111 (587)
Q Consensus       107 a~~~~  111 (587)
                      +.+++
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            98543

>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=99.65  E-value=7.4e-17  Score=128.60  Aligned_cols=68  Identities=29%  Similarity=0.587  Sum_probs=64.8

Q ss_pred             eEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       518 ~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      +|||+|||+++||+||+++|++||.|.++++..+ |+|||+|++.++|++||+.|||.+|.|+.|+|.+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~   69 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   69 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCB
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeE
Confidence            7999999999999999999999999999999776 9999999999999999999999999999988754

>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=99.65  E-value=1.1e-16  Score=130.19  Aligned_cols=78  Identities=17%  Similarity=0.224  Sum_probs=70.5

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++|||+|||+++++++| ++|++||+|..++    .+++++|||||+|.+.++|++|++.||+..|.|++|+|.++.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            35678999999999999999 8999999987664    267789999999999999999999999999999999999998


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      ++.
T Consensus        90 ~k~   92 (96)
T d1fjca_          90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.64  E-value=1.8e-16  Score=130.45  Aligned_cols=82  Identities=22%  Similarity=0.345  Sum_probs=74.6

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ....+|||+|||+++|++||+++|+.|| |..|.++++.+++++|||||+|.+.++|++|++ ||++.|.||.|+|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            3457999999999999999999999997 568889999889999999999999999999985 89999999999999987


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      ....
T Consensus        91 ~~~~   94 (102)
T d1weza_          91 TAGT   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.64  E-value=3.1e-16  Score=130.94  Aligned_cols=77  Identities=23%  Similarity=0.373  Sum_probs=71.1

Q ss_pred             CcEEEEecCCC-CCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      +++|||+|||+ .+++++|+++|+.||.|.+|.|++++    +|||||+|.+.++|.+|++.||+..|.|+.|+|++++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            46999999965 59999999999999999999999875    78999999999999999999999999999999999875


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      ..
T Consensus        78 ~~   79 (109)
T d2adca1          78 QN   79 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.64  E-value=1.8e-16  Score=132.81  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=70.8

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .++|||+|||+++++++|+++|++||.|..|.|.+     ++|||||+|.+.++|.+||+.|||..|.|++|.|+|+...
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            57999999999999999999999999999998854     4789999999999999999999999999999999998765


Q ss_pred             C
Q psy1534         239 D  239 (587)
Q Consensus       239 ~  239 (587)
                      .
T Consensus        85 ~   85 (111)
T d1whxa_          85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            4

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.7e-16  Score=124.28  Aligned_cols=76  Identities=12%  Similarity=0.044  Sum_probs=69.4

Q ss_pred             CCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          31 LEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        31 ~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..++|||+|||+++++++| ++|++||.|..+.+.+     +||||||+|.+.++|.+|++.||+..|.|++|+|.++.+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            4578999999999999999 8999999998888765     479999999999999999999999999999999999875


Q ss_pred             cc
Q psy1534         110 DK  111 (587)
Q Consensus       110 ~~  111 (587)
                      +.
T Consensus        82 ~~   83 (86)
T d2cpda1          82 VD   83 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.64  E-value=2.4e-16  Score=128.38  Aligned_cols=75  Identities=16%  Similarity=0.246  Sum_probs=69.3

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ....+|||+|||+++++++| ++|++||+|++|+|.+      +|||||+|.+.++|++||+.||+..|.|+.|+|.++.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            35668999999999999999 8999999999999875      4899999999999999999999999999999999987


Q ss_pred             cc
Q psy1534         109 ED  110 (587)
Q Consensus       109 ~~  110 (587)
                      .+
T Consensus        87 ~~   88 (98)
T d1wg4a_          87 VY   88 (98)
T ss_dssp             EE
T ss_pred             cC
Confidence            44

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1e-16  Score=128.02  Aligned_cols=76  Identities=22%  Similarity=0.225  Sum_probs=68.2

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      ...++|||+|||+++|+++| ++|++||+|.+|++..+    ++|||||+|.+.++|++|+.  ++..|.|++|.|.++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            45689999999999999999 89999999999987654    67899999999999999995  7889999999999997


Q ss_pred             ccc
Q psy1534         109 EDK  111 (587)
Q Consensus       109 ~~~  111 (587)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.64  E-value=2e-16  Score=132.62  Aligned_cols=71  Identities=17%  Similarity=0.315  Sum_probs=68.4

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      .++|||+|||+++|++||+++|++||+|..+.+.+.+++|||+|.+.++|++||+.|||..|.|++|+|.+
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~   80 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEE
Confidence            56999999999999999999999999999999988889999999999999999999999999999999975

>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=99.64  E-value=1.7e-16  Score=126.94  Aligned_cols=75  Identities=23%  Similarity=0.299  Sum_probs=68.6

Q ss_pred             CcEEEEecCCCCCcHHHH---HHHHHhcCCeeEEEEeeCCC----CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         159 INKVFVANLDYKVDEKKL---REVFRLAGKVENVEIALDKD----GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l---~~~F~~~G~i~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      .++|||+|||+++++++|   +++|++||.|.+|.|++++.    +.++|||||+|.+.++|.+|++.|||..+.|++|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999   77899999999999999874    33459999999999999999999999999999999


Q ss_pred             EE
Q psy1534         232 VR  233 (587)
Q Consensus       232 v~  233 (587)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.63  E-value=1.7e-16  Score=126.72  Aligned_cols=70  Identities=24%  Similarity=0.380  Sum_probs=64.3

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      ..+|||.|||+++|++||+++|++|| +..+.+...+++|||+|++.++|++||+.||+++|+|++|+|++
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~   74 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35999999999999999999999999 44566667779999999999999999999999999999999986

>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=99.63  E-value=6.1e-16  Score=119.27  Aligned_cols=74  Identities=22%  Similarity=0.277  Sum_probs=68.3

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      ++|||+|||+++++++|+++|+.||.|..|++.+++.+. ++||||+|.+.++|.+|+ .+|++.|.|++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            489999999999999999999999999999999988654 579999999999999999 58999999999999864

>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=99.63  E-value=1.1e-16  Score=128.89  Aligned_cols=77  Identities=18%  Similarity=0.252  Sum_probs=69.7

Q ss_pred             CCcEEEcCCCCCCCHHHH-----HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          32 EVPVVMDLIQGDASLYQI-----SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-----~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      .++|||+|||.+++++||     ++|++||+|.+|++.+  +++++|||||+|.+.++|.+|++.||+..+.|++|.|.+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            478999999999999988     3589999999998754  567789999999999999999999999999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +..+
T Consensus        81 ak~~   84 (91)
T d1nu4a_          81 AKTD   84 (91)
T ss_dssp             CSSC
T ss_pred             eCCC
Confidence            9844

>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=99.63  E-value=1.1e-15  Score=124.47  Aligned_cols=71  Identities=20%  Similarity=0.305  Sum_probs=67.0

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccC--ceEEEEE
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDG--KIIDVTF  586 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g--~~i~v~~  586 (587)
                      ..+|||.|||+++|+++|+++|++||.|..+++.+++++|||+|.+.++|++|++.||+.+|.|  ++|+|.+
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4699999999999999999999999999999999999999999999999999999999999987  4788875

>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=99.63  E-value=4.8e-16  Score=126.51  Aligned_cols=78  Identities=14%  Similarity=0.230  Sum_probs=71.0

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE--RRITVRM  234 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~  234 (587)
                      +++++|||+|||+++++++|+++|++||.|..|++.++     ++||||+|.+.++|++|++.||+..|.|  ++|+|+|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            45789999999999999999999999999999999875     6799999999999999999999999976  5799999


Q ss_pred             ccCCC
Q psy1534         235 DRVAD  239 (587)
Q Consensus       235 a~~~~  239 (587)
                      +++.+
T Consensus        90 ak~~~   94 (97)
T d1whya_          90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.62  E-value=2.4e-16  Score=126.79  Aligned_cols=80  Identities=15%  Similarity=0.368  Sum_probs=71.6

Q ss_pred             CCcEEEEecCCCCCcHHHHHH----HHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         158 LINKVFVANLDYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~----~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      |+++|||+|||++++++||++    +|++||+|.+|++.+  +++++|||||+|.+.++|.+|++.||+..+.|++|.|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            468999999999999999864    689999999988754  35678999999999999999999999999999999999


Q ss_pred             EccCCC
Q psy1534         234 MDRVAD  239 (587)
Q Consensus       234 ~a~~~~  239 (587)
                      |++.+.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            997654

>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=99.62  E-value=2.2e-16  Score=126.14  Aligned_cols=77  Identities=22%  Similarity=0.199  Sum_probs=69.2

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      .+++|||+|||+++++++|+++|++||.|.+|++..+    +++||||+|.+.++|++||.  +++.|.|++|.|+++.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCC
Confidence            4679999999999999999999999999999987654    57899999999999999984  78899999999999876


Q ss_pred             CCC
Q psy1534         238 ADR  240 (587)
Q Consensus       238 ~~~  240 (587)
                      +..
T Consensus        78 k~~   80 (88)
T d1wf0a_          78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.62  E-value=8.4e-16  Score=122.72  Aligned_cols=78  Identities=13%  Similarity=0.180  Sum_probs=70.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM--HRFETKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l--~g~~l~gr~i~V~  105 (587)
                      .++.++|||+|||.++++++| ++|++||.|.+|+++++     ++||||+|.+.++|++|++.+  ++..+.|++|+|.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            467789999999999999999 89999999999999875     689999999999999999865  5789999999999


Q ss_pred             eccccc
Q psy1534         106 EAVEDK  111 (587)
Q Consensus       106 ~a~~~~  111 (587)
                      ++..++
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            998553

>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=99.62  E-value=1.9e-16  Score=130.65  Aligned_cols=81  Identities=21%  Similarity=0.299  Sum_probs=71.6

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEE-EEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEe
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYV-EILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE  106 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v-~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~  106 (587)
                      ......|||+|||+++|+++| ++|+.||.|..+ .++.+.+|+++|||||+|.+.++|++||+ ||+..|.||+|.|.+
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            345578999999999999999 899999999874 45555699999999999999999999995 899999999999999


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +.++
T Consensus        84 ~~~~   87 (103)
T d2cpya1          84 VTLE   87 (103)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8743

>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=99.62  E-value=6.6e-16  Score=119.08  Aligned_cols=70  Identities=21%  Similarity=0.357  Sum_probs=63.3

Q ss_pred             EEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecccc
Q psy1534          35 VVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED  110 (587)
Q Consensus        35 vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~~  110 (587)
                      |||+|||+++++++| ++|++|| +..+++.     +++|||||+|.+.++|++|++.||+..+.|++|+|+++..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            799999999999999 8999999 5565553     45899999999999999999999999999999999999744

>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=99.62  E-value=3.5e-16  Score=130.60  Aligned_cols=75  Identities=15%  Similarity=0.267  Sum_probs=68.6

Q ss_pred             CCcEEEcCCCC-CCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEeccc
Q psy1534          32 EVPVVMDLIQG-DASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE  109 (587)
Q Consensus        32 ~~~vfV~nlp~-~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~~  109 (587)
                      ..+|||+|||+ .+++++| ++|++||+|.+|+|++++    ||||||+|.+.++|++|++.||+..|.|++|+|.++..
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            46899999954 5899999 899999999999999873    68999999999999999999999999999999999873


Q ss_pred             c
Q psy1534         110 D  110 (587)
Q Consensus       110 ~  110 (587)
                      +
T Consensus        78 ~   78 (109)
T d2adca1          78 Q   78 (109)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.62  E-value=3.6e-16  Score=124.99  Aligned_cols=76  Identities=17%  Similarity=0.173  Sum_probs=68.4

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCcee-CCeEEEEEec
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET-KGRKLVIKEA  107 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l-~gr~i~V~~a  107 (587)
                      |+.++|||+|||+++++++| ++|++||.|.++.++.+   +++|||||+|.+.++|.+|+..|++..+ .|++|+|.++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            45678999999999999999 89999999998877654   3468999999999999999999999988 5899999998


Q ss_pred             c
Q psy1534         108 V  108 (587)
Q Consensus       108 ~  108 (587)
                      +
T Consensus        85 k   85 (88)
T d2adca2          85 K   85 (88)
T ss_dssp             S
T ss_pred             C
Confidence            6

>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=99.62  E-value=9.6e-17  Score=123.16  Aligned_cols=70  Identities=23%  Similarity=0.464  Sum_probs=66.6

Q ss_pred             EEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q psy1534         162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT  231 (587)
Q Consensus       162 l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  231 (587)
                      |||+|||+++|+++|+++|++||.|..+++.+++. +.++|||||+|.+.++|++|++.|||+.|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999885 89999999999999999999999999999998763

>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=99.62  E-value=8.2e-16  Score=118.56  Aligned_cols=67  Identities=19%  Similarity=0.370  Sum_probs=64.1

Q ss_pred             EEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEEE
Q psy1534         519 VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF  586 (587)
Q Consensus       519 v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~  586 (587)
                      |||+|||++++++||+++|++|| +..+.+.+.+++|||+|.+.++|++||+.|||+.|+|++|+|++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~   67 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQL   67 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEE
Confidence            79999999999999999999999 77788888899999999999999999999999999999999986

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.61  E-value=5.8e-16  Score=125.83  Aligned_cols=78  Identities=23%  Similarity=0.393  Sum_probs=70.9

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..++|||+|||+++++++|+++|++||.|..+..    .++++|||||+|.+.++|++|++.||+..|.|++|+|.|+.+
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            4679999999999999999999999998766542    467899999999999999999999999999999999999987


Q ss_pred             CC
Q psy1534         238 AD  239 (587)
Q Consensus       238 ~~  239 (587)
                      +.
T Consensus        91 k~   92 (96)
T d1fjca_          91 KG   92 (96)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.61  E-value=1.2e-15  Score=125.73  Aligned_cols=80  Identities=15%  Similarity=0.191  Sum_probs=71.0

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEE
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM--HRFETKGRKLVIK  105 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l--~g~~l~gr~i~V~  105 (587)
                      .++.+.|||+|||.++++++| ++|++||+|++|++.++     |++|||+|.+.++|++|++.|  ++..+.|++|+|.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            356778999999999999999 89999999999999864     789999999999999999987  4677889999999


Q ss_pred             ecccccCC
Q psy1534         106 EAVEDKGG  113 (587)
Q Consensus       106 ~a~~~~~~  113 (587)
                      ++..++..
T Consensus        87 ~s~~~~~~   94 (104)
T d1wexa_          87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EcCCCccC
Confidence            99865543

>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=99.61  E-value=1.4e-15  Score=121.38  Aligned_cols=80  Identities=14%  Similarity=0.147  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCeEEEE
Q psy1534         155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML--NNQNLFERRITV  232 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~v  232 (587)
                      ..+++++|||+|||+++++++|+++|++||.|.++++.++     ++||||+|.+.++|++|++.+  ++..+.|++|+|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            4567899999999999999999999999999999998865     579999999999999999865  577899999999


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      +|++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9987654

>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=99.61  E-value=3.4e-16  Score=130.18  Aligned_cols=78  Identities=12%  Similarity=0.109  Sum_probs=70.1

Q ss_pred             CCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCcee--CCeEEEEEe
Q psy1534          30 PLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET--KGRKLVIKE  106 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l--~gr~i~V~~  106 (587)
                      .+..+|||+|||+++|+++| ++|++||+|.+|+|++++   ++|||||+|.++++|++|++.||+..|  .+++|+|.+
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            35568999999999999999 899999999999999874   579999999999999999999999998  478899998


Q ss_pred             cccc
Q psy1534         107 AVED  110 (587)
Q Consensus       107 a~~~  110 (587)
                      +..+
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            8744

>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=99.61  E-value=1.1e-15  Score=126.20  Aligned_cols=82  Identities=18%  Similarity=0.147  Sum_probs=72.0

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEee-CCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENVEIAL-DKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ...+|||+|||+++||+||+++|+.+|.|..+.++. +.+++++|||||+|.++++|++|++ +|++.|.||.|.|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            346899999999999999999999999887754444 4569999999999999999999995 89999999999999987


Q ss_pred             CCCC
Q psy1534         237 VADR  240 (587)
Q Consensus       237 ~~~~  240 (587)
                      ..+.
T Consensus        93 ~~~~   96 (104)
T d1wg5a_          93 RAEV   96 (104)
T ss_dssp             TTTS
T ss_pred             HHHh
Confidence            7653

>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=99.60  E-value=1.2e-15  Score=126.88  Aligned_cols=80  Identities=19%  Similarity=0.317  Sum_probs=71.3

Q ss_pred             CCCcEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEEE
Q psy1534         157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF--ERRITVRM  234 (587)
Q Consensus       157 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~~  234 (587)
                      .+..+|||+|||+.+|+++|+++|++||.|.+|.|++++   ++|||||+|.+.++|++||+.||+..|.  +++|+|.+
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            345789999999999999999999999999999998874   4899999999999999999999999984  77888888


Q ss_pred             ccCCC
Q psy1534         235 DRVAD  239 (587)
Q Consensus       235 a~~~~  239 (587)
                      ++.+.
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            76543

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=3.6e-16  Score=130.81  Aligned_cols=83  Identities=14%  Similarity=0.144  Sum_probs=72.5

Q ss_pred             CCCCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEe-eCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          27 TGAPLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEIL-NDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        27 ~~~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~-~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      ........|||+|||+++|+++| ++|+.||.|..+.++ .+.+|.++|||||+|.+.++|++|++ ||+..|+||.|.|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V   91 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   91 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEE
Confidence            33445668999999999999999 899999999875544 45699999999999999999999995 8999999999999


Q ss_pred             Eecccc
Q psy1534         105 KEAVED  110 (587)
Q Consensus       105 ~~a~~~  110 (587)
                      .++.++
T Consensus        92 ~~~~~~   97 (112)
T d1wela1          92 HPITKK   97 (112)
T ss_dssp             EEECHH
T ss_pred             EEcChH
Confidence            998744

>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=99.59  E-value=9.1e-16  Score=125.19  Aligned_cols=76  Identities=11%  Similarity=0.101  Sum_probs=68.4

Q ss_pred             CCCCcEEEcCCCCC-CCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHH--HhCCceeCCeEEEEE
Q psy1534          30 PLEVPVVMDLIQGD-ASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVN--KMHRFETKGRKLVIK  105 (587)
Q Consensus        30 ~~~~~vfV~nlp~~-~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~--~l~g~~l~gr~i~V~  105 (587)
                      ...++|||+|||.+ +|+++| ++|++||+|.+|+++++     ||||||+|.+.++|.+|++  .+++..|.|++|+|.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            45578999999986 799999 89999999999999875     6899999999999999997  578889999999999


Q ss_pred             ecccc
Q psy1534         106 EAVED  110 (587)
Q Consensus       106 ~a~~~  110 (587)
                      ++.++
T Consensus        91 ~s~~~   95 (99)
T d1x4fa1          91 LSEKY   95 (99)
T ss_dssp             EECSC
T ss_pred             EcCCc
Confidence            99754

>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=99.57  E-value=2e-15  Score=124.44  Aligned_cols=79  Identities=19%  Similarity=0.272  Sum_probs=70.6

Q ss_pred             CcEEEEecCCCCCcHHHHHHHHHhcCCeeE-EEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q psy1534         159 INKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV  237 (587)
Q Consensus       159 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~~  237 (587)
                      ..+|||+|||+++|+++|+++|+.||.|.. +.++.+..|+++|||||+|.+.++|++||+ ||+..|.|+.|.|.++..
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            467999999999999999999999999876 455555679999999999999999999995 899999999999998754


Q ss_pred             C
Q psy1534         238 A  238 (587)
Q Consensus       238 ~  238 (587)
                      .
T Consensus        87 ~   87 (103)
T d2cpya1          87 E   87 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.56  E-value=1.2e-14  Score=119.63  Aligned_cols=73  Identities=18%  Similarity=0.206  Sum_probs=67.7

Q ss_pred             CCCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHh--CCCcccCceEEEEE
Q psy1534         514 IERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMM--DRTRIDGKIIDVTF  586 (587)
Q Consensus       514 ~~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l--~g~~~~g~~i~v~~  586 (587)
                      .+..+|+|+|||.++|++||+++|++||.|..+.+.+++++|||+|++.++|+.||+.|  ++..+.|++|+|.+
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~   87 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEE
Confidence            34679999999999999999999999999999999999999999999999999999988  55678899999986

>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=99.56  E-value=4.2e-15  Score=118.56  Aligned_cols=76  Identities=17%  Similarity=0.146  Sum_probs=68.1

Q ss_pred             CCCCcEEEcCCCCC-CCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHh--CCceeCCeEEEEE
Q psy1534          30 PLEVPVVMDLIQGD-ASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM--HRFETKGRKLVIK  105 (587)
Q Consensus        30 ~~~~~vfV~nlp~~-~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l--~g~~l~gr~i~V~  105 (587)
                      ...+.|||+|||.. +|++|| ++|++||+|.+|+++++     +++|||+|.+.++|..|++.|  ++..+.|++|+|.
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~   80 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   80 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEE
Confidence            46678999999986 789999 89999999999999876     579999999999999999965  6789999999999


Q ss_pred             ecccc
Q psy1534         106 EAVED  110 (587)
Q Consensus       106 ~a~~~  110 (587)
                      ++.+.
T Consensus        81 ~s~~~   85 (89)
T d1x4da1          81 LSQKY   85 (89)
T ss_dssp             EECCC
T ss_pred             ECCCc
Confidence            99743

>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=99.55  E-value=3e-16  Score=129.03  Aligned_cols=74  Identities=15%  Similarity=0.109  Sum_probs=70.3

Q ss_pred             cEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEec
Q psy1534          34 PVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA  107 (587)
Q Consensus        34 ~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a  107 (587)
                      .++|++++.+++|++| ++|++||+|++|+|+++.++++||||||+|.+.++|++|++.|||+.|.||+|+|+++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            5888999999999999 8899999999999998889999999999999999999999999999999999999876

>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=99.53  E-value=5.7e-15  Score=121.24  Aligned_cols=80  Identities=11%  Similarity=0.116  Sum_probs=70.7

Q ss_pred             CCcEEEEecCCCCCc-----HHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534         158 LINKVFVANLDYKVD-----EKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV  232 (587)
Q Consensus       158 ~~~~l~V~nLp~~~t-----e~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  232 (587)
                      ..++|||+||+.++.     +++|+++|+.||.|+++++++.     ++||||+|.+.++|.+|++.|||..|.|++|+|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-----CCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            467999999998763     3569999999999999999864     689999999999999999999999999999999


Q ss_pred             EEccCCCCCC
Q psy1534         233 RMDRVADRLD  242 (587)
Q Consensus       233 ~~a~~~~~~~  242 (587)
                      .|++......
T Consensus        79 ~~a~~~~~~~   88 (104)
T d1weya_          79 YFAQTLHIGS   88 (104)
T ss_dssp             ECCCCSSCCS
T ss_pred             eecccCCCCC
Confidence            9998776443

>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=99.53  E-value=1.2e-14  Score=115.76  Aligned_cols=79  Identities=11%  Similarity=0.109  Sum_probs=70.2

Q ss_pred             CCCCcEEEEecCCCC-CcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCeEEEE
Q psy1534         156 CPLINKVFVANLDYK-VDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML--NNQNLFERRITV  232 (587)
Q Consensus       156 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~v  232 (587)
                      ..++++|||+|||.. +|++||.++|++||.|.+|.++++     +++|||+|++.++|.+|++.|  ++..+.|++|+|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            345789999999986 899999999999999999999876     469999999999999999966  677899999999


Q ss_pred             EEccCCC
Q psy1534         233 RMDRVAD  239 (587)
Q Consensus       233 ~~a~~~~  239 (587)
                      .|+....
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9987543

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=4.4e-15  Score=124.11  Aligned_cols=80  Identities=24%  Similarity=0.299  Sum_probs=70.4

Q ss_pred             CCcEEEEecCCCCCcHHHHHHHHHhcCCeeEE-EEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         158 LINKVFVANLDYKVDEKKLREVFRLAGKVENV-EIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       158 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      ..++|||+|||+++|++||+++|+.||.|..+ .+..+.+|+++|||||+|.+.++|++|++ ||+..|.||.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            45689999999999999999999999998664 44555579999999999999999999995 89999999999998865


Q ss_pred             CC
Q psy1534         237 VA  238 (587)
Q Consensus       237 ~~  238 (587)
                      ..
T Consensus        96 ~~   97 (112)
T d1wela1          96 KK   97 (112)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>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=99.50  E-value=2.1e-14  Score=116.88  Aligned_cols=72  Identities=14%  Similarity=0.191  Sum_probs=66.9

Q ss_pred             CCCeEEEeCCCCC-CChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHH--HhCCCcccCceEEEEE
Q psy1534         515 ERDTVVVKNLPPT-ITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAID--MMDRTRIDGKIIDVTF  586 (587)
Q Consensus       515 ~~~~v~V~~Lp~~-~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~--~l~g~~~~g~~i~v~~  586 (587)
                      +..+|||+|||.+ +|++||+++|++||.|..+.+.+++++|||+|++.++|.+||+  .+++..|+|++|+|.+
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~   91 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   91 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEE
Confidence            4579999999985 8999999999999999999999999999999999999999998  5788899999999975

>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=99.50  E-value=1.5e-16  Score=127.83  Aligned_cols=76  Identities=13%  Similarity=0.108  Sum_probs=66.3

Q ss_pred             CCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEe-----eC-CCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEE
Q psy1534          32 EVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEIL-----ND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI  104 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~-----~d-~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V  104 (587)
                      .++|||+|||+++|+++| ++|++||.|..+.+.     .+ .++++||||||+|.++|+|++|+ .|||..|.|++|+|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI   79 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEE
Confidence            378999999999999999 899999988876654     23 36788999999999999999999 49999999999999


Q ss_pred             Eecc
Q psy1534         105 KEAV  108 (587)
Q Consensus       105 ~~a~  108 (587)
                      +++.
T Consensus        80 ~r~k   83 (90)
T d1u2fa_          80 RRPH   83 (90)
T ss_dssp             BCTT
T ss_pred             CCCC
Confidence            7544

>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=99.49  E-value=9.5e-15  Score=119.88  Aligned_cols=77  Identities=16%  Similarity=0.125  Sum_probs=67.6

Q ss_pred             CCCCcEEEcCCCCCC-CH----HHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEE
Q psy1534          30 PLEVPVVMDLIQGDA-SL----YQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLV  103 (587)
Q Consensus        30 ~~~~~vfV~nlp~~~-t~----~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~  103 (587)
                      +...+|||+||+.++ ++    ++| ++|++||+|.+|++++     +++||||+|.+.++|.+|++.|||..|.|++|+
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            456789999999886 43    345 6899999999999986     478999999999999999999999999999999


Q ss_pred             EEeccccc
Q psy1534         104 IKEAVEDK  111 (587)
Q Consensus       104 V~~a~~~~  111 (587)
                      |.++....
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997443

>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=99.48  E-value=4.4e-15  Score=121.93  Aligned_cols=76  Identities=18%  Similarity=0.164  Sum_probs=72.2

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEc
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD  235 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a  235 (587)
                      +.++|.+++.+++|++|+++|++||.|.+|+|+++.+++++|||||+|.+.++|.+|++.|||+.+.||+|+|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3588899999999999999999999999999998888999999999999999999999999999999999999985

>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=99.42  E-value=2.6e-15  Score=120.41  Aligned_cols=74  Identities=15%  Similarity=0.327  Sum_probs=65.0

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEee-----CC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIAL-----DK-DGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR  233 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  233 (587)
                      ++|||+|||+++||++|+++|+.||.|..+.+..     +. .++++|||||+|.+.++|++|+ .|||..+.|++|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            5899999999999999999999999887665542     22 3788999999999999999998 599999999999996


Q ss_pred             E
Q psy1534         234 M  234 (587)
Q Consensus       234 ~  234 (587)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=3.4e-13  Score=109.83  Aligned_cols=63  Identities=17%  Similarity=0.300  Sum_probs=59.6

Q ss_pred             CCCeEEEeC--CCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcc
Q psy1534         515 ERDTVVVKN--LPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI  577 (587)
Q Consensus       515 ~~~~v~V~~--Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~  577 (587)
                      +..+|+|.|  ||.++|+++|+++|++||.|..+.+.+++++|||+|.+.++|++|++.|||++|
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            356899976  999999999999999999999999999999999999999999999999999987

>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=99.40  E-value=3.2e-13  Score=110.01  Aligned_cols=76  Identities=18%  Similarity=0.305  Sum_probs=64.4

Q ss_pred             CCCCCcEEEEec--CCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CeE
Q psy1534         155 NCPLINKVFVAN--LDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLF---ERR  229 (587)
Q Consensus       155 ~~~~~~~l~V~n--Lp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~  229 (587)
                      ...++++|||.|  ||.++|+++|+++|++||.|..|.++++     ++||||+|.+.++|.+|++.|||+.+.   +.+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~   88 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcE
Confidence            455678899965  9999999999999999999999998875     579999999999999999999999873   345


Q ss_pred             EEEEEc
Q psy1534         230 ITVRMD  235 (587)
Q Consensus       230 l~v~~a  235 (587)
                      +.+.+.
T Consensus        89 i~~~~~   94 (101)
T d2cq2a1          89 ITLYLN   94 (101)
T ss_dssp             EECEEE
T ss_pred             EEEEEE
Confidence            444333

>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=99.39  E-value=1.6e-13  Score=106.65  Aligned_cols=73  Identities=14%  Similarity=0.109  Sum_probs=64.0

Q ss_pred             CCcEEEcCCCCCCCHHHHHhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeE-EEEEecccc
Q psy1534          32 EVPVVMDLIQGDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK-LVIKEAVED  110 (587)
Q Consensus        32 ~~~vfV~nlp~~~t~~~l~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~-i~V~~a~~~  110 (587)
                      ...|||.++|++.+++.|++|++||+|.++++.+     +++||||+|.++++|++||+ +||..|.|+. |.|.++..+
T Consensus         4 ~~wV~V~G~p~~~~~~il~~F~~~G~I~~~~~~~-----~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           4 DTWVTVFGFPQASASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGEEEEECCCGGGHHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             ccEEEEECCChHHHHHHHHHHHhhhhhheEEecC-----CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            4579999999999988778999999999998865     37999999999999999995 8999999985 678887643

>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=99.38  E-value=3.9e-13  Score=112.08  Aligned_cols=68  Identities=18%  Similarity=0.222  Sum_probs=62.2

Q ss_pred             eEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCH-HHHHHHHHHhCCCcccCceEEEE
Q psy1534         518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSE-WTAKRAIDMMDRTRIDGKIIDVT  585 (587)
Q Consensus       518 ~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~-~~a~~Ai~~l~g~~~~g~~i~v~  585 (587)
                      .+||.|||+.+|+++|+++|++||+|.+++|.+++++|||.|.++ ++|..|++.||+..+.++.++|.
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~   81 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   81 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEE
Confidence            458999999999999999999999999999999999999999986 78999999999999887766554

>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=99.35  E-value=4e-13  Score=112.00  Aligned_cols=73  Identities=22%  Similarity=0.257  Sum_probs=65.1

Q ss_pred             EEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCH-HHHHHHHHHhCCceeCCeEEEEEEccCC
Q psy1534         161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHP-VEAVQSISMLNNQNLFERRITVRMDRVA  238 (587)
Q Consensus       161 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~-~~A~~Al~~l~g~~~~g~~l~v~~a~~~  238 (587)
                      .+||+|||+++|+++|+++|++||+|.+|.|+++     +|||||+|.++ ++|..|+..||+..+.++.+.|.++...
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            4599999999999999999999999999999875     68999999996 7899999999999998888778776543

>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=99.31  E-value=1.5e-12  Score=105.60  Aligned_cols=77  Identities=17%  Similarity=0.239  Sum_probs=65.4

Q ss_pred             CCCCCcEEEcCC--CCCCC---------HHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCce
Q psy1534          29 APLEVPVVMDLI--QGDAS---------LYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE   96 (587)
Q Consensus        29 ~~~~~~vfV~nl--p~~~t---------~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~   96 (587)
                      ....+.|+|+|+  |.++.         ++|| +.|++||+|.+|++..+   .++|||||+|.++++|.+|++.|||..
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            346678999999  55432         2355 67999999999998765   356999999999999999999999999


Q ss_pred             eCCeEEEEEecc
Q psy1534          97 TKGRKLVIKEAV  108 (587)
Q Consensus        97 l~gr~i~V~~a~  108 (587)
                      |.||+|.|.++.
T Consensus        82 ~~gr~i~v~~~~   93 (99)
T d2dita1          82 FGGRQITAQAWD   93 (99)
T ss_dssp             ETTEECEEEECC
T ss_pred             ECCEEEEEEEeC
Confidence            999999999986

>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=99.31  E-value=3.3e-12  Score=103.50  Aligned_cols=80  Identities=20%  Similarity=0.232  Sum_probs=69.4

Q ss_pred             CCCcEEEEecC--CCCCc---------HHHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy1534         157 PLINKVFVANL--DYKVD---------EKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL  225 (587)
Q Consensus       157 ~~~~~l~V~nL--p~~~t---------e~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  225 (587)
                      ..+++|+|.||  |.++.         ++||++.|++||.|..|.+..+   .++||+||+|.+.++|.+|+..|||+.+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            34679999999  55432         3689999999999999998775   4579999999999999999999999999


Q ss_pred             CCeEEEEEEccCCC
Q psy1534         226 FERRITVRMDRVAD  239 (587)
Q Consensus       226 ~g~~l~v~~a~~~~  239 (587)
                      .||+|+|.+...+.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987665

>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=99.29  E-value=2.7e-12  Score=99.49  Aligned_cols=70  Identities=23%  Similarity=0.284  Sum_probs=62.2

Q ss_pred             CCCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCce-EEEEE
Q psy1534         515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKI-IDVTF  586 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~-i~v~~  586 (587)
                      .++.|+|.|||++.+++.| .+|++||.|+.+++.++++++||+|+++++|++||+ +||..|+|+. |.|..
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~   73 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   73 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEe
Confidence            3568999999999997655 589999999999998888999999999999999996 8999999985 66764

>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=99.26  E-value=2.9e-12  Score=104.99  Aligned_cols=81  Identities=16%  Similarity=0.165  Sum_probs=69.9

Q ss_pred             CCCcEEEEecC--CCCCc--------HHHHHHHHHhcCCeeEEEEeeCCC---CCcceEEEEEecCHHHHHHHHHHhCCc
Q psy1534         157 PLINKVFVANL--DYKVD--------EKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQSISMLNNQ  223 (587)
Q Consensus       157 ~~~~~l~V~nL--p~~~t--------e~~l~~~F~~~G~i~~v~i~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~g~  223 (587)
                      +|++.|.|.|+  |.++.        .+||++.|++||.|++|.|+++..   ....|++||+|.+.++|.+|+..|||+
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            45789999999  55432        367999999999999999998764   345699999999999999999999999


Q ss_pred             eeCCeEEEEEEccC
Q psy1534         224 NLFERRITVRMDRV  237 (587)
Q Consensus       224 ~~~g~~l~v~~a~~  237 (587)
                      .+.||+|.|.+...
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999754

>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=99.23  E-value=3.2e-12  Score=104.71  Aligned_cols=81  Identities=20%  Similarity=0.109  Sum_probs=66.9

Q ss_pred             CCCCcEEEcCC--CCCCC--------HHHH-HhcccCCCeEEEEEeeCCC---CCcceEEEEEECCHHHHHHHHHHhCCc
Q psy1534          30 PLEVPVVMDLI--QGDAS--------LYQI-SHLSTVGDVTYVEILNDDT---GKPRGSAIVEFQSPDLVRKAVNKMHRF   95 (587)
Q Consensus        30 ~~~~~vfV~nl--p~~~t--------~~~l-~~F~~~G~V~~v~i~~d~~---g~skG~aFV~F~~~e~A~~Al~~l~g~   95 (587)
                      ++.+.|.|+|+  |.++.        .+|| +.|++||+|++|+|++++.   ...+|++||+|.+.++|.+|++.|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            45667889999  44432        2345 6799999999999998753   345699999999999999999999999


Q ss_pred             eeCCeEEEEEecccc
Q psy1534          96 ETKGRKLVIKEAVED  110 (587)
Q Consensus        96 ~l~gr~i~V~~a~~~  110 (587)
                      .+.||+|.|.++...
T Consensus        82 ~f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          82 KFANRVVVTKYCDPD   96 (104)
T ss_dssp             CSSSSCCEEEEECHH
T ss_pred             EECCeEEEEEEcCHH
Confidence            999999999998744

>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=97.65  E-value=0.00013  Score=51.99  Aligned_cols=57  Identities=23%  Similarity=0.346  Sum_probs=51.9

Q ss_pred             HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCceeCCeEEEEEecc
Q psy1534          50 SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV  108 (587)
Q Consensus        50 ~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~g~~l~gr~i~V~~a~  108 (587)
                      +.|.++++|.+|.|....++..  .|-|...+.++|.-|+..|+..+|++++|.|.++.
T Consensus        15 ~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          15 EAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            6799999999999988767765  58999999999999999999999999999998875

>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=97.47  E-value=0.0004  Score=49.39  Aligned_cols=61  Identities=23%  Similarity=0.370  Sum_probs=54.0

Q ss_pred             HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q psy1534         174 KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR  236 (587)
Q Consensus       174 ~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~a~  236 (587)
                      +-|.+.|.+++.|.++.|....++..  .|-|...+..+|.-|+..|+.++|+.++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            34567899999999999988777666  48999999999999999999999999999999874

>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=97.35  E-value=0.00023  Score=53.38  Aligned_cols=69  Identities=26%  Similarity=0.373  Sum_probs=56.7

Q ss_pred             CCCeEEEeCCCCCCCh---------HHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhCCCcccCceEEEE
Q psy1534         515 ERDTVVVKNLPPTITW---------QELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT  585 (587)
Q Consensus       515 ~~~~v~V~~Lp~~~~~---------~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~g~~~~g~~i~v~  585 (587)
                      ++-||.|.=...+..+         .+|.+-|..||+|+-++...+  .-+|+|++-++|.+|++. +|.+++|+.|+|.
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--~mwVTF~dG~SAL~al~l-~g~~v~G~~l~It   90 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--QMLVTFADSHSALSVLDV-DGMKVKGRAVKIS   90 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--EEEEECSCSHHHHHHHHG-GGSEETTEEEEEE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--eEEEEECCcHHHHHHhcc-CCeEEcceEEEEe
Confidence            3568888644333322         468888999999999999887  999999999999999985 9999999999986


Q ss_pred             E
Q psy1534         586 F  586 (587)
Q Consensus       586 ~  586 (587)
                      .
T Consensus        91 ~   91 (95)
T d1ufwa_          91 G   91 (95)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=97.32  E-value=0.00045  Score=51.75  Aligned_cols=73  Identities=18%  Similarity=0.182  Sum_probs=58.6

Q ss_pred             CCCCCcEEEEecCCCCCcH---------HHHHHHHHhcCCeeEEEEeeCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q psy1534         155 NCPLINKVFVANLDYKVDE---------KKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNL  225 (587)
Q Consensus       155 ~~~~~~~l~V~nLp~~~te---------~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  225 (587)
                      ..|+.-+|.|.=..++..+         .+|.+.|..||+|.-|++..+       -..|+|.+-+.|.+|+ .+++.++
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al-~l~g~~v   82 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVL-DVDGMKV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHH-HGGGSEE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHh-ccCCeEE
Confidence            3455667777655444333         468889999999999999876       5899999999999999 5699999


Q ss_pred             CCeEEEEEEc
Q psy1534         226 FERRITVRMD  235 (587)
Q Consensus       226 ~g~~l~v~~a  235 (587)
                      +|+.|+|...
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999999763

>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=97.16  E-value=0.0011  Score=50.61  Aligned_cols=77  Identities=10%  Similarity=0.142  Sum_probs=61.8

Q ss_pred             cEEEEecCCCCCcHHHHHHHHHhcCCeeEEEEeeCCC--C-CcceEEEEEecCHHHHHHHHHHhCCceeCCe-----EEE
Q psy1534         160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--G-KSRGFGTVEFDHPVEAVQSISMLNNQNLFER-----RIT  231 (587)
Q Consensus       160 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--g-~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-----~l~  231 (587)
                      ++|.|+.||+.+||+++.+.+...+.+........+.  + ..-.-|+|.|.+.++...-.+.++|+.+.+.     +-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            5899999999999999999999999988877776653  2 2235699999999999999999999987531     345


Q ss_pred             EEEcc
Q psy1534         232 VRMDR  236 (587)
Q Consensus       232 v~~a~  236 (587)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            55553

>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=96.70  E-value=0.0024  Score=48.64  Aligned_cols=64  Identities=19%  Similarity=0.289  Sum_probs=55.4

Q ss_pred             CeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCC--------CeEEEEECCHHHHHHHHHHhCCCcccCc
Q psy1534         517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKG--------DIGLVRFDSEWTAKRAIDMMDRTRIDGK  580 (587)
Q Consensus       517 ~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~--------g~g~v~f~~~~~a~~Ai~~l~g~~~~g~  580 (587)
                      ++|.||.||+..|++++.+.+.+.+++.+..-...+        -.|.|.|.+.+++..-.+.++|+.|...
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~   73 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcC
Confidence            489999999999999999999999998776654321        5699999999999999999999988643

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.64  E-value=0.098  Score=39.48  Aligned_cols=56  Identities=20%  Similarity=0.289  Sum_probs=47.8

Q ss_pred             CCeEEEeCCCCCCChHHHHHHHhhcCCeeEEEeecCCCeEEEEECCHHHHHHHHHHhC
Q psy1534         516 RDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMD  573 (587)
Q Consensus       516 ~~~v~V~~Lp~~~~~~~l~~~f~~~G~v~~~~~~~~~g~g~v~f~~~~~a~~Ai~~l~  573 (587)
                      +--||.-..|..+.-.||.++|++||.|.-.-|..  ..|+|...++++++.+++.++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIdd--TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDD--TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEET--TEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEecC--ceEEEEecCHHHHHHHHHHhc
Confidence            45788888999999999999999999987666644  499999999999999887654

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.46  E-value=0.045  Score=41.41  Aligned_cols=58  Identities=22%  Similarity=0.335  Sum_probs=47.5

Q ss_pred             CCCCCcEEEcCCCCCCCHHHH-HhcccCCCeEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhC
Q psy1534          29 APLEVPVVMDLIQGDASLYQI-SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH   93 (587)
Q Consensus        29 ~~~~~~vfV~nlp~~~t~~~l-~~F~~~G~V~~v~i~~d~~g~skG~aFV~F~~~e~A~~Al~~l~   93 (587)
                      .|...-||.=.+|.++..-|| ++|+.||.|. |.-+-|      --|||...+.|+|+.++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC------ceEEEEecCHHHHHHHHHHhc
Confidence            355567999999999999999 9999999975 434444      369999999999999987654